RECON-1.08/0000755000076400007640000000000012274532636012046 5ustar rhubleyrepeatRECON-1.08/00README0000644000076400007640000001110112274532636013060 0ustar rhubleyrepeatRECON -- finding repeat families from biological sequences Version 1.08 (Jan 2014) Copyright (C) 2001 Washington University School of Medicine Copyright (C) 2011-2014 Institute for Systems Biology ------------------------------------------------------------------ About the package The RECON package implements a de novo algorithm for the indentification of repeat families from biological sequences. For details about the algorithm, see Bao Z. and Eddy S.R. (2002) Automated de novo Identification of Repeat Sequence Families in Sequenced Genomes. Submitted. and http://www.genetics.wustl.edu/eddy/recon Source code of RECON is freely available under the GNU General Public License. For details on the copyright and licensing, see the COPYRIGHT and LICENSE file. This distribution includes two Perl scripts and several C programs. Most users only need to run the scripts and the C programs should be transparent. What's new? RECON1.08: Wed Feb 5 14:04:25 PST 2014 - Robert Hubley ISB - New checks in eleredef.c for failed memory allocation/file operations. - A buffer overrun bug fix provided by Stephen Ficklin in eledef.c. RECON1.07: Wed Jun 8 10:00:55 PDT 2011 - Robert Hubley ISB - Another problem with the eleredef program has appeared a couple of times. A divide by zero error in one of Zhirong's routines. I have applied a workaround to the divide by zero but not a fix to the real problem. The program will now warn the user if the workaround was exercised during a run. RECON1.06: Tue May 20 15:19:30 PDT 2008 - Robert Hubley ISB - 64 bit compiler fixes: Previous versions of RECON used the "long" data type under the assumption that was 32bits. This caused the program to crash or lock up during analysis. Bug fix for RECON1.02 in the eleredef program. Programs and input The RECON algorithm defines repeat families on the basis of pairwise similarity between the input biological sequences. We do not provide pairwise sequence comparison tools in the package. However, we provide a tool (MSPCollect) which converts a BLAST output into an MSP file, which is used by the package as input. In the MSP file, each MSP that BLAST reports is turned into a one-line summary in the following format: score %iden start end query_name start end subject_name \n The command line format for MSPCollect is MSPCollect BLAST_output_file > name_of_your_MSP_file If you have multiple BLAST output files, you have to run MSPCollect multiple times and concatenate the result into one MSP file. The recon script drives the running of the package. The command line format is as follows: recon.pl seq_name_list_file MSP_file integer The seq_name_list_file contains the names of the input sequences, one per line. The lines can be just the names, or it may be in the FASTA format (starting with ">"). The names should be sorted in lexical order. The very first line of file should be an integer which is the number of names listed in the file. If the input sequences are stored in one FASTA file, one can construct the seq_name_list_file as follows: grep ">" FASTA_file | sort > name_of_your_seq_name_list_file One can then add the number of names to the top of the file. As one of the early steps, the script sort the MSPs. If there are too many MSPs in the input, one may consider sorting a subsection at a time. The third integer argument specifies how many sections you want to divide the sorting process into. The default is 1. (Notice, as the file size gets big, the sorting process becomes inefficient, and may even cause the process to crash.) If you know the RECON algorithm, then the names of C programs are self explanatory. Output of the package The package generates several directories along the way. All of them, except for the summary directory, stores intermediate results. The ele_def_res, ele_redef_res and edge_redef_res directories contain files for the elements defined at the corresponding step, one file per element. Elements are indexed using integers and are named as e123, e987, etc.. If you are not interested in the details about the elements, you can remove all these directories. Two files in the summary directory are the "official" output of the package -- eles and families. Each line in "eles" is a summary of an element defined in the following format: family_index element_index strand sequence_name start end Each line in "families" is a summary of a family defined in the following format: family_index copy_number_in_the_family The Demo To get examples of (the format of) the input and output files, see the README file in the Demos directory. RECON-1.08/INSTALL0000644000076400007640000000121612274532636013077 0ustar rhubleyrepeatThe RECON package includes three parts -- the C source code in the src directory, the Perl scripts in the scripts directory, and a Demos directory containing examplory data. To install the package, run "make" and then "make install" in the src directory. You may have to modify the Makefile in the src directory to choose the proper C compliler (cc or gcc). Before you can use the package, you need one more modification in the script "recon.pl" in the scripts directory -- on the third line, add the path to the binaries (the bin directory here) between the double quotes. Now the package is up for running. See 00README on how to use the package. 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07666464 07666203 ChrX 17250650 17250912 ChrX 000617 83.0 17030585 17030761 ChrX 17250712 17250893 ChrX 000401 69.1 16963270 16963486 ChrX 17250719 17250935 ChrX 001142 93.8 16609724 16609515 ChrX 17250725 17250934 ChrX 001057 92.8 07921528 07921734 ChrX 17250731 17250935 ChrX 000518 76.1 09183982 09184178 ChrX 17250732 17250936 ChrX 000674 81.8 06917173 06917364 ChrX 17250745 17250934 ChrX 000660 85.3 15021982 15021807 ChrX 17250765 17250935 ChrX 000452 79.7 05416956 05417107 ChrX 17250791 17250941 ChrX 000518 83.7 12567167 12567028 ChrX 17250794 17250934 ChrX RECON-1.08/Demos/README0000644000076400007640000000320312274532636013773 0ustar rhubleyrepeatThe Demos directory contains an example from the C. elegans genome. You have three directories to start with -- input, standard and output. The input directory contains two files for the input of the RECON package -- the seq_name_list_file "seqnames" and MSP_file "elegans.msps". The elegans.msps contains MSPs from an all-vs-all comparison of the elegans genome which cover regions similar to Tc3 (a transposable element in elegans), directly or by transitive similarity. These include both the Tc3 copies in the genome, as well as certain Tc3-related but distinct transposable elements. The standard directory also contains two files -- Tc3.list and Tc3.msps. The former file is a manually curated list of Tc3 copies/fragments in the genome. For the more critical users, the latter file is a manually curated list of MSPs from a search with the canonical Tc3 against the genome, which we believe are hits to true Tc3 copies. You can compare this file with the "elegans.msps" to check whether our curation is reasonable. The empty directory of output is where you can run the RECON package on this example (after installation, of course). Within the output directory, type ../../scripts/recon.pl ../input/seqnames ../input/elegans.msps 1 The process will generate several directories to store the output. All these directories, except for the summary directory stores intermediate results (see 00README). You can find that in summary/eles, the Tc3 copies are defined as family six. Do awk '$1==6' summary/eles to get the list of members in this defined family and compare it to standard/Tc3.list to evaluate the result of this automatic clustering. RECON-1.08/scripts/0000755000076400007640000000000012274532636013535 5ustar rhubleyrepeatRECON-1.08/scripts/recon.pl0000755000076400007640000000345112274532636015206 0ustar rhubleyrepeat#! /usr/bin/perl $path = ""; if (!$path) { die "Please modifiy this script to specify the path to the binaries.\n"; } if (@ARGV < 2) { die "usage: recon seq_name_list_file MSP_file integer\nSee 00README for details.\n"; } open(SEQ, "$ARGV[0]") || die "usage: recon seq_name_list_file MSP_file integer\nCan not open the seq_name_list_file $ARGV[0].\nSee 00README for details.\n"; close SEQ; open(MSP, "$ARGV[1]") || die "usage: recon seq_name_list_file MSP_file integer\nCan not open the MSP_file $ARGV[1].\nSee 00README for details.\n"; close MSP; `rm -f core`; `rm -rf summary`; `mkdir summary`; # prepare images `rm -rf images`; `mkdir images`; `$path/imagespread $ARGV[0] $ARGV[1] $ARGV[2]`; if ($?) {die "imagespread failed. Exit code $?\n";} if (@ARGV < 3) { $sect = 1; } else { $sect = $ARGV[2]; } for ($i=1; $i<=$sect; $i++) { $spread = "images/spread" . $i; `sort -k 3,3 -k 4n,4n -k 5nr,5nr $spread >> images/images_sorted`; if ($?) {die "sort failed for $spread.\n";} } `rm -f images/spread*`; # initial definition of elements `rm -rf ele_def_res`; `mkdir ele_def_res`; `$path/eledef $ARGV[0] $ARGV[1] single`; if ($?) {die "eledef failed. Exit code $?\n";} # re-defining elements `rm -rf ele_redef_res`; `mkdir ele_redef_res`; `rm -f tmp tmp2`; `ln -s ele_def_res tmp`; `ln -s ele_redef_res tmp2`; `$path/eleredef $ARGV[0]`; if ($?) {die "eleredef failed. Exit code $?\n";} `rm -f tmp tmp2`; # re-defining edges `rm -rf edge_redef_res`; `mkdir edge_redef_res`; `rm -f tmp tmp2`; `ln -s ele_redef_res tmp`; `ln -s edge_redef_res tmp2`; `$path/edgeredef $ARGV[0]`; if ($?) {die "edgeredef failed. Exit code $?\n";} # famdef `rm -f tmp tmp2`; `ln -s edge_redef_res tmp`; `$path/famdef $ARGV[0]`; if ($?) {die "famdef failed. Exit code $?\n";} `rm -f tmp`; RECON-1.08/scripts/MSPCollect.pl0000755000076400007640000000253212274532636016044 0ustar rhubleyrepeat#! /usr/bin/perl if (!@ARGV) { die "usage: MSPCollect BLAST_output_file\n"; } open (BLST, "$ARGV[0]") || die "usage: MSPCollect BLAST_output_file\nCan not open the BLAST_output_file $ARGV[0]\n"; $score_cutoff = 0; $iden_cutoff = 0; $score = -1; while () { if (/^Query=\s+(\S+)/) { $query = $1; } elsif (/^>(\S+)/) { $sbjct_current = $1; } elsif (/^\s+Score =\s*(\S+)/) { if (&filter) { &report; } $head_q_boolean = 1; $head_s_boolean = 1; $sbjct = $sbjct_current; $score_string = $1; if ($score_string =~ /(\S+)(e|E)\+(\d+)/) { $score = $1 * exp($3*log(10)); } else {$score = $score_string;} } elsif (/^\s+Identities =\s+(\d+)\/(\d+)/) { $iden = $1/$2*100; } elsif (/^Query:\s+(\d+)\s+(\S+)\s+(\d+)/) { if ($head_q_boolean) { $head_query = $1; $head_q_boolean = 0; } $tail_query = $3; } elsif (/^Sbjct:\s+(\d+)\s+(\S+)\s+(\d+)/) { if ($head_s_boolean) { $head_sbjct = $1; $head_s_boolean = 0; } $tail_sbjct = $3; } elsif (/^Parameters:/) { if (&filter) {&report;} $score = -1; } } sub filter { if ($score > 0 && $score > $score_cutoff && $iden > $iden_cutoff) {return 1;} return 0; } sub report { printf("%06d %03d %05d %05d %s %05d %05d %s \n", $score, $iden, $head_query, $tail_query, $query, $head_sbjct, $tail_sbjct, $sbjct); } RECON-1.08/COPYRIGHT0000640000076400007640000000337512274532636013345 0ustar rhubleyrepeatRECON -- finding repeat families from biological sequences Version 1.01 (Nov 2001) Copyright (C) 2001 Washington University School of Medicine ------------------------------------------------------------------ This suite of programs is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. In other words, you are free to modify, copy, or redistribute this source code and its documentation in any way you like, but you must distribute all derivative versions as free software under the same terms that I've provided my code to you (i.e. the GNU General Public License). This precludes any use of the code in proprietary or commercial software unless your source code is made freely available. If you wish to use RECON code under a different Open Source license that's not compatible with the GPL (like the Artistic License, BSD license, or the Netscape Public License), please contact Sean Eddy (eddy@genetics.wustl.edu) for permission. Incorporation into commercial software under non-GPL terms is possible by obtaining a specially licensed version from Washington University School of Medicine. Contact Jack Pincus (jhpincus@cris.com) to arrange licensing terms. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this RECON release, in the file LICENSE; if not, write to the Free Software Foundation, Inc., 675 Mass. Ave, Cambridge, MA 02139 USA. RECON-1.08/src/0000755000076400007640000000000012274532636012635 5ustar rhubleyrepeatRECON-1.08/src/famdef.c0000644000076400007640000001446712274532636014237 0ustar rhubleyrepeat#include "ele.h" typedef struct Dirs { int dir; struct Dirs *next; } Dirs_t; FAMILY_t *new_family(); void build_family(FAMILY_t *, ELE_INFO_t *, short, int *); void recruit_partner(ELE_INFO_t *, EDGE_TREE_t *, ELE_DATA_t **, Dirs_t *, Dirs_t **); int main (int argc, char *argv[]) { int i, rounds=0, ei; char line[35], stat; FAM_DATA_t *fam; FAMILY_t *family; FILE *seq_list, *ele_no, *redef_stat; FILE *fam_no, *final_ele_no; int tot_ele; /* processing command line */ if (argc == 1) { printf("usage: famdef seq_list\n where seq_list is the list of sequence names.\n"); exit(1); } seq_list = fopen(argv[1], "r"); if (!seq_list) { printf("Input file for sequence name list %s not found. Exit.\n", argv[1]); exit(2); } GetSeqNames(seq_list); ele_no = fopen("summary/redef_ele_no", "r"); if(!ele_no) { printf("Can not open redef_ele_no. Exiting\n"); exit(2); } redef_stat = fopen("tmp/redef_stat", "r"); if (!redef_stat) { printf("Can not open redef_stat. Exiting\n"); exit(2); } eles = fopen("summary/eles", "w"); fams = fopen("summary/families", "w"); fam_no = fopen("summary/fam_no", "w"); final_ele_no = fopen("summary/ele_no", "w"); log_file = fopen("tmp/log2", "w"); while (fgets(line, 15, ele_no)) { ele_ct = atoi(line); } fclose(ele_no); ele_array_size = ele_ct; all_ele = (ELE_INFO_t **) malloc(ele_array_size*sizeof(ELE_INFO_t *)); for (i=0; istat = stat; } msp_in_mem = 0; msp_left = 0; msp_ct = 0; edge_ct = 0; edge_in_mem = 0; edge_left = 0; files_read = 0; clan_ct = 0; err_no = 0; /* define families */ fam_ct = 0; tot_ele = 0; fprintf(eles, "# fam ele dir sequence start end\n"); fprintf(fams, "# fam cp-no name\n"); for (i=0; istat != 'O' && (*(all_ele+i))->stat != 'X') { fprintf(log_file, "evaluating family membership of element %d\n", (*(all_ele+i))->index); fflush(log_file); if ((*(all_ele+i))->stat == 'y') { /* starting a new family! */ family = new_family(); build_family(family, *(all_ele+i), 1, &tot_ele); } else if ((*(all_ele+i))->stat != 'x') { err_no ++; fprintf(log_file, "ele %d %c not properly filtered\n", (*(all_ele+i))->index, (*(all_ele+i))->stat); fflush(log_file); exit(5); } } } fprintf(fam_no, "%d\n", fam_ct); fclose(fam_no); fprintf(final_ele_no, "%d\n", tot_ele); fclose(final_ele_no); fprintf(log_file, "total numbers: %d elements, %d msps, %d edges\n", ele_ct, msp_index+1, edge_index+1); fprintf(log_file, "%d files read, %d msps seen, %d edges seen\n", files_read, msp_ct, edge_ct); fprintf(log_file, "%d errors, %d msps and %d edges left in memory, \n", err_no, msp_left, edge_left); fflush(log_file); fclose(log_file); exit(0); } /************************************** ************************************** ** ** ** CLUSTERING, YEAH BABY YEAH! ** ** ** ************************************** **************************************/ FAMILY_t *new_family() { FAMILY_t *fam; FAM_DATA_t *fam_data; fam_ct ++; fam = (FAMILY_t *) malloc(sizeof(FAMILY_t)); fam->index = fam_ct; fam->members = NULL; fam->relatives = NULL; return fam; } void build_family(FAMILY_t *fam, ELE_INFO_t *ele_info, short dir, int *te) { /* standard breath first traverse for connected components */ ELE_DATA_t *mem_tail, *seed, *cur_mem; ELE_INFO_t *cei; int mem_ct = 0; Dirs_t *dirs, *dirs_t, *cur_dir; ele_info->stat = 'x'; seed = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t)); seed->ele_info = ele_info; seed->next = NULL; fam->members = seed; mem_tail = seed; dirs = (Dirs_t *) malloc(sizeof(Dirs_t)); dirs->dir = 1; dirs->next = NULL; dirs_t = dirs; /* recruiting new members */ cur_mem = fam->members; cur_dir = dirs; while (cur_mem) { mem_ct ++; cei = cur_mem->ele_info; if (cei->ele) { fprintf(log_file, "ele %d is in memory unexpectedly\n", cei->index); fflush(log_file); exit(3); } else ele_read_in(cei, 4); cei->to_family = fam; /* output the element */ /* to the list of all elements */ /*fprintf(eles, "%6d %6d %2d %10s %8d %8d \n", fam->index, cei->index, cei->ele->direction, cei->ele->frag.seq_name, cei->ele->frag.lb, cei->ele->frag.rb);*/ fprintf(eles, "%6d %6d %2d %10s %8d %8d \n", fam->index, cei->index, cur_dir->dir, cei->ele->frag.seq_name, cei->ele->frag.lb, cei->ele->frag.rb); /* recruit its partners (that have not been recruited) */ if (cei->ele->edges) recruit_partner(cei, cei->ele->edges, &mem_tail, cur_dir, &dirs_t); else if (cur_mem != seed) { fprintf(log_file, "error: ele %d edge tree missing\n", cei->index); fflush(log_file); exit(4); } ele_cleanup(&cei->ele); cur_mem = cur_mem->next; cur_dir = cur_dir->next; } fprintf(fams, "%d %d unknown \n", fam->index, mem_ct); fflush(fams); *te += mem_ct; fprintf(log_file, "new family with %d members\n", mem_ct); fflush(log_file); fam_cleanup(&fam); } void recruit_partner(ELE_INFO_t *ele_info, EDGE_TREE_t *rt, ELE_DATA_t **tail, Dirs_t *cur_dir, Dirs_t **dtail){ ELE_INFO_t *epi; ELE_DATA_t *new_mem; Dirs_t *new_dir; if (rt->l) recruit_partner(ele_info, rt->l, tail, cur_dir, dtail); if (rt->to_edge->type == 'p' || rt->to_edge->type == 'P') { epi = linked_ele(ele_info, rt->to_edge); if (epi->stat == 'y') { epi->stat = 'x'; new_mem = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t)); new_mem->ele_info = epi; new_mem->next = NULL; (*tail)->next = new_mem; *tail = new_mem; new_dir = (Dirs_t *) malloc(sizeof(Dirs_t)); new_dir->dir = cur_dir->dir * rt->to_edge->direction; new_dir->next = NULL; (*dtail)->next = new_dir; *dtail = new_dir; } } if (rt->r) recruit_partner(ele_info, rt->r, tail, cur_dir, dtail); } RECON-1.08/src/edgeredef.c0000644000076400007640000002676512274532636014733 0ustar rhubleyrepeat#include "ele.h" #define CUTOFF3 0.7 void report_redef_stat(); void general_edge_redef(ELE_INFO_t *); void build_local_edge_net(ELE_INFO_t *, int, ELE_DATA_t **); void local_edge_net_walk(ELE_INFO_t *, EDGE_TREE_t *, int, ELE_DATA_t **); void cruise_local_edge_net(ELE_DATA_t *); void dissolve_local_edge_net(ELE_DATA_t **); void stage_exit(int ); void edge_filt(ELE_INFO_t *); EDGE_TREE_t *find_PPS(ELE_INFO_t *, EDGE_TREE_t *); EDGE_TREE_t * edge_update(ELE_INFO_t *, EDGE_TREE_t *, EDGE_TREE_t *); void edge_repair(ELE_INFO_t *); EDGE_TREE_t *best_link(ELE_INFO_t *, EDGE_TREE_t *); int main (int argc, char *argv[]) { int i, rounds=0, ei, start; short to_march; char line[35], stat; FILE *seq_list, *ele_no, *redef_stat; /* processing command line */ if (argc == 1) { printf("usage: fam_def seq_list start\n where seq_list is the list of sequence names, start is the index of the element to start defining families. The latter one is optional.\n"); exit(1); } seq_list = fopen(argv[1], "r"); if (!seq_list) { printf("Input file for sequence name list %s not found. Exit.\n", argv[1]); exit(2); } GetSeqNames(seq_list); if (argc > 2) start = atoi(argv[2]) - 1; else start = 0; ele_no = fopen("summary/redef_ele_no", "r"); if(!ele_no) { printf("Can not open redef_ele_no. Exiting\n"); exit(1); } redef_stat = fopen("tmp/redef_stat", "r"); if (!redef_stat) { printf("Can not open redef_stat. Exiting\n"); exit(1); } log_file = fopen("tmp2/log", "w"); if (!log_file) { printf("Can not open log_file. Exiting\n"); exit(1); } while (fgets(line, 15, ele_no)) { ele_ct = atoi(line); } fclose(ele_no); ele_array_size = ele_ct; all_ele = (ELE_INFO_t **) malloc(ele_array_size*sizeof(ELE_INFO_t *)); for (i=0; istat = stat; } msp_in_mem = 0; msp_left = 0; msp_ct = 0; edge_ct = 0; edge_in_mem = 0; edge_left = 0; files_read = 0; clan_ct = 0; err_no = 0; /* update edges, to get rid of PPS */ for (i=start; istat != 'O' && (*(all_ele+i))->stat != 'X') { fprintf(log_file, "evaluating edges of element %d\n", (*(all_ele+i))->index); fflush(log_file); if ((*(all_ele+i))->stat == 'v') { general_edge_redef(*(all_ele+i)); report_redef_stat(); } else if((*(all_ele+i))->stat != 'y') { err_no ++; fprintf(log_file, "ele %d %c not properly defined\n", (*(all_ele+i))->index, (*(all_ele+i))->stat); fflush(log_file); exit(5); } } } for (i=start; istat != 'O' && (*(all_ele+i))->stat != 'X') { fprintf(log_file, "repairing edges of element %d\n", (*(all_ele+i))->index); fflush(log_file); if ((*(all_ele+i))->stat == 'y') { edge_repair(*(all_ele+i)); } else { err_no ++; fprintf(log_file, "ele %d %c edges not properly redefined\n", (*(all_ele+i))->index, (*(all_ele+i))->stat); fflush(log_file); exit(5); } } } fprintf(log_file, "total numbers: %d elements, %d msps, %d edges\n", ele_ct, msp_index+1, edge_index+1); fprintf(log_file, "%d files read, %d msps seen, %d edges seen\n", files_read, msp_ct, edge_ct); fprintf(log_file, "%d errors, %d msps and %d edges left in memory, \n", err_no, msp_left, edge_left); fflush(log_file); fclose(log_file); exit(0); } void report_redef_stat() { int i; FILE *redef_stat; redef_stat = fopen("tmp2/redef_stat", "w"); for (i=0; iindex, (*(all_ele+i))->stat, (*(all_ele+i))->file_updated); } fclose(redef_stat); } /*********************************** *********************************** ** ** ** UPDATING THE EDGES ** ** ** *********************************** ***********************************/ void general_edge_redef(ELE_INFO_t *ele_info) { ELE_DATA_t *local_net=NULL; char *command; if (!ele_info->ele) ele_read_in(ele_info, 2); if (ele_info->ele->edges) { clan_ct ++; clan_size = 0; clan_core_size = 0; fprintf(log_file, "new clan: %d for ele %d\n", clan_ct, ele_info->index); fflush(log_file); build_local_edge_net(ele_info, 1, &local_net); /*notice level here is 0, not 1 */ fprintf(log_file, "clan size: %d, clan core size: %d\n", clan_size, clan_core_size); fflush(log_file); cruise_local_edge_net(local_net); dissolve_local_edge_net(&local_net); } else { ele_info->stat = 'y'; ele_cleanup(&ele_info->ele); command = (char *) malloc(80*sizeof(char)); sprintf(command, "cp tmp/e%d tmp2/.", ele_info->index); system(command); free(command); } } /* notice the structural similarity and difference b/t the following two functions and the corresponding ones in redef.c */ /* notice that it's much simpler here */ void build_local_edge_net(ELE_INFO_t *ele_info, int level, ELE_DATA_t **net_p) { ELE_INFO_t *epi; ELE_DATA_t *que; ELEMENT_t *ele; clan_size ++; que = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t)); que->ele_info = ele_info; que->next = *net_p; *net_p = que; if (!ele_info->ele) ele_read_in(ele_info, 1); ele = ele_info->ele; if (level < DEPTH) { if (ele_info->stat != 'y') { ele->l_hold = 1; clan_core_size ++; /*fprintf(log_file, " %d\n", ele_info->index); fflush(log_file);*/ level ++; if (ele->edges) local_edge_net_walk(ele_info, ele->edges, level, net_p); else { err_no ++; fprintf(log_file, "error: edge tree missing in ele %d\n", ele_info->index); fflush(log_file); } } else ele->l_hold = 2; } else ele->l_hold = 2; } void local_edge_net_walk(ELE_INFO_t *ele_info, EDGE_TREE_t *rt, int level, ELE_DATA_t **net_p) { ELE_INFO_t *epi; ELEMENT_t *ele=ele_info->ele; if (rt->l) local_edge_net_walk(ele_info, rt->l, level, net_p); if (rt->to_edge->type == 'p' || rt->to_edge->type == 'S' || rt->to_edge->type == 'P') { epi = linked_ele(ele_info, rt->to_edge); if (!epi->ele) ele_read_in(epi, 2); if (!epi->ele->l_hold) build_local_edge_net(epi, level, net_p); } if (rt->r) local_edge_net_walk(ele_info, rt->r, level, net_p); } void cruise_local_edge_net(ELE_DATA_t *local_net) { ELE_DATA_t *que; que = local_net; while (que) { /* here, all elements in the local_network are explicitly hung in ques, unlike in the local_network for ele_ref, where some are hung in redef of other elements */ /* also, no need to march for a second time, since once edge_filt is done, the status will not be affected by the processing of other elements, so no need to come back and re-do it */ if (que->ele_info->ele->l_hold == 1) { if (que->ele_info->stat != 'y') { if (que->ele_info->ele->edges) edge_filt(que->ele_info); else if (que != local_net) { fprintf(log_file, "error: ele %d edge tree missing\n", que->ele_info->index); fflush(log_file); exit(4); } que->ele_info->stat = 'y'; } else { fprintf(log_file, "error: ele %d conflicting status in local network\n", que->ele_info->index); fflush(log_file); exit(5); } } que = que->next; } } void dissolve_local_edge_net(ELE_DATA_t **net_p) { ELE_DATA_t *que; char *command; int i, ele_left=0; que = *net_p; while (que) { que->ele_info->ele->l_hold = 0; ele_write_out(que->ele_info, 2); ele_cleanup(&que->ele_info->ele); que = que->next; } ele_data_free(net_p); if (msp_in_mem) { err_no ++; fprintf(log_file, "error: error in bookkeeping: %d msps total, %d seen, %d left in memory\n", msp_index+1, msp_ct, msp_in_mem); fflush(log_file); msp_left += msp_in_mem; } if (edge_in_mem) { err_no ++; fprintf(log_file, "error: error in bookkeeping: %d edges total, %d seen, %d left in memory\n", edge_index+1, edge_ct, edge_in_mem); fflush(log_file); edge_left += edge_in_mem; edge_in_mem = 0; } for (i=0; iele) { ele_left ++; err_no ++; fprintf(log_file, "error: element %d not cleaned from memory. stat = %c\n", i+1, (*(all_ele+i))->stat); fflush(log_file); } } if (ele_left) { err_no ++; fprintf(log_file, "error: %d elements left in memory\n", ele_left); fflush(log_file); } if (err_no) exit(3); #if 0 command = (char *) malloc(50*sizeof(char)); sprintf(command, "mv -f tmp2/clan/e* tmp2/."); if (system(command)) { fprintf(log_file, "error moving files from tmp2/clan/\n"); fflush(log_file); stage_exit(6); } free(command); #endif } void stage_exit(int code) { char *command = (char *) malloc(50*sizeof(char)); sprintf(command, "mv -f tmp2/redef_stat tmp2/redef_stat_prev"); if (system(command)) { fprintf(log_file, "error in moving tmp2/redef_stat\n"); fflush(log_file); exit(code); } report_redef_stat(); exit(code); } void edge_filt(ELE_INFO_t *ele_info) { EDGE_TREE_t *max; max = find_PPS(ele_info, ele_info->ele->edges); if (max) { max = edge_update(ele_info, ele_info->ele->edges, max); max->to_edge->type = 'P'; } } EDGE_TREE_t *find_PPS(ELE_INFO_t *ele_info, EDGE_TREE_t *rt) { ELE_INFO_t *epi; EDGE_TREE_t *res=NULL; if (rt->to_edge->type == 'p' || rt->to_edge->type == 'S') { epi = linked_ele(ele_info, rt->to_edge); if (((float) ele_info->ele->frag.rb - ele_info->ele->frag.lb)/(epi->ele->frag.rb - epi->ele->frag.lb) < CUTOFF3) res = rt; } if (!res && rt->l) res = find_PPS(ele_info, rt->l); if (!res && rt->r) res = find_PPS(ele_info, rt->r); return res; } EDGE_TREE_t *edge_update(ELE_INFO_t *ele_info, EDGE_TREE_t *rt, EDGE_TREE_t *ref) { ELE_INFO_t *epi; if (rt->l) ref = edge_update(ele_info, rt->l, ref); if (rt->r) ref = edge_update(ele_info, rt->r, ref); epi = linked_ele(ele_info, rt->to_edge); if (rt->to_edge->type == 'p' || rt->to_edge->type == 'S') { if (((float) ele_info->ele->frag.rb - ele_info->ele->frag.lb)/(epi->ele->frag.rb - epi->ele->frag.lb) < CUTOFF3) { if (rt->to_edge->score > ref->to_edge->score) { ref->to_edge->type = 'S'; ref = rt; } else { rt->to_edge->type = 'S'; } } else { if (rt->to_edge->type == 'p') rt->to_edge->type = 'S'; } } return ref; } void edge_repair(ELE_INFO_t *ele_info) { EDGE_TREE_t *hanger; ele_read_in(ele_info, 2); if (ele_info->ele->edges) { hanger = best_link(ele_info, ele_info->ele->edges); if (!hanger) { fprintf(log_file, "ele %d can not be repaired.\n", ele_info->index); } else if (hanger->to_edge->type == 'S') { hanger->to_edge->type == 'P'; ele_write_out(ele_info, 2); } } ele_cleanup(&ele_info->ele); } EDGE_TREE_t *best_link(ELE_INFO_t *ele_info, EDGE_TREE_t *rt) { EDGE_TREE_t *res=NULL; if (rt->to_edge->type == 'p') res = rt; else if (rt->to_edge->type == 'P' || rt->to_edge->type == 'S') { if (!res || rt->to_edge->score > res->to_edge->score) res = rt; } if ((!res || res->to_edge->type != 'p') && rt->l) res = best_link(ele_info, rt->l); if ((!res || res->to_edge->type != 'p') && rt->r) res = best_link(ele_info, rt->r); return res; } RECON-1.08/src/msps.h0000644000076400007640000001376512274532636014004 0ustar rhubleyrepeat/* standard stuff */ #include "bolts.h" #include "seqlist.h" /* A collection of structures and functions to handle MSPs */ /* BASIC structures */ typedef struct frag { char *seq_name; int32_t lb, rb; /* char lst, rst; type of ends, can be used to mark physical ends */ } FRAG_t; typedef struct frag_list { FRAG_t *to_frag; struct frag_list *next; } FRAG_DATA_t; typedef struct image { int index; FRAG_t frag; struct msp *to_msp; struct ele_info *ele_info; } IMAGE_t; typedef struct image_list { IMAGE_t *to_image; struct image_list *next; } IMG_DATA_t; typedef struct img_tree { IMAGE_t *to_image; struct img_tree *p, *l, *r; } IMG_TREE_t; /*typedef struct img_rec { int msp_index; struct img_rec *next; } IMG_REC_t; */ typedef struct msp { /*struct msp_list *hanger;*/ char stat; /* 'p', 's' */ int32_t score; float iden; int direction; IMAGE_t query, sbjct; } MSP_t; typedef struct msp_list { MSP_t *to_msp; struct msp_list *next; } MSP_DATA_t; /* funtions prototypes */ int print_msp(MSP_t *); int fprint_msp(FILE *, MSP_t *); int scan_msp(MSP_t *, char *); int merge_msp(MSP_t *, MSP_t *); IMAGE_t *partner(IMAGE_t *); int doub_cov(FRAG_t *, FRAG_t *, float); int sing_cov(FRAG_t *, FRAG_t *, float); int print_msp(MSP_t *m) { if (m->direction == 1) { if (printf("%06d %3.1f %08d %08d %s %08d %08d %s \n", m->score, m->iden, m->query.frag.lb, m->query.frag.rb, m->query.frag.seq_name, m->sbjct.frag.lb, m->sbjct.frag.rb, m->sbjct.frag.seq_name) > 0) { return 0; } else { return 1; } } else if (m->direction == -1) { if (printf("%06d %3.1f %08d %08d %s %08d %08d %s \n", m->score, m->iden, m->query.frag.rb, m->query.frag.lb, m->query.frag.seq_name, m->sbjct.frag.lb, m->sbjct.frag.rb, m->sbjct.frag.seq_name) > 0) { return 0; } else { return 1; } } else { return 1; } } int fprint_msp(FILE *ofp, MSP_t *m) { if (m->direction == 1) { if (fprintf(ofp, "%06d %3.1f %08d %08d %s %08d %08d %s \n", m->score, m->iden, m->query.frag.lb, m->query.frag.rb, m->query.frag.seq_name, m->sbjct.frag.lb, m->sbjct.frag.rb, m->sbjct.frag.seq_name) > 0) { return 0; } else { return 1; } } else if (m->direction == -1) { if (fprintf(ofp, "%06d %3.1f %08d %08d %s %08d %08d %s \n", m->score, m->iden, m->query.frag.rb, m->query.frag.lb, m->query.frag.seq_name, m->sbjct.frag.lb, m->sbjct.frag.rb, m->sbjct.frag.seq_name) > 0) { return 0; } else { return 1; } } else { return 1; } } int scan_msp(MSP_t *m, char *line) { int32_t bd_tmp; char qname[NAME_LEN], sname[NAME_LEN]; int pos; if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { return 1; } else { pos = GetSeqIndex(0, seq_no-1, qname); if (pos<0) {return pos;} m->query.frag.seq_name = *(seq_names+pos); pos = GetSeqIndex(0, seq_no-1, sname); if (pos<0) {return pos;} m->sbjct.frag.seq_name = *(seq_names+pos); m->direction = 1; m->stat = 's'; /*m->score = m->score;*/ m->query.to_msp = m; m->sbjct.to_msp = m; /* indices and ele_info pointer are not taken care of here */ /* m->query.frag.lst = 'n'; m->query.frag.rst = 'n'; m->sbjct.frag.lst = 'n'; m->sbjct.frag.rst = 'n'; */ if (m->query.frag.lb > m->query.frag.rb) { m->direction *= -1; bd_tmp = m->query.frag.lb; m->query.frag.lb = m->query.frag.rb; m->query.frag.rb = bd_tmp; } if (m->sbjct.frag.lb > m->sbjct.frag.rb) { m->direction *= -1; bd_tmp = m->sbjct.frag.lb; m->sbjct.frag.lb = m->sbjct.frag.rb; m->sbjct.frag.rb = bd_tmp; } return 0; } } /* archaine */ #if 0 int merge_msp(MSP_t *m1, MSP_t *m2) { /* merge two MSPs into the first one */ int32_t l1, l2; /* no need for changing direction */ /* iden */ l1 = m1->sbjct.frag.rb - m1->sbjct.frag.lb; l2 = m2->sbjct.frag.rb - m2->sbjct.frag.lb; m1->iden = (m1->iden*l1 + m2->iden*l2)/(l1+l2); /* query */ /* links and seq_name do not need to change */ /* query boundaries */ m1->query.frag.lb = m2->query.frag.lb < m1->query.frag.lb ? m2->query.frag.lb : m1->query.frag.lb; m1->query.frag.rb = m2->query.frag.rb > m1->query.frag.rb ? m2->query.frag.rb : m1->query.frag.rb; /* sbjct */ /* links and seq_name do not need to change */ /* sbjct boundaries */ m1->sbjct.frag.lb = m2->sbjct.frag.lb < m1->sbjct.frag.lb ? m2->sbjct.frag.lb : m1->sbjct.frag.lb; m1->sbjct.frag.rb = m2->sbjct.frag.rb > m1->sbjct.frag.rb ? m2->sbjct.frag.rb : m1->sbjct.frag.rb; /* score */ if (m1->score == 999999 || m2->score == 999999) { m1->score = 999999; } else { m1->score = (m1->score%800000 + m2->score%800000)*(m1->sbjct.frag.rb - m1->sbjct.frag.lb)/(l1+l2); /* notice that the boundaries of m1 are now for the merged MSP */ if (m1->score + 800000 < 999999) { m1->score += 800000; } else { m1->score = 999999; } } return 0; } #endif IMAGE_t *partner(IMAGE_t *i) { if (i == &(i->to_msp->query)) { return &(i->to_msp->sbjct); } return &(i->to_msp->query); } int sing_cov(FRAG_t *f1, FRAG_t *f2, float cutoff) { int32_t l1, l2, l, lb, rb; if (f1->seq_name == f2->seq_name /*!strncmp(f1->seq_name, f2->seq_name, NAME_LEN)*/) { l1 = f1->rb - f1->lb; l2 = f2->rb - f2->lb; lb = f1->lb > f2->lb ? f1->lb : f2->lb; rb = f1->rb < f2->rb ? f1->rb : f2->rb; l = rb - lb; if ( (float) l/l1 >= cutoff || (float) l/l2 >= cutoff) { return 1; } } return 0; } int doub_cov(FRAG_t *f1, FRAG_t *f2, float cutoff) { int32_t l1, l2, l, lb, rb; if (f1->seq_name == f2->seq_name /*!strncmp(f1->seq_name, f2->seq_name, NAME_LEN)*/) { l1 = f1->rb - f1->lb; l2 = f2->rb - f2->lb; lb = f1->lb > f2->lb ? f1->lb : f2->lb; rb = f1->rb < f2->rb ? f1->rb : f2->rb; l = rb - lb; if ( (float) l/l1 >= cutoff && (float) l/l2 >= cutoff) { return 1; } } return 0; } RECON-1.08/src/ele.h0000644000076400007640000010251112274532636013553 0ustar rhubleyrepeat#include "msps.h" #define SIZE_LIMIT 500 #define TANDEM 5 typedef struct cp_list { int32_t cp; struct ele_info *contributor; struct cp_list *next; } CP_t; typedef struct bd_list { int32_t bd; int support; struct bd_list *next; } BD_t; typedef struct edge { int index; char type; /* 'p', 's', 'c' */ int direction; /* for clustering elements in consistent directions */ int32_t score; /* for edge_filt, to solve the PPS problem */ struct ele_info *ele1_info, *ele2_info; } EDGE_t; /* typedef struct edge_list { EDGE_t *to_edge; struct edge_list *next; } EDGE_DATA_t; */ typedef struct edge_tree { EDGE_t *to_edge; struct edge_tree *p, *l, *r; } EDGE_TREE_t; typedef struct element { int index; FRAG_t frag; int direction; short update, l_hold; int img_no, flimg_no, edge_no; IMG_TREE_t *to_img_tree; IMG_DATA_t *to_img_data; EDGE_TREE_t *edges; CP_t *PCP; BD_t *TBD; struct ele_list *redef; /* IMG_REC_t *ignored, *dissected; */ } ELEMENT_t; typedef struct ele_info { int index; ELEMENT_t *ele; char stat; /* 'z', 't', 'v', 'w', 'y', 'x' and 'X' */ short file_updated; struct family *to_family; struct ele_info *next; } ELE_INFO_t; typedef struct ele_list { struct ele_info *ele_info; struct ele_list *next; } ELE_DATA_t; typedef struct family { int index; char name[10]; ELE_DATA_t *members; struct fam_list *relatives; } FAMILY_t; typedef struct fam_list { struct family *to_family; struct fam_list *next; } FAM_DATA_t; ELEMENT_t *ele_init(int); ELE_INFO_t *ele_info_init(int); MSP_t *MSP_malloc(); void MSP_free(MSP_t *); EDGE_t *EDGE_malloc(); void EDGE_free(EDGE_t *); ELE_INFO_t *linked_ele(ELE_INFO_t *, EDGE_t *); void outthrow_big_tandems(FILE *); int int_cmp(const void *, const void *); void spit_out_ele(ELE_INFO_t *); ELEMENT_t *ele_read_in(ELE_INFO_t *, int); void img_scan(ELE_INFO_t *, char *, IMAGE_t **, int *); void edge_scan(char *, EDGE_t **, ELE_INFO_t *, int *); ELE_INFO_t *get_ele_info(int); void ele_write_out(ELE_INFO_t *, int); int img_index_cmp(const void *, const void *); int edge_index_cmp(const void *, const void *); void write_out_msps(FILE *, IMG_TREE_t *); void write_out_edges(FILE *, EDGE_TREE_t *, ELE_INFO_t *); void build_img_tree(IMG_TREE_t **, IMAGE_t **, int, int); int count_img_nodes(IMG_TREE_t *); void insert_image(IMG_TREE_t **, IMAGE_t *); void delete_image(IMG_TREE_t **, IMAGE_t *); IMG_TREE_t *minimal_image(IMG_TREE_t *); IMG_TREE_t *find_image(IMG_TREE_t *, int); IMG_DATA_t **listify(IMG_TREE_t *, IMG_DATA_t **); void build_edge_tree(EDGE_TREE_t **, EDGE_t **, int, int); int count_edge_nodes(EDGE_TREE_t *); int count_total_edges(EDGE_TREE_t *); void insert_edge(EDGE_TREE_t **, EDGE_t *); void delete_edge(EDGE_TREE_t **, EDGE_t *); EDGE_TREE_t *minimal_edge(EDGE_TREE_t *); EDGE_TREE_t *find_edge(EDGE_TREE_t *, int); void ele_info_free(ELE_INFO_t **); void ele_cleanup(ELEMENT_t **); void BD_free(BD_t **); void CP_free(CP_t **); void ele_data_free(ELE_DATA_t **); void img_data_free (IMG_DATA_t **); void img_tree_free(IMG_TREE_t **, ELE_INFO_t *); void img_tree_cleanup(IMG_TREE_t **, ELE_INFO_t *); void msp_data_free(MSP_DATA_t **); void edge_tree_cleanup(ELE_INFO_t *, EDGE_TREE_t **); void edge_tree_free(EDGE_TREE_t **); void fam_data_free(FAM_DATA_t **); void fam_data_cleanup(FAM_DATA_t **); void fam_cleanup(FAMILY_t **); void frag_data_free(FRAG_DATA_t **); void frag_data_cleanup(FRAG_DATA_t **); void print_ele_info(ELE_INFO_t *rt); void print_ele_data(ELE_DATA_t *rt); /*MSP_DATA_t *all_msps=NULL; EDGE_t *efav=NULL;*/ ELE_INFO_t **all_ele; int ele_ct, ele_array_size, fam_ct; int clan_size, clan_core_size; int32_t msp_in_mem, msp_left, msp_ct, msp_index; int32_t edge_index, edge_in_mem, edge_left, edge_ct; int32_t files_read, clan_ct, err_no; ELE_INFO_t *ele_info_data, *ele_info_tail; FAM_DATA_t *FAMs; FILE *err, *new_msps, *eles, *unproc, *combo, *obs, *fams, *log_file; /*************** * DEBUG * ***************/ void print_ele_data(ELE_DATA_t *rt) { if (!rt) return; print_ele_info( rt->ele_info ); if (rt->next) print_ele_data(rt->next); } void print_ele_info(ELE_INFO_t *rt) { if (!rt) return; printf("ele: index=%d, stat=%c, file_update=%d", rt->index, rt->stat, rt->file_updated ); if ( rt->to_family ) printf(" family_index=%d,", rt->to_family->index ); if ( rt->ele ) printf(" ele_index=%d", rt->ele->index ); else printf(" ele=NULL"); printf("\n"); } /*************** * Initializer * ***************/ ELEMENT_t *ele_init(int index) { ELEMENT_t *ele_tmp = (ELEMENT_t *) malloc(sizeof(ELEMENT_t)); ele_tmp->index = index; ele_tmp->direction = 1; ele_tmp->update = 0; ele_tmp->l_hold = 0; ele_tmp->img_no = 0; ele_tmp->flimg_no = 0; ele_tmp->edge_no = 0; ele_tmp->to_img_data = NULL; ele_tmp->to_img_tree = NULL; ele_tmp->edges = NULL; ele_tmp->PCP = NULL; ele_tmp->TBD = NULL; ele_tmp->redef = NULL; return ele_tmp; } ELE_INFO_t *ele_info_init(int index) { ELE_INFO_t *ele_info_tmp; ele_info_tmp = (ELE_INFO_t *) malloc(sizeof(ELE_INFO_t)); ele_info_tmp->index = index; ele_info_tmp->file_updated = 0; ele_info_tmp->stat = 'z'; ele_info_tmp->ele = NULL; ele_info_tmp->to_family = NULL; ele_info_tmp->next = NULL; return ele_info_tmp; } MSP_t *MSP_malloc() { MSP_t *msp_tmp = (MSP_t *) malloc(sizeof(MSP_t)); /*MSP_DATA_t *new_hanger = (MSP_DATA_t *) malloc(sizeof(MSP_DATA_t *));*/ msp_in_mem ++; msp_ct ++; /*new_hanger->to_msp = msp_tmp; new_hanger->next = all_msps; all_msps = new_hanger; msp_tmp->hanger = new_hanger;*/ return msp_tmp; } void MSP_free(MSP_t *m) { msp_in_mem --; /*m->hanger->to_msp = NULL;*/ free(m); } EDGE_t *EDGE_malloc() { EDGE_t *edge_tmp = (EDGE_t *) malloc(sizeof(EDGE_t)); edge_in_mem ++; edge_ct ++; return edge_tmp; } void EDGE_free(EDGE_t *ed) { edge_in_mem --; free(ed); } /*************** * Small Tools * ***************/ ELE_INFO_t *linked_ele(ELE_INFO_t *ele_info, EDGE_t *edge) { if (ele_info->index == edge->ele1_info->index) return edge->ele2_info; return edge->ele1_info; } void outthrow_big_tandems(FILE *size_list){ int ei, ino; FILE *ele_file; char ele_name[50], line[150], head[10], *msp = "msp"; int id, ele1, ele2; int *partners, i_ct, i, p_id, p_ct; int ratio; while (fgets(line, 25, size_list)) { sscanf(line, "%d %d\n", &ei, &ino); if (ino > SIZE_LIMIT) { sprintf(ele_name, "tmp/e%d", ei); ele_file = fopen(ele_name, "r"); if (!ele_file) { fprintf(log_file, "Can not open ele file %s. Exit.\n", ele_name); exit(2); } partners = (int *) malloc(ino*sizeof(int)); p_ct = 0; i_ct = -1; p_id = -1; while (fgets(line, 150, ele_file)) { sscanf(line, "%s %*s", head); if (!strncmp(head, msp, 3)) { sscanf(line, "msp %d %*c %*d %*f %*d %d %*s %*d %*d %d %*s %*d %*d\n", &id, &ele1, &ele2); i_ct ++; if (id%2) *(partners+i_ct) = ele1; else *(partners+i_ct) = ele2; } } qsort(partners, i_ct+1, sizeof(int), int_cmp); for (i=0; i<=i_ct; i++) { if (*(partners+i) != p_id) { p_id = *(partners+i); p_ct ++; } } if (ino/p_ct > TANDEM) { (*(all_ele+ei-1))->stat = 'O'; spit_out_ele(*(all_ele+ei-1)); } free(partners); fclose(ele_file); } } } int int_cmp(const void *i1, const void *i2) { return *((int *) i1) - *((int *) i2); } void spit_out_ele(ELE_INFO_t *ele_info) { /* char *command = (char *) malloc(100*sizeof(char));*/ ele_info->file_updated = 1; /* the reason for using ln instead of mv is to avoid changing files in tmp/ */ #if 0 sprintf(command, "ln -s tmp/e%d unproc/.\n", ele_info->index); if (system(command)) { fprintf(log_file, "error linking tmp/e%d to unproc/\n", ele_info->index); fflush(log_file); exit(6); } #endif fprintf(unproc, "%d\n", ele_info->index); /* free(command);*/ } /********************** * Read in an element * **********************/ ELEMENT_t *ele_read_in(ELE_INFO_t *ele_info, int stage) { char line[200], head[10], rest[150], *fn = (char *) malloc(20*sizeof(char)); char fragname[NAME_LEN]; int pos; FILE *fp; IMAGE_t **img_array; EDGE_t **edge_array; int holder, img_encountered=0, edge_encountered=0, ct; CP_t *new_pcp; BD_t *new_tbd; ELE_DATA_t *cur_ele_data; char *index="index", *stat = "stat", *file_updated="file_updated", *family="family", *direc="direc", *update="update", *l_hold="l_hold", *img_no="img_no", *flimg_no="flimg_no", *edge_no="edge_no", *frag="frag", *pcp="pcp", *tbd="tbd", *redef="redef", *msp="msp", *edge="edge"; if (ele_info->file_updated) sprintf(fn, "tmp2/e%d", ele_info->index); else sprintf(fn, "tmp/e%d", ele_info->index); fp = fopen(fn, "r"); /*if (!fp) { sprintf(fn, "tmp/e%d", ele_info->index); fp = fopen(fn, "r"); }*/ files_read ++; ele_info->ele = ele_init(ele_info->index); while (fgets(line, 200, fp)) { sscanf(line, "%s %*s", head); /* if (!strncmp(head, index, 10)) sscanf(rest, "%d\n", ele_info->index); if (!strncmp(head, stat, 10)) sscanf(rest, "%c\n", ele_info->stat); if (!strncmp(head, file_updated, 10)) sscanf(rest, "%d\n", ele_info->file_updated); */ /* if (!strncmp(head, l_hold, 10)) {sscanf(line, "%*s %d\n", &ele_info->ele->l_hold); continue;} */ if (!strncmp(head, update, 10)) {sscanf(line, "%*s %hd\n", &ele_info->ele->update); continue;} if (!strncmp(head, direc, 10)) {sscanf(line, "%*s %d\n", &ele_info->ele->direction); continue;} if (!strncmp(head, flimg_no, 10)) {sscanf(line, "%*s %d\n", &ele_info->ele->flimg_no); continue;} if (!strncmp(head, frag, 10)) { sscanf(line, "%*s %s %d %d\n", fragname, &ele_info->ele->frag.lb, &ele_info->ele->frag.rb); pos = GetSeqIndex(0, seq_no-1, fragname); ele_info->ele->frag.seq_name = *(seq_names+pos); if (ele_info->ele->frag.lb > ele_info->ele->frag.rb) { fprintf(log_file, "error: ele %d reversed from read_in\n", ele_info->index); fflush(log_file); exit(3); } continue; } if (!strncmp(head, edge_no, 10)) { sscanf(line, "%*s %d\n", &ele_info->ele->edge_no); if (ele_info->ele->edge_no) edge_array = (EDGE_t **) malloc(ele_info->ele->edge_no*sizeof(EDGE_t *)); continue; } if (!strncmp(head, edge, 10)) { if (edge_encountered < ele_info->ele->edge_no) { edge_scan(line, edge_array, ele_info, &edge_encountered); } else { err_no ++; fprintf(log_file, "error: more edges in file for ele %d\n", ele_info->index); fflush(log_file); exit(4); } continue; } if (!strncmp(head, img_no, 10)) { sscanf(line, "%*s %d\n", &ele_info->ele->img_no); if (stage != 3 && ele_info->ele->img_no) img_array = (IMAGE_t **) malloc(ele_info->ele->img_no*sizeof(IMAGE_t *)); continue; } if (stage != 3 && !strncmp(head, msp, 10)) { if (img_encountered < ele_info->ele->img_no) { img_scan(ele_info, line, img_array, &img_encountered); } else { err_no ++; fprintf(log_file, "error: more image in file for ele %d\n", ele_info->index); fflush(log_file); exit(2); } continue; } if (stage < 2 && !strncmp(head, pcp, 10)) { new_pcp = (CP_t *) malloc(sizeof(CP_t)); sscanf(line, "%*s %d %d\n", &new_pcp->cp, &holder); new_pcp->contributor = get_ele_info(holder); new_pcp->next = ele_info->ele->PCP; ele_info->ele->PCP = new_pcp; continue; } if (!strncmp(head, tbd, 10)) { new_tbd = (BD_t *) malloc(sizeof(BD_t)); sscanf(line, "%*s %d %d\n", &new_tbd->bd, &new_tbd->support); new_tbd->next = ele_info->ele->TBD; ele_info->ele->TBD = new_tbd; continue; } if (!strncmp(head, redef, 10)) { sscanf(line, "%*s %d\n", &holder); cur_ele_data = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t)); cur_ele_data->ele_info = get_ele_info(holder); cur_ele_data->next = ele_info->ele->redef; ele_info->ele->redef = cur_ele_data->next; continue; } } fclose(fp); free(fn); if (stage != 3 && img_encountered != ele_info->ele->img_no) { if (ele_info->file_updated) { /* we spit out elements with too many images, so some of their partners might have less images left than img_no */ err_no ++; fprintf(log_file, "error: %d: image number not matched.\n", ele_info->index); fflush(log_file); exit(2); } ele_info->ele->img_no = img_encountered; } if (edge_encountered != ele_info->ele->edge_no) { err_no ++; fprintf(log_file, "error: %d: edge number not matched.\n", ele_info->index); fflush(log_file); exit(4); ele_info->ele->edge_no = edge_encountered; } /*ele_info->ele->index = ele_info->index;*/ if (edge_encountered) { qsort(edge_array, edge_encountered, sizeof(EDGE_t *), edge_index_cmp); build_edge_tree(&ele_info->ele->edges, edge_array, 0, edge_encountered-1); /*ct = count_edge_nodes(ele_info->ele->edges); if (ct != edge_encountered) { err_no ++; fprintf(log_file, "error: trouble building edge tree: %d %d\n", edge_encountered, ct); fflush(log_file); exit(4); }*/ free(edge_array); } if (stage != 3 && ele_info->ele->img_no) { qsort(img_array, img_encountered, sizeof(IMAGE_t *), img_index_cmp); build_img_tree(&ele_info->ele->to_img_tree, img_array, 0, img_encountered-1); /*ct = count_img_nodes(ele_info->ele->to_img_tree); if (ct != img_encountered) { err_no ++; fprintf(log_file, "error: trouble building the image tree: %d %d\n", img_encountered, ct); fflush(log_file); exit(2); }*/ free(img_array); } ele_info->file_updated = 1; return ele_info->ele; } void img_scan(ELE_INFO_t *ele_info, char *line, IMAGE_t **img_array, int *img_encountered_ptr) { MSP_t *msp_tmp = MSP_malloc(); int id, ele1, ele2, id2; ELE_INFO_t *epi; IMAGE_t *ip; char qname[NAME_LEN], sname[NAME_LEN]; int pos; /*printf("%s", line);*/ sscanf(line, "msp %d %c %d %f %d %d %s %d %d %d %s %d %d\n", &id, &msp_tmp->stat, &msp_tmp->score, &msp_tmp->iden, &msp_tmp->direction, &ele1, qname, &msp_tmp->query.frag.lb, &msp_tmp->query.frag.rb, &ele2, sname, &msp_tmp->sbjct.frag.lb, &msp_tmp->sbjct.frag.rb); pos = GetSeqIndex(0, seq_no-1, qname); msp_tmp->query.frag.seq_name = *(seq_names+pos); pos = GetSeqIndex(0, seq_no-1, sname); msp_tmp->sbjct.frag.seq_name = *(seq_names+pos); if (id%2) { epi = get_ele_info(ele1); id2 = id - 1; } else { epi = get_ele_info(ele2); id2 = id + 1; } if (epi->stat == 'O') { MSP_free(msp_tmp); } else { if (ele1 != ele2) { if (epi->ele) { ip = find_image(epi->ele->to_img_tree, id2)->to_image; if (id%2) *(img_array+*img_encountered_ptr) = &ip->to_msp->sbjct; else *(img_array+*img_encountered_ptr) = &ip->to_msp->query; MSP_free(msp_tmp); } else { if (id%2) { msp_tmp->query.index = id2; msp_tmp->sbjct.index = id; *(img_array+*img_encountered_ptr) = &msp_tmp->sbjct; msp_tmp->query.ele_info = epi; msp_tmp->sbjct.ele_info = ele_info; } else { msp_tmp->query.index = id; msp_tmp->sbjct.index = id2; *(img_array+*img_encountered_ptr) = &msp_tmp->query; msp_tmp->query.ele_info = ele_info; msp_tmp->sbjct.ele_info = epi; } msp_tmp->query.to_msp = msp_tmp; msp_tmp->sbjct.to_msp = msp_tmp; /*msp_in_mem ++;*/ /*msp_ct ++;*/ } (*img_encountered_ptr) ++; } else { if (id%2) { msp_tmp->query.index = id2; msp_tmp->sbjct.index = id; msp_tmp->query.ele_info = epi; msp_tmp->sbjct.ele_info = ele_info; } else { msp_tmp->query.index = id; msp_tmp->sbjct.index = id2; msp_tmp->query.ele_info = ele_info; msp_tmp->sbjct.ele_info = epi; } msp_tmp->query.to_msp = msp_tmp; msp_tmp->sbjct.to_msp = msp_tmp; *(img_array+*img_encountered_ptr) = &msp_tmp->sbjct; (*img_encountered_ptr) ++; *(img_array+*img_encountered_ptr) = &msp_tmp->query; (*img_encountered_ptr) ++; /*msp_in_mem ++;*/ /*msp_ct ++;*/ } } } void edge_scan(char *line, EDGE_t **edge_array, ELE_INFO_t *ele_info, int *edge_encountered_ptr){ EDGE_t *new = EDGE_malloc(); int ele1, ele2; ELE_INFO_t *epi; sscanf(line, "edge %d %c %d %d %d %d\n", &new->index, &new->type, &new->direction, &new->score, &ele1, &ele2); if (ele1 != ele2 && new->type != 'c') { /* bullet proof */ if (ele_info->index == ele1) { epi = get_ele_info(ele2); new->ele1_info = ele_info; new->ele2_info = epi; } else { epi = get_ele_info(ele1); new->ele1_info = epi; new->ele2_info = ele_info; } if (epi->ele) { *(edge_array+*edge_encountered_ptr) = find_edge(epi->ele->edges, new->index)->to_edge; EDGE_free(new); } else { *(edge_array+*edge_encountered_ptr) = new; } (*edge_encountered_ptr) ++; }else EDGE_free(new); } ELE_INFO_t *get_ele_info(int index) { ELE_INFO_t *cur; if (index <= ele_array_size) return *(all_ele+index-1); cur = ele_info_data; while (cur && cur->index < index) { cur = cur->next; } if (cur && cur->index == index) return cur; return NULL; } int img_index_cmp(const void *i1, const void *i2) { return (*((IMAGE_t **) i1))->index - (*((IMAGE_t **) i2))->index; } int edge_index_cmp(const void *ed1, const void *ed2) { return (*((EDGE_t **) ed1))->index - (*((EDGE_t **) ed2))->index; } /************************ * Write out an element * ************************/ void ele_write_out(ELE_INFO_t *ele_info, int stage) { char *fn = (char *) malloc(50*sizeof(char)); FILE *fp; CP_t *cur_pcp; BD_t *cur_bd; ELE_DATA_t *cur_ele_data; int ct; /* sprintf(fn, "tmp2/clan/e%d", ele_info->index);*/ sprintf(fn, "tmp2/e%d", ele_info->index); fp = fopen(fn, "w"); /* fprintf(fp, "index %d\n", ele_info->index); fprintf(fp, "stat %s\n", ele_info->stat); fprintf(fp, "file_updated %d\n", ele_info->file_updated); if (ele_info->to_family) fprintf(fp, "family %d\n", ele_info->to_family->index); */ fprintf(fp, "frag %s %d %d\n", ele_info->ele->frag.seq_name, ele_info->ele->frag.lb, ele_info->ele->frag.rb); /* if (ele_info->ele->l_hold) fprintf(fp, "l_hold %d\n", ele_info->ele->l_hold); */ if (ele_info->ele->direction != 1) fprintf(fp, "direc %d\n", ele_info->ele->direction); if (ele_info->ele->update) fprintf(fp, "update %d\n", ele_info->ele->update); /*ct = count_edge_nodes(ele_info->ele->edges); if (ct > ele_info->ele->edge_no) { err_no ++; fprintf(log_file, "error: more edges than known: ele %d, %d, %d\n", ele_info->index, ele_info->ele->edge_no, ct); fflush(log_file); exit(4); } else if (ct < ele_info->ele->edge_no) { err_no ++; fprintf(log_file, "error: less edges than known: ele %d, %d, %d\n", ele_info->index, ele_info->ele->edge_no, ct); fflush(log_file); exit(4); }*/ /*ct = count_img_nodes(ele_info->ele->to_img_tree); if (ct > ele_info->ele->img_no) { err_no ++; fprintf(log_file, "error: more images than known: ele %d, %d, %d\n", ele_info->index, ele_info->ele->img_no, ct); fflush(log_file); exit(2); } else if (ct < ele_info->ele->img_no) { err_no ++; fprintf(log_file, "error: less images than known: ele %d, %d, %d\n", ele_info->index, ele_info->ele->img_no, ct); fflush(log_file); exit(2); }*/ fprintf(fp, "img_no %d\n", ele_info->ele->img_no); if (ele_info->ele->flimg_no) fprintf(fp, "flimg_no %d\n", ele_info->ele->flimg_no); fprintf(fp, "edge_no %d\n", ele_info->ele->edge_no); if (ele_info->ele->img_no) write_out_msps(fp, ele_info->ele->to_img_tree); if (ele_info->ele->edge_no) write_out_edges(fp, ele_info->ele->edges, ele_info); if (stage < 2 && ele_info->ele->PCP) { /*fprintf(fp, "PCPs \n");*/ cur_pcp = ele_info->ele->PCP; while (cur_pcp) { fprintf(fp, "pcp %d %d\n", cur_pcp->cp, cur_pcp->contributor->index); cur_pcp = cur_pcp->next; } } if (ele_info->ele->TBD) { /*fprintf(fp, "TBDs \n");*/ cur_bd = ele_info->ele->TBD; while (cur_bd) { fprintf(fp, "tbd %d %d\n", cur_bd->bd, cur_bd->support); cur_bd = cur_bd->next; } } if (ele_info->ele->redef) { /*fprintf(fp, "redefs \n");*/ cur_ele_data = ele_info->ele->redef; while (cur_ele_data) { fprintf(fp, "redef %d\n", cur_ele_data->ele_info->index); cur_ele_data = cur_ele_data->next; } } fclose(fp); free(fn); } void write_out_msps(FILE *fp, IMG_TREE_t *rt) { if (rt->l) write_out_msps(fp, rt->l); if (rt->to_image->to_msp->query.ele_info->index != rt->to_image->to_msp->sbjct.ele_info->index || rt->to_image == &rt->to_image->to_msp->sbjct) { /* trick to report self MSPs only once */ fprintf(fp, "msp %d ", rt->to_image->index); fprintf(fp, "%c ", rt->to_image->to_msp->stat); fprintf(fp, "%d %3.1f %d ", rt->to_image->to_msp->score, rt->to_image->to_msp->iden, rt->to_image->to_msp->direction); fprintf(fp, "%d %s %d %d ", rt->to_image->to_msp->query.ele_info->index, rt->to_image->to_msp->query.frag.seq_name, rt->to_image->to_msp->query.frag.lb, rt->to_image->to_msp->query.frag.rb); fprintf(fp, "%d %s %d %d\n", rt->to_image->to_msp->sbjct.ele_info->index, rt->to_image->to_msp->sbjct.frag.seq_name, rt->to_image->to_msp->sbjct.frag.lb, rt->to_image->to_msp->sbjct.frag.rb); } if (rt->r) write_out_msps(fp, rt->r); } void write_out_edges(FILE *fp, EDGE_TREE_t *rt, ELE_INFO_t *ele_info) { if (rt->l) write_out_edges(fp, rt->l, ele_info); if (rt->to_edge->type != 'c' && rt->to_edge->ele1_info->index != rt->to_edge->ele2_info->index) { fprintf(fp, "edge %d %c %d %d %d %d\n", rt->to_edge->index, rt->to_edge->type, rt->to_edge->direction, rt->to_edge->score, rt->to_edge->ele1_info->index, rt->to_edge->ele2_info->index); } else { fprintf(log_file, "error: illegitimate edges in ele %d\n", ele_info->index); fflush(log_file); exit(4); } if (rt->r) write_out_edges(fp, rt->r, ele_info); } /*************************** * manipulating image tree * ***************************/ void build_img_tree(IMG_TREE_t **rt_ptr, IMAGE_t **img_array, int ori, int end) { int mid = (ori+end)/2; IMG_TREE_t *new = (IMG_TREE_t *) malloc(sizeof(IMG_TREE_t)); new->to_image = *(img_array+mid); new->l = NULL; new->r = NULL; new->p = NULL; *rt_ptr = new; if (mid > ori) { build_img_tree(&new->l, img_array, ori, mid-1); new->l->p = new; } if (mid < end) { build_img_tree(&new->r, img_array, mid+1, end); new->r->p = new; } } int count_img_nodes(IMG_TREE_t *rt) { int ct=0; if (!rt) return 0; if (rt->l) ct += count_img_nodes(rt->l); if (rt->r) ct += count_img_nodes(rt->r); ct ++; return ct; } void insert_image(IMG_TREE_t **rt_ptr, IMAGE_t *i) { IMG_TREE_t *new, *x, *y; new = (IMG_TREE_t *) malloc(sizeof(IMG_TREE_t)); new->to_image = i; new->p = NULL; new->l = NULL; new->r = NULL; y = NULL; x = *rt_ptr; while (x) { y = x; if (new->to_image->index < x->to_image->index) x = x->l; else x = x->r; } new->p = y; if (!y) *rt_ptr = new; else { if (new->to_image->index < y->to_image->index) y->l = new; else y->r = new; } } void delete_image(IMG_TREE_t **rt_ptr, IMAGE_t *i) { IMG_TREE_t *x, *y, *z; if (!(*rt_ptr)) { err_no ++; fprintf(log_file, "error: Image tree does not exist: %d\n", i->ele_info->index); fflush(log_file); exit(2); return; } z= find_image(*rt_ptr, i->index); if (z) { if (!z->l || !z->r) y = z; else y = minimal_image(z->r); if (y->l) x = y->l; else x = y->r; if (x) x->p = y->p; if (!y->p) *rt_ptr = x; else { if (y == y->p->l) y->p->l = x; else y->p->r = x; } if (y != z) z->to_image = y->to_image; free(y); } else { err_no ++; fprintf(log_file, "error: Can not find the image in the tree: %d %d\n", i->ele_info->index, i->index); fflush(log_file); exit(2); return; } } IMG_TREE_t *minimal_image(IMG_TREE_t *rt) { while (rt->l) { rt = rt->l; } return rt; } IMG_TREE_t *find_image(IMG_TREE_t *rt, int index) { while (rt && index != rt->to_image->index) { if (index < rt->to_image->index) rt = rt->l; else rt = rt->r; } return rt; } IMG_DATA_t **listify(IMG_TREE_t *rt, IMG_DATA_t **tail_ptr) { IMG_DATA_t *new, **new_tail_ptr; if (!rt) return NULL; if (rt->l) tail_ptr = listify(rt->l, tail_ptr); new = (IMG_DATA_t *) malloc(sizeof(IMG_DATA_t)); new->to_image = rt->to_image; new->next = NULL; *tail_ptr = new; tail_ptr = &new->next; if (rt->r) tail_ptr = listify(rt->r, tail_ptr); return tail_ptr; } /************************** * Manipulating edge tree * **************************/ void build_edge_tree(EDGE_TREE_t **rt_ptr, EDGE_t **edge_array, int ori, int end) { int mid = (ori+end)/2; EDGE_TREE_t *new = (EDGE_TREE_t *) malloc(sizeof(EDGE_TREE_t)); new->to_edge = *(edge_array+mid); new->l = NULL; new->r = NULL; new->p = NULL; *rt_ptr = new; if (mid > ori) { build_edge_tree(&new->l, edge_array, ori, mid-1); new->l->p = new; } if (mid < end) { build_edge_tree(&new->r, edge_array, mid+1, end); new->r->p = new; } } int count_edge_nodes(EDGE_TREE_t *rt) { int ct=0; if (!rt) return 0; if (rt->l) ct += count_edge_nodes(rt->l); if (rt->r) ct += count_edge_nodes(rt->r); if (rt->to_edge->type != 'c' && rt->to_edge->ele1_info->index != rt->to_edge->ele2_info->index) ct ++; return ct; } int count_total_edges(EDGE_TREE_t *rt) { int ct=0; if (!rt) return 0; if (rt->l) ct += count_total_edges(rt->l); if (rt->r) ct += count_total_edges(rt->r); ct ++; return ct; } void insert_edge(EDGE_TREE_t **rt_ptr, EDGE_t *ed) { EDGE_TREE_t *new, *x, *y; new = (EDGE_TREE_t *) malloc(sizeof(EDGE_TREE_t)); new->to_edge = ed; new->p = NULL; new->l = NULL; new->r = NULL; y = NULL; x = *rt_ptr; while (x) { y = x; if (new->to_edge->index < x->to_edge->index) x = x->l; else x = x->r; } new->p = y; if (!y) *rt_ptr = new; else { if (new->to_edge->index < y->to_edge->index) y->l = new; else y->r = new; } } void delete_edge(EDGE_TREE_t **rt_ptr, EDGE_t *ed) { EDGE_TREE_t *x, *y, *z; if (!(*rt_ptr)) { err_no ++; fprintf(log_file, "error: edge tree empty: %d %d %d\n", ed->index, ed->ele1_info->index, ed->ele2_info->index); fflush(log_file); exit(4); } z= find_edge(*rt_ptr, ed->index); if (z) { if (!z->l || !z->r) y = z; else y = minimal_edge(z->r); if (y->l) x = y->l; else x = y->r; if (x) x->p = y->p; if (!y->p) *rt_ptr = x; else { if (y == y->p->l) y->p->l = x; else y->p->r = x; } if (y != z) z->to_edge = y->to_edge; free(y); } else { err_no ++; fprintf(log_file, "error: Can not find edge %d between ele %d and %d\n", ed->index, ed->ele1_info->index, ed->ele2_info->index); fflush(log_file); exit(4); } } EDGE_TREE_t *minimal_edge(EDGE_TREE_t *rt) { while (rt->l) { rt = rt->l; } return rt; } EDGE_TREE_t *find_edge(EDGE_TREE_t *rt, int index) { while (rt && index != rt->to_edge->index) { if (index < rt->to_edge->index) rt = rt->l; else rt = rt->r; } return rt; } /************************ ************************ *** *** *** CLEANING UPS *** *** *** ************************ ************************/ void ele_info_free(ELE_INFO_t **ei) { ELE_INFO_t *cur, *next; cur = *ei; while (cur) { next = cur->next; free(cur); cur = next; } *ei = NULL; } void ele_data_free (ELE_DATA_t **e) { ELE_DATA_t *cur, *next; cur = *e; while (cur != NULL) { next = cur->next; free(cur); cur = next; } *e = NULL; } /* void ele_data_cleanup (ELE_DATA_t **e) { ELE_DATA_t *cur, *next, *dangler; cur = *e; while (cur != NULL) { next = cur->next; if (cur->ele_info->ele->redef) { ele_data_cleanup(&cur->ele_info->ele->redef); } ele_cleanup(&cur->ele_info->ele); free(cur); cur = next; } *e = NULL; } */ void ele_cleanup(ELEMENT_t **e) { ELE_INFO_t *ele_info; int ct; if (!(*e)) return; if ((*e)->frag.lb > (*e)->frag.rb) { fprintf(log_file, "error: ele %d reversed before clean up\n", (*e)->index); fflush(log_file); exit(3); } /* reason for finding ele_info here instead of passing it over when calling the function is that this way, ele_cleanup() will be more independent of the ele_info structure */ ele_info = get_ele_info((*e)->index); if ((*e)->to_img_data) img_data_free(&(*e)->to_img_data); if ((*e)->PCP) CP_free(&(*e)->PCP); if ((*e)->TBD) BD_free(&(*e)->TBD); if ((*e)->edges) edge_tree_cleanup(ele_info, &(*e)->edges); if ((*e)->edge_no) { err_no ++; fprintf(log_file, "error: element %d, %d edges left\n", (*e)->index, (*e)->edge_no); fflush(log_file); exit(4); } if ((*e)->to_img_tree) { /*ct = count_img_nodes((*e)->to_img_tree); if (ct != (*e)->img_no) { err_no ++; fprintf(log_file, "error: image keeping not synchronized: ele %d %d %d\n", (*e)->index, (*e)->img_no, ct); fflush(log_file); exit(2); }*/ img_tree_cleanup(&(*e)->to_img_tree, ele_info); if ((*e)->img_no) { err_no ++; fprintf(log_file, "error: element %d, %d images left\n", (*e)->index, (*e)->img_no); fflush(log_file); exit(2); } } if ((*e)->redef) ele_data_free(&(*e)->redef); free(*e); *e = NULL; } void BD_free (BD_t **bds) { BD_t *cur, *next; cur = *bds; while (cur != NULL) { next = cur->next; free(cur); cur = next; } *bds = NULL; } void CP_free (CP_t **cps) { CP_t *cur, *next; cur = *cps; while (cur != NULL) { next = cur->next; free(cur); cur = next; } *cps = NULL; } void img_data_free (IMG_DATA_t **i) { IMG_DATA_t *cur, *next; cur = *i; while (cur != NULL) { next = cur->next; free(cur); cur = next; } *i = NULL; } void img_tree_cleanup(IMG_TREE_t **rt_p, ELE_INFO_t *ele_info) { ELE_INFO_t *ep; if ((*rt_p)->l) img_tree_cleanup(&(*rt_p)->l, ele_info); if ((*rt_p)->r) img_tree_cleanup(&(*rt_p)->r, ele_info); ele_info->ele->img_no --; ep = partner((*rt_p)->to_image)->ele_info; if (ep == (*rt_p)->to_image->ele_info) { /* this is a hack here. we cann't simply free self msps 'cuz that way when we run across the second image in the tree, the to_image pointer will be pointing to space already freed. So we mark a self msp by changing its stat when we first see it, and when we see it the second time, which means when a self msp is alredy marked, we free it. Same thing for self edges. only we change the type of the edge to 'm' */ if ((*rt_p)->to_image->to_msp->stat != 'm') (*rt_p)->to_image->to_msp->stat = 'm'; else { MSP_free((*rt_p)->to_image->to_msp); /*msp_in_mem --;*/ } } else if (!ep->ele) { MSP_free((*rt_p)->to_image->to_msp); /*msp_in_mem --;*/ } free(*rt_p); *rt_p = NULL; } void img_tree_free(IMG_TREE_t **rt_p, ELE_INFO_t *ele_info) { if ((*rt_p)->l) img_tree_free(&(*rt_p)->l, ele_info); if ((*rt_p)->r) img_tree_free(&(*rt_p)->r, ele_info); ele_info->ele->img_no --; free(*rt_p); *rt_p = NULL; } void edge_tree_cleanup(ELE_INFO_t *ele_info, EDGE_TREE_t **rt_p) { ELE_INFO_t *ep; if ((*rt_p)->l) edge_tree_cleanup(ele_info, &(*rt_p)->l); if ((*rt_p)->r) edge_tree_cleanup(ele_info, &(*rt_p)->r); if (ele_info->index == (*rt_p)->to_edge->ele1_info->index) ep = (*rt_p)->to_edge->ele2_info; else ep = (*rt_p)->to_edge->ele1_info; if (!ep->ele) EDGE_free((*rt_p)->to_edge); ele_info->ele->edge_no --; free(*rt_p); *rt_p = NULL; } void edge_tree_free(EDGE_TREE_t **rt_p) { if ((*rt_p)->l) edge_tree_free(&(*rt_p)->l); if ((*rt_p)->r) edge_tree_free(&(*rt_p)->r); free(*rt_p); *rt_p = NULL; } /* void img_data_cleanup (IMG_DATA_t **i) { IMG_DATA_t *cur, *next; cur = *i; while (cur != NULL) { next = cur->next; free(cur->to_image); free(cur); cur = next; } *i = NULL; } */ void fam_data_free(FAM_DATA_t **fd) { FAM_DATA_t *cur, *next; cur = *fd; while (cur != NULL) { next = cur->next; free(cur); cur = next; } *fd = NULL; } void fam_data_cleanup(FAM_DATA_t **fd) { FAM_DATA_t *cur, *next; cur = *fd; while (cur != NULL) { next = cur->next; fam_cleanup(&cur->to_family); free(cur); cur = next; } *fd = NULL; } void fam_cleanup(FAMILY_t **f) { if ((*f)->members != NULL) ele_data_free(&(*f)->members); if ((*f)->relatives != NULL) fam_data_free(&(*f)->relatives); free(*f); *f = NULL; } /* Unused */ void msp_data_free(MSP_DATA_t **md) { MSP_DATA_t *cur, *next; cur = *md; while (cur != NULL) { next = cur->next; /*if (cur->to_msp) MSP_free(cur->to_msp);*/ free(cur); cur = next; } *md = NULL; } /* void edge_data_free(EDGE_DATA_t **ed) { EDGE_DATA_t *cur, *next; cur = *ed; while (cur != NULL) { next = cur->next; free(cur); cur = next; } *ed = NULL; } void edge_data_cleanup(EDGE_DATA_t **ed) { EDGE_DATA_t *cur, *next; cur = *ed; while (cur != NULL) { next = cur->next; free(cur->to_edge); free(cur); cur = next; } *ed = NULL; } */ void frag_data_free(FRAG_DATA_t **fd) { FRAG_DATA_t *cur, *next; cur = *fd; while (cur != NULL) { next = cur->next; free(cur); cur = next; } *fd = NULL; } void frag_data_cleanup(FRAG_DATA_t **fd) { FRAG_DATA_t *cur, *next; cur = *fd; while (cur != NULL) { next = cur->next; free(cur->to_frag); free(cur); cur = next; } *fd = NULL; } RECON-1.08/src/eledef.c0000644000076400007640000003204012274532636014224 0ustar rhubleyrepeat#include "msps.h" #define IMG_CAP 500000 #define INCLUDE_IMAGE if (method == 1) {cov=sing_cov(&ele_frag, &cur->to_image->frag, cutoff);}\ else {cov=doub_cov(&ele_frag, &cur->to_image->frag, cutoff);}\ if (cov) {\ img_ct ++;\ if (cur->to_image->index%2) {\ (*(all_mprot+cur->to_image->index/2))->se = (*ecp);\ } else {\ (*(all_mprot+cur->to_image->index/2))->pe = (*ecp);\ }\ fprintf(img_prot, "%d %d\n", (*ecp), cur->to_image->index);\ fflush(img_prot);\ if (!cur->next) tail = prev;\ if (prev) prev->next = cur->next;\ else remain = cur->next;\ if (ele_frag.rb < cur->to_image->frag.rb) {\ ele_frag.rb = cur->to_image->frag.rb;\ free(cur->to_image);\ free(cur);\ cur = remain;\ prev = NULL;\ } else {\ free(cur->to_image);\ free(cur);\ if (prev) cur = prev->next;\ else cur = remain;\ }\ } else {\ prev = cur;\ cur = cur->next;\ } #define ADD_EP ep_tmp = (EPROT_t *) malloc(sizeof(EPROT_t));\ ep_tmp->flag = 0;\ ep_tmp->index = (*ecp);\ ep_tmp->img_no = img_ct;\ ep_tmp->frag = ele_frag;\ ep_tmp->next = NULL;\ if (*all_epp) ep_tail->next = ep_tmp;\ else *all_epp = ep_tmp;\ ep_tail = ep_tmp;\ fprintf(all_ele, "%d %s %d %d\n", (*ecp), ele_frag.seq_name, ele_frag.lb, ele_frag.rb) #define RITE_THING ritetime = 0;\ (*ecp) ++;\ img_ct = 1;\ ele_frag = cur->to_image->frag;\ if (cur->to_image->index%2) {\ (*(all_mprot+cur->to_image->index/2))->se = (*ecp);\ } else {\ (*(all_mprot+cur->to_image->index/2))->pe = (*ecp);\ }\ fprintf(img_prot, "%d %d\n", (*ecp), cur->to_image->index);\ fflush(img_prot);\ remain = cur->next;\ free(cur->to_image);\ free(cur);\ prev = NULL;\ cur = remain #define DO_IT if (ele_frag.seq_name == cur->to_image->frag.seq_name /*!strncmp(ele_frag.seq_name, cur->to_image->frag.seq_name, NAME_LEN)*/ && ele_frag.rb - cur->to_image->frag.lb > 10) {\ INCLUDE_IMAGE;\ } else {\ ADD_EP;\ ritetime = 1;\ break;\ } #define BACK_UP imgp = (IMAGE_t *) malloc(sizeof(IMAGE_t));\ *imgp = img;\ tmp = (IMG_DATA_t *) malloc(sizeof(IMG_DATA_t));\ tmp->to_image = imgp;\ tmp->next = NULL;\ if (!remain) {\ remain = tmp;\ } else {\ tail->next = tmp;\ }\ tail = tmp #define DUMBBELL img_charge(iprot_shadow, iprot_ct, msp_file);\ for (i=0; iindex%2) {\ partner_index = (*(all_mprot+(*(all_iprot+i))->index/2))->pe;\ } else {\ partner_index = (*(all_mprot+(*(all_iprot+i))->index/2))->se;\ }\ if ((*(all_iprot+i))->to_msp->score) {\ if (!(*(ep_array+((*(all_iprot+i))->ele_index-1)))->flag) {\ sprintf(ele_name, "ele_def_res/e%d", (*(all_iprot+i))->ele_index);\ freopen(ele_name, "w", all_ele);\ fprintf(all_ele, "index %d\n", (*(all_iprot+i))->ele_index);\ fprintf(all_ele, "frag %s %d %d\n", (*(ep_array+((*(all_iprot+i))->ele_index-1)))->frag.seq_name, (*(ep_array+((*(all_iprot+i))->ele_index-1)))->frag.lb, (*(ep_array+((*(all_iprot+i))->ele_index-1)))->frag.rb);\ fprintf(all_ele, "img_no %d\n", (*(ep_array+((*(all_iprot+i))->ele_index-1)))->img_no);\ fprintf(size_list, "%d %d\n", (*(all_iprot+i))->ele_index, (*(ep_array+((*(all_iprot+i))->ele_index-1)))->img_no);\ (*(ep_array+((*(all_iprot+i))->ele_index-1)))->flag = 1;\ }\ if (partner_index != (*(all_iprot+i))->ele_index) {\ if ((*(all_iprot+i))->index%2) fprintf(all_ele, "msp %d s %d %.1f %d %d %s %d %d %d %s %d %d\n", (*(all_iprot+i))->index, (*(all_iprot+i))->to_msp->score, (*(all_iprot+i))->to_msp->iden, (*(all_iprot+i))->to_msp->direction, partner_index, (*(all_iprot+i))->to_msp->query.frag.seq_name, (*(all_iprot+i))->to_msp->query.frag.lb, (*(all_iprot+i))->to_msp->query.frag.rb, (*(all_iprot+i))->ele_index, (*(all_iprot+i))->to_msp->sbjct.frag.seq_name, (*(all_iprot+i))->to_msp->sbjct.frag.lb, (*(all_iprot+i))->to_msp->sbjct.frag.rb);\ else fprintf(all_ele, "msp %d s %d %.1f %d %d %s %d %d %d %s %d %d\n", (*(all_iprot+i))->index, (*(all_iprot+i))->to_msp->score, (*(all_iprot+i))->to_msp->iden, (*(all_iprot+i))->to_msp->direction, (*(all_iprot+i))->ele_index, (*(all_iprot+i))->to_msp->query.frag.seq_name, (*(all_iprot+i))->to_msp->query.frag.lb, (*(all_iprot+i))->to_msp->query.frag.rb, partner_index, (*(all_iprot+i))->to_msp->sbjct.frag.seq_name, (*(all_iprot+i))->to_msp->sbjct.frag.lb, (*(all_iprot+i))->to_msp->sbjct.frag.rb);\ } else {\ if ((*(all_iprot+i))->index%2) fprintf(all_ele, "msp %d s %d %.1f %d %d %s %d %d %d %s %d %d\n", (*(all_iprot+i))->index, (*(all_iprot+i))->to_msp->score, (*(all_iprot+i))->to_msp->iden, (*(all_iprot+i))->to_msp->direction, partner_index, (*(all_iprot+i))->to_msp->query.frag.seq_name, (*(all_iprot+i))->to_msp->query.frag.lb, (*(all_iprot+i))->to_msp->query.frag.rb, (*(all_iprot+i))->ele_index, (*(all_iprot+i))->to_msp->sbjct.frag.seq_name, (*(all_iprot+i))->to_msp->sbjct.frag.lb, (*(all_iprot+i))->to_msp->sbjct.frag.rb);\ }\ }\ } typedef struct msp_prototype { int pe, se; } MPROT_t; typedef struct img_prototype { int index, ele_index; MSP_t *to_msp; } IPROT_t; typedef struct ele_prototype { short flag; int index, img_no; FRAG_t frag; struct ele_prototype *next; } EPROT_t; void ele_def(int, FILE *, float, EPROT_t **, int *, MPROT_t **); void img_charge(IPROT_t **, int, FILE *); int index_cmp(const void *, const void *); FILE *msp_no, *all_ele, *img_prot, *ele_no, *err, *size_list; int main (int argc, char *argv[]) { int ele_ct=0, msp_ct, i, method; float cutoff; char line[150], *m1="single", *m2="double"; MPROT_t **all_mprot; EPROT_t *all_ep=NULL, **ep_array, *ep_tmp; IPROT_t **all_iprot, **iprot_shadow; int iprot_ct=0, partner_index; char ele_name[50]; /*name of element used as name of the ele file*/ FILE *frags, *seq_list, *msp_file; /* processing command line */ if (argc == 1) { printf("usage: ele_def seq_list msp_file method cut_off\nfor method, choose 'single' or 'double'\ncutoff is optional\n"); exit(1); } seq_list = fopen(argv[1], "r"); if (!seq_list) { printf("Input file for sequence name list %s not found. Exit.\n", argv[1]); exit(2); } GetSeqNames(seq_list); msp_file = fopen(argv[2], "r"); if (!msp_file) { printf("Input file of MSPs %s not found. Exit.\n", argv[2]); exit(2); } if (!strcmp(argv[3], m1)) {method = 1;} else if (!strcmp(argv[3], m2)) {method = 2;} else { printf("please choose single or double to indicate the method to evaluate overlap.\n"); printf("%s is not a valid option. Exit.\n", argv[3]); exit(2); } if (argc > 4) cutoff = atof(argv[4]); else { if (method == 1) {cutoff = 0.5;} else {cutoff = 0.9;} } /* opening files */ if (!(frags = fopen("images/images_sorted", "r"))) { printf("Can not open the fragment list file, exiting.\n"); exit(1); } if (!(msp_no = fopen("summary/ori_msp_no", "r"))) { printf("Can not open msp_no, exiting.\n"); exit(1); } err = fopen("ele_def_res/errors", "w"); all_ele = fopen("summary/naive_eles", "w"); img_prot = fopen("ele_def_res/img_prot", "w"); ele_no = fopen("summary/naive_ele_no", "w"); size_list = fopen("ele_def_res/size_list", "w"); while(fgets(line, 100, msp_no)) { msp_ct = atoi(line); } all_mprot = (MPROT_t **) malloc(msp_ct*sizeof(MPROT_t *)); for (i=0; ipe = 0; (*(all_mprot+i))->se = 0; } ele_def(method, frags, cutoff, &all_ep, &ele_ct, all_mprot); /*for (i=0; ipe > ele_ct || (*(all_mprot+i))->se > ele_ct) { printf("not OK\n"); exit(1); } }*/ fclose(ele_no); fclose(img_prot); fclose(msp_no); fclose(frags); img_prot = fopen("ele_def_res/img_prot", "r"); ep_array = (EPROT_t **) malloc(ele_ct*sizeof(EPROT_t *)); ep_tmp = all_ep; i = 0; while (ep_tmp) { *(ep_array+i) = ep_tmp; i ++; ep_tmp = ep_tmp->next; } all_iprot = (IPROT_t **) malloc(IMG_CAP*sizeof(IPROT_t *)); iprot_shadow = (IPROT_t **) malloc(IMG_CAP*sizeof(IPROT_t *)); for (i=0; ito_msp = (MSP_t *) malloc(sizeof(MSP_t)); *(iprot_shadow+i) = *(all_iprot+i); } while (fgets(line, 100, img_prot)) { sscanf(line, "%d %d\n", &(*(all_iprot+iprot_ct))->ele_index, &(*(all_iprot+iprot_ct))->index); iprot_ct ++; if (iprot_ct == IMG_CAP) { DUMBBELL; iprot_ct = 0; } } if (iprot_ct) { for (i=0; ito_msp); free(*(all_iprot+i)); } free(all_iprot); free(iprot_shadow); for (i=0; ise = (*ecp); } else { (*(all_mprot+img.index/2))->pe = (*ecp); } fprintf(img_prot, "%d %d\n", (*ecp), img.index); fflush(img_prot); continue; } if (ele_frag.seq_name == img.frag.seq_name /*!strncmp(ele_frag.seq_name, img.frag.seq_name, NAME_LEN)*/ && ele_frag.rb - img.frag.lb > 10) { /* checking possible images */ if (method == 1) {cov = sing_cov(&ele_frag, &img.frag, cutoff);} else {cov = doub_cov(&ele_frag, &img.frag, cutoff);} if (cov) { /* a good image */ /* include the current frag in the current element*/ img_ct ++; if (img.index%2) { (*(all_mprot+img.index/2))->se = (*ecp); } else { (*(all_mprot+img.index/2))->pe = (*ecp); } fprintf(img_prot, "%d %d\n", (*ecp), img.index); fflush(img_prot); /* updating definition of the element if necessary */ /* notice that it is a bit complicated than above */ if (ele_frag.rb < img.frag.rb) { ele_frag.rb = img.frag.rb; /* time to go back and check if previously unqualified images are now good to be participated to the updated element */ cur = remain; prev = NULL; while (cur) { INCLUDE_IMAGE; } } } else { /* current image not good for the current ele, keep it in the remaining list and move on */ /*printf("1st backing up\n");*/ BACK_UP; } } else { /* time to finish defining of ele_tmp */ /* output the element */ ADD_EP; /*printf("2nd backing up\n");*/ BACK_UP; /* start a new element, finish the remain list */ ritetime = 1; /* if (remain) printf("2nd look back\n"); else printf("no need for 2nd look back\n"); */ while (remain && ritetime) { cur = remain; RITE_THING; while (cur) { DO_IT; } } } } ADD_EP; if (remain) ritetime = 1; /* add the last element to the list of elements */ /* if (remain) printf("finishing\n"); else printf("no need to finish\n"); */ while (remain) { cur = remain; prev = NULL; while (cur) { if (ritetime) { RITE_THING; continue; } DO_IT; } if (!cur) { ADD_EP; ritetime = 1; } } fprintf(ele_no, "%d\n", (*ecp)); } void img_charge(IPROT_t **shadow, int ct, FILE *input) { int i=0, pos=0; char line[151]; int scan_flag; MSP_t msp; qsort(shadow, ct, sizeof(IPROT_t *), index_cmp); while (fgets(line, 150, input)) { if (pos == (*(shadow+i))->index/2) { scan_flag = scan_msp(&msp, line); if (scan_flag) { (*(shadow+i))->to_msp->score = 0; fprintf(err, "Wrong format in the MSP file line %d for image %d\n", pos, (*(shadow+i))->index); } else { *((*(shadow+i))->to_msp) = msp; } i ++; if (i == ct) break; if (pos == (*(shadow+i))->index/2) { /* in case the next image is from the same MSP line */ if (scan_flag) { (*(shadow+i))->to_msp->score = 0; /*(*(shadow+i))->to_msp = NULL;*/ fprintf(err, "Wrong format in the MSP file line %d for image %d\n", pos, (*(shadow+i))->index); } else { *((*(shadow+i))->to_msp) = msp; } i ++; if (i == ct) break; } } pos ++; } rewind(input); } int index_cmp(const void *i1, const void *i2) { return (*((IPROT_t **) i1))->index - (*((IPROT_t **) i2))->index; } RECON-1.08/src/seqlist.h0000644000076400007640000000371512274532636014500 0ustar rhubleyrepeat #include "bolts.h" #include "string.h" #ifndef _seqlist_h #define _seqlist_h void GetSeqNames(FILE *); int GetSeqIndex(int, int, char *); void GetSeqNames(FILE *seq_list) { char line[256]; int seq_ct = -1; char *name_start; /* get the number of sequences in the list, and generates an array of proper size to hold the list */ fgets(line, 255, seq_list); seq_no = atoi(line); if (!seq_no) { printf("First line in the list of sequences must be an integer,\nwhich is the number of sequences in the list. Exit\n"); exit(2); } seq_names = (char **) malloc(seq_no*sizeof(char *)); /* get the names of the sequences */ while (fgets(line, 255, seq_list)) { seq_ct ++; if (seq_ct == seq_no) { printf("More sequence names than indicated at the begining of the file. Exit.\n"); exit(2); } *(seq_names+seq_ct) = (char *) malloc(NAME_LEN*sizeof(char)); /* skip the '>' and possilbe spaces following it at the beginning of the line, in case the name is grepped directly from a fasta file */ name_start = line; if (line[0] == '>') { name_start++; while (isspace(*name_start)) name_start++; } strncpy(*(seq_names+seq_ct), name_start, NAME_LEN-1); /* mark the end of the string */ name_start = *(seq_names+seq_ct); while (/**name_start != EOF &&*/ !isspace(*name_start)) name_start++; *name_start = '\0'; } /* we assume that the list is already sorted lexically, which is done in get-names.pl */ } /* binary search of a sorted list of sequence names */ /* returns position in the array if found */ /* returns -1 if not found */ int GetSeqIndex(int left, int right, char *seq_name) { int pos, dir; if (left <= right) { pos = (left+right)/2; dir = strncmp(seq_name, *(seq_names+pos), NAME_LEN); if (dir < 0) return GetSeqIndex(left, pos-1, seq_name); else if (dir > 0) return GetSeqIndex(pos+1, right, seq_name); else return pos; } else { return -1; } } #endif RECON-1.08/src/imagespread.c0000644000076400007640000000542112274532636015264 0ustar rhubleyrepeat #include "msps.h" int GetOutputInterval(char *, int, int); int main (int argc, char *argv[]) { FILE *msp_file, *seq_list; /* input files */ FILE **output, *err, *msp_no; /* output files */ int noof=1, i; /* noof == Number Of Output Files */ char line[150], output_name[50]; MSP_t cur; int img_ct=-1; /* checking command line */ if (argc < 3) { printf("usage:\n imagespread seq_name_list msp_list number_of_output_files\nlast parameter optional with default of 1\n"); exit(1); } /* checking input */ seq_list = fopen(argv[1], "r"); if (!seq_list) { printf("Input file for sequence name list %s not found. Exit.\n", argv[1]); exit(2); } msp_file = fopen(argv[2], "r"); if (!msp_file) { printf("Input MSP file %s not found. Exit.\n", argv[2]); exit(2); } if (argc == 4) {noof = atoi(argv[3]);} if (noof < 1) noof = 1; /*files for output */ err = fopen("images/errors", "w"); if (!err) { printf("Can not open images/errors for output. Exit.\n"); exit(3); } msp_no = fopen("summary/ori_msp_no", "w"); if (!msp_no) { printf("Can not open images/msp_no for output. Exit.\n"); exit(3); } output = (FILE **) malloc(noof*sizeof(FILE *)); for (i=0; i noof-1) interval=noof-1; /* the last few ones */ return interval; } RECON-1.08/src/eleredef.c0000644000076400007640000020647012274532636014565 0ustar rhubleyrepeat#include #include #include #include "ele.h" #define CUTOFF1 0.5 #define CUTOFF2 0.9 #define MAX_IMG 1200 #define TOO_SHORT 30 #define FUDGE 2 #define MARGIN 10000 #define FLURRY 10 typedef struct img_node { short recorded; IMAGE_t *to_image; struct img_node *sib; struct img_node *children; } IMG_NODE_t; void report_cts(); void report_redef_stat(); ELE_DATA_t *ele_def(IMG_DATA_t **, float); void generate_img_tree(ELEMENT_t *); ELE_INFO_t *new_element(); void add_ele_info(ELE_INFO_t *); void general_ele_redef(ELE_INFO_t *, IMAGE_t **); /*void build_local_network(ELE_INFO_t *, int, ELE_DATA_t **, IMAGE_t **); void local_net_walk(ELE_INFO_t *, int, EDGE_TREE_t *, ELE_DATA_t **, IMAGE_t **);*/ void build_local_network(ELE_INFO_t *, ELE_DATA_t **, ELE_DATA_t **, IMAGE_t **); void recruit(ELE_INFO_t *, EDGE_TREE_t *, ELE_DATA_t **, IMAGE_t **); void cruise_local_net(ELE_DATA_t *, IMAGE_t **); void local_ele_redef(ELE_INFO_t *, IMAGE_t **, int*); void dissolve_local_network(ELE_DATA_t **); int emptyDir(char *); void stage_exit(int); void dismiss_element(ELE_INFO_t *); void remove_ele(ELE_INFO_t *); void ele_redef(ELE_INFO_t *, IMAGE_t **); IMG_DATA_t *img_data_sort(IMG_DATA_t *, int); void PCP_to_TBDs(ELEMENT_t *); BD_t *CP_cluster(CP_t *); void CP_sort(CP_t **); void BD_sort(BD_t **); int span(ELEMENT_t *, int32_t); void TBD_merge(ELEMENT_t *); void dissect(ELE_INFO_t *); int too_short(FRAG_t *); MSP_t *add_msp(MSP_t *); void register_image(IMAGE_t *, ELEMENT_t *); void put_image(IMG_DATA_t **, IMAGE_t *); void dump_image(IMAGE_t *); void remove_image(IMAGE_t *); void combo_update(ELE_INFO_t *); void combo_edge_update(ELE_INFO_t *, EDGE_TREE_t **); void CP_clean(CP_t **, ELE_INFO_t *); void edges_and_cps(ELE_INFO_t *, IMAGE_t **); int full_length(IMAGE_t *, float); void add_CP(CP_t **, int32_t, ELE_INFO_t *); void add_edge(ELE_INFO_t *, ELE_INFO_t *, char, int32_t, short); void adjust_edge_tree(ELE_INFO_t *); int charge_edge_array(EDGE_t **, EDGE_TREE_t *, int); int consis_tree_build(IMG_NODE_t *, IMAGE_t *, int); int consis(IMAGE_t *, IMAGE_t *, float); IMG_NODE_t **node_entry(IMG_NODE_t **); void consis_tree_free(IMG_NODE_t *); /*int find_prim(struct img_node *, float, int32_t, int32_t, short, int32_t *, short *);*/ int find_prim(IMG_NODE_t *, float, int32_t, int32_t, int32_t, int32_t, int32_t, int32_t, int32_t, int *, int32_t *, short *); void combo_output(ELE_INFO_t *); void obs_output(ELE_INFO_t *); void fprint_ele_obs(FILE *, ELE_INFO_t *); int frag_cmp(const void *, const void *); int partner_cmp(const void *, const void *); int CP_cmp(const void *, const void *); int BD_cmp(const void *, const void *); int fam_cmp(const void *, const void *); int main (int argc, char *argv[]) { ELE_INFO_t *cur_ele_info; int i, ele_march, ei, rounds=0, start; char line[35], stat; short fu, to_march; IMAGE_t **img_ptr; FILE *ele_no, *msp_no, *edge_no, *size_list, *new_stat; FILE *seq_list; /* processing command line */ if (argc == 1) { printf("usage: redef seq_list start clan_ct\n where seq_list is the list of sequence names, start is the index of the element to start redefining, and clan_ct is the number to start counting the number of clans. The latter two are optional.\n"); exit(1); } seq_list = fopen(argv[1], "r"); if (!seq_list) { printf("Input file for sequence name list %s not found. Exit.\n", argv[1]); exit(2); } GetSeqNames(seq_list); if (argc > 2) start = atoi(argv[2]) - 1; else start = 0; if (argc > 3) clan_ct = atoi(argv[3]); else clan_ct = 0; ele_no = fopen("summary/naive_ele_no", "r"); if(!ele_no) { printf("Can not open naive_ele_no. Exiting\n"); exit(1); } msp_no = fopen("summary/redef_msp_no", "r"); if (!msp_no) msp_no = fopen("summary/ori_msp_no", "r"); if (!msp_no) { printf("Can not open msp_no. Exiting\n"); exit(1); } // May or may not exist. All uses of edge_no first check for // its existence. edge_no = fopen("summary/naive_edge_no", "r"); // May or may not exist. All uses are checked. size_list = fopen("tmp/size_list", "r"); // May or may not exist. All uses are checked. new_stat = fopen("tmp2/redef_stat", "r"); new_msps = fopen("summary/new_msps", "a"); if ( !new_msps ) { printf("Can not open summary/new_msps for writing! Exiting\n"); exit(1); } unproc = fopen("summary/unproc", "a"); if ( !unproc ) { printf("Can not open summary/unproc for writing! Exiting\n"); exit(1); } combo = fopen("summary/combo", "a"); if ( !combo ) { printf("Can not open summary/combo for writing! Exiting\n"); exit(1); } obs = fopen("summary/obsolete", "a"); if ( !obs ) { printf("Can not open summary/obsolete for writing! Exiting\n"); exit(1); } log_file = fopen("tmp2/log", "a"); if ( !log_file ) { printf("Can not open tmp2/log for writing! Exiting\n"); exit(1); } while (fgets(line, 15, ele_no)) { ele_ct = atoi(line); } fclose(ele_no); while (fgets(line, 15, msp_no)) { msp_index = atoi(line) - 1; } fclose(msp_no); if (edge_no) { while (fgets(line, 15, edge_no)) { edge_index = atoi(line) - 1; } } else edge_index = -1; ele_array_size = 2*ele_ct; all_ele = (ELE_INFO_t **) malloc(ele_array_size*sizeof(ELE_INFO_t *)); for (i=0; istat = stat; (*(all_ele+ei-1))->file_updated = fu; } else { cur_ele_info = ele_info_init(ei); cur_ele_info->stat = stat; cur_ele_info->file_updated = fu; add_ele_info(cur_ele_info); } } } msp_in_mem = 0; msp_left = 0; msp_ct = 0; edge_ct = 0; edge_in_mem = 0; edge_left = 0; files_read = 0; err_no = 0; /* re-define elements using the syntopy algorithm, and build edges */ img_ptr = (IMAGE_t **) malloc(MAX_IMG*sizeof(IMAGE_t *)); if ( ! img_ptr ) { printf("eleredef: Error! Could not allocate memory for img_ptr: %d bytes requested\n", ( MAX_IMG*sizeof(IMAGE_t *) ) ); exit(-1); } to_march = 1; while (to_march) { to_march = 0; rounds ++; for (i=start; iindex); fflush(log_file); if ((*(all_ele+i))->stat == 'z' || (*(all_ele+i))->stat == 'w' || (*(all_ele+i))->stat == 't') { to_march = 1; general_ele_redef(*(all_ele+i), img_ptr); #if 0 report_redef_stat(); #endif } /*else if ((*(all_ele+i))->stat == 'O' && !(*(all_ele+i))->file_updated) spit_out_ele(*(all_ele+i));*/ } start = 0; cur_ele_info = ele_info_data; while(cur_ele_info) { fprintf(log_file, "evaluating definition of element %d\n", cur_ele_info->index); fflush(log_file); if (cur_ele_info->stat == 'z' || cur_ele_info->stat == 'w' || cur_ele_info->stat == 't') { to_march = 1; general_ele_redef(cur_ele_info, img_ptr); #if 0 report_redef_stat(); #endif } /*else if (cur_ele_info->stat == 'O' && !cur_ele_info->file_updated) spit_out_ele(cur_ele_info);*/ cur_ele_info = cur_ele_info->next; } } report_cts(); report_redef_stat(); free(img_ptr); #if 0 for (i=start; istat == 'X') remove_ele(*(all_ele+i)); } cur_ele_info = ele_info_data; while(cur_ele_info) { if (cur_ele_info->stat == 'X') remove_ele(cur_ele_info); cur_ele_info = cur_ele_info->next; } #endif fprintf(log_file, "total numbers: %d elements, %d msps, %d edges\n", ele_ct, msp_index+1, edge_index+1); fprintf(log_file, "%d rounds, %d files read, %d msps seen, %d edges seen\n", rounds, files_read, msp_ct, edge_ct); fprintf(log_file, "%d errors, %d msps and %d edges left in memory, \n", err_no, msp_left, edge_left); fflush(log_file); fclose(log_file); exit(0); } void report_cts() { FILE *fp; fp = fopen("summary/redef_ele_no", "w"); fprintf(fp, "%d\n", ele_ct); fclose(fp); } void report_redef_stat() { int i, ele_march = ele_ct < ele_array_size ? ele_ct : ele_array_size; FILE *redef_stat, *fp; ELE_INFO_t *cur_ele_info = ele_info_data; redef_stat = fopen("tmp2/redef_stat", "w"); for (i=0; iindex, (*(all_ele+i))->stat, (*(all_ele+i))->file_updated); } while(cur_ele_info) { fprintf(redef_stat, "%d %c %d\n", cur_ele_info->index, cur_ele_info->stat, cur_ele_info->file_updated); cur_ele_info = cur_ele_info->next; } fclose(redef_stat); fp = fopen("summary/redef_msp_no", "w"); fprintf(fp, "%d\n", msp_index+1); fclose(fp); fp = fopen("summary/naive_edge_no", "w"); fprintf(fp, "%d\n", edge_index+1); fclose(fp); } /*********************************** *********************************** ** ** ** DEFINING ELEMENTS ** ** ** *********************************** ***********************************/ ELE_DATA_t *ele_def(IMG_DATA_t **img_data_p, float cutoff) { /* this function assumes that the images are SORTED according to frag_cmp. defining elements is in essence partitioning images in the original list. cur_img_data marks the current image under inspection; *img_data_p and prev_img_data are used to maintain the un-participated list; *img_data_p marks the first (un-participated) image in the remaining list; prev_img_data marks the last un-participated image proceding cur_img_data, so that when cur_img_data is removed from the origial list and participated into an element, we know where the tail of the unparticipated list, used to be pointed by cur_img_data->next, should be appended to */ IMG_DATA_t *cur_img_data, *prev_img_data; ELEMENT_t *ele_tmp; ELE_INFO_t *ele_info_tmp; ELE_DATA_t *ele_data=NULL, *ele_data_tmp; short ritetime; int ct; while (*img_data_p) { cur_img_data = *img_data_p; prev_img_data = NULL; ritetime = 1; /* ritetime marks the right time to start a new element */ while(cur_img_data != NULL) { if (ritetime) { /* starting a new element */ ele_info_tmp = new_element(); ele_tmp = ele_info_tmp->ele; /* start the definition of the element */ ele_tmp->img_no = 1; ele_tmp->frag = cur_img_data->to_image->frag; /* lst and rst included */ /* kick cur_img_data out of the original list */ /* notice that whenever we're here, cur_img_data points to the first image in the remaining list, which is also pointed to by *img_data_p */ *img_data_p = cur_img_data->next; /* updat the current image and move it to the image list of ele_tmp */ /* notice that here it's always the first one for ele_tmp */ cur_img_data->to_image->ele_info = ele_info_tmp; cur_img_data->next = NULL; ele_tmp->to_img_data = cur_img_data; /* move pointer cur_img_data to the next one */ cur_img_data = *img_data_p; ritetime = 0; continue; } if (/*!strncmp(ele_tmp->frag.seq_name, cur_img_data->to_image->frag.seq_name, NAME_LEN)*/ ele_tmp->frag.seq_name == cur_img_data->to_image->frag.seq_name && ele_tmp->frag.rb - cur_img_data->to_image->frag.lb > 10) { /*checking possible images */ if (sing_cov(&ele_tmp->frag, &cur_img_data->to_image->frag, cutoff)) { /* a good image */ ele_tmp->img_no ++; /* move cur_img_data from the original list */ /* notice that it's a bit more complicated than above */ if (prev_img_data != NULL) { prev_img_data->next = cur_img_data->next; } else { *img_data_p = cur_img_data->next; } /* update the current image and move it to the image_list of ele_tmp */ cur_img_data->to_image->ele_info = ele_info_tmp; cur_img_data->next = ele_tmp->to_img_data; ele_tmp->to_img_data = cur_img_data; /* updating definition of the element if necessary, and move cur_img_data to the right place */ /* notice that it is a bit complicated than above */ if (ele_tmp->frag.rb < cur_img_data->to_image->frag.rb) { ele_tmp->frag.rb = cur_img_data->to_image->frag.rb; /* ele_tmp->frag.rst = cur_img_data->to_image->frag.rst; */ /* time to go back and check if previously unqualified images are now good to be participated to the updated element */ cur_img_data = *img_data_p; prev_img_data = NULL; } else { if (prev_img_data != NULL) cur_img_data = prev_img_data->next; else cur_img_data = *img_data_p; } } else { /* current image not good for the ele_tmp, keep it in the remaining list and move on */ prev_img_data = cur_img_data; cur_img_data = cur_img_data->next; } } else { /* time to finish defining of ele_tmp */ /* add the element to the list of elements */ ele_data_tmp = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t)); ele_data_tmp->ele_info = ele_info_tmp; ele_data_tmp->next = ele_data; ele_data = ele_data_tmp; /* if (!strncmp(ele_tmp->frag.seq_name, target, NAME_LEN)) printf("%d %s %d %d\n", ele_tmp->index, ele_tmp->frag.seq_name, ele_tmp->frag.lb, ele_tmp->frag.rb); */ /* time to go back to the head of the remaining list and start a new element */ ritetime = 1; cur_img_data = *img_data_p; prev_img_data = NULL; } } /* add the last element to the list of elements */ ele_data_tmp = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t)); ele_data_tmp->ele_info = ele_info_tmp; ele_data_tmp->next = ele_data; ele_data = ele_data_tmp; } ele_data_tmp = ele_data; while (ele_data_tmp) { if (ele_data_tmp->ele_info->ele->frag.lb > ele_data_tmp->ele_info->ele->frag.rb) { fprintf(log_file, "error: ele %d reversed after ele_def\n", ele_data_tmp->ele_info->index); fflush(log_file); exit(3); } generate_img_tree(ele_data_tmp->ele_info->ele); /*ct = count_img_nodes(ele_data_tmp->ele_info->ele->to_img_tree); if (ct != ele_data_tmp->ele_info->ele->img_no) { err_no ++; fprintf(log_file, "error: trouble generating image tree for redefed offsprings: ele %d %d %d\n", ele_data_tmp->ele_info->index, ele_data_tmp->ele_info->ele->img_no, ct); fflush(log_file); exit(2); }*/ ele_data_tmp = ele_data_tmp->next; } return ele_data; } void generate_img_tree(ELEMENT_t *ele) { IMAGE_t **img_array = (IMAGE_t **) malloc(ele->img_no*sizeof(IMAGE_t *)); IMG_DATA_t *cur; int ct=0; cur = ele->to_img_data; while (cur) { *(img_array+ct) = cur->to_image; ct ++; cur = cur->next; } qsort(img_array, ct, sizeof(IMAGE_t *), img_index_cmp); build_img_tree(&ele->to_img_tree, img_array, 0, ct-1); free(img_array); } ELE_INFO_t *new_element() { ELE_INFO_t *ele_info_tmp; ele_ct ++; if (ele_ct <= ele_array_size) ele_info_tmp = *(all_ele+ele_ct-1); else { ele_info_tmp = ele_info_init(ele_ct); add_ele_info(ele_info_tmp); } ele_info_tmp->ele = ele_init(ele_ct); ele_info_tmp->file_updated = 1; return ele_info_tmp; } void add_ele_info(ELE_INFO_t *ele_info_tmp) { if (!ele_info_data) ele_info_data = ele_info_tmp; else ele_info_tail->next = ele_info_tmp; ele_info_tail = ele_info_tmp; } /*********************************** *********************************** ** ** ** REDEFINING THE ELEMENTS ** ** ** *********************************** ***********************************/ /********************************************** * Organizing the traverse of the local graph * **********************************************/ void general_ele_redef(ELE_INFO_t *ele_info, IMAGE_t **img_ptr) { ELE_DATA_t *local_net=NULL, *local_net_tail=NULL; if (!ele_info->ele) ele_read_in(ele_info, 1); /* an element could have lost all its images during the re-evaluation of its partners */ if (!ele_info->ele->img_no) { combo_update(ele_info); remove_ele(ele_info); ele_cleanup(&ele_info->ele); } else { /* redefining cur_ele and its adjacent neighbors */ fprintf(new_msps, "new clan for ele %d\n", ele_info->index); fflush(new_msps); fprintf(combo, "new clan for ele %d\n", ele_info->index); fflush(combo); fprintf(obs, "new clan for ele %d\n", ele_info->index); fflush(obs); /* set up the local network */ clan_ct ++; clan_size = 0; clan_core_size = 0; fprintf(log_file, "new clan: %d for ele %d\n", clan_ct, ele_info->index); fflush(log_file); build_local_network(ele_info, &local_net, &local_net_tail, img_ptr); if ( ele_info->index == 362 || ele_info->index == 10 ) { printf("Printing local net for 362\n"); print_ele_data( local_net ); } fprintf(log_file, "clan size: %d, clan core size: %d\n", clan_size, clan_core_size); fflush(log_file); /* redefining elements in the local network */ /* local_ele_redef(ele_info, img_ptr); */ cruise_local_net(local_net, img_ptr); /* clearing up the local network */ fflush(new_msps); fflush(combo); fflush(obs); dissolve_local_network(&local_net); } } #if 0 void build_local_network(ELE_INFO_t *ele_info, int level, ELE_DATA_t **net_p, IMAGE_t **img_ptr) { ELEMENT_t *ele; ELE_DATA_t *que; clan_size ++; que = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t)); que->ele_info = ele_info; que->next = *net_p; *net_p = que; if (!ele_info->ele) ele_read_in(ele_info, 1); ele = ele_info->ele; if (level < DEPTH) { ele->l_hold = 1; clan_core_size ++; /*fprintf(log_file, " %d\n", ele_info->index); fflush(log_file);*/ if (ele_info->stat != 'v') { if (ele_info->stat == 'z') edges_and_cps(ele_info, img_ptr); level ++; if (ele->edges) local_net_walk(ele_info, level, ele->edges, net_p, img_ptr); } else { if (ele->edges) local_net_walk(ele_info, DEPTH, ele->edges, net_p, img_ptr); } } else ele->l_hold = 2; } void local_net_walk(ELE_INFO_t *ele_info, int level, EDGE_TREE_t *edge_node, ELE_DATA_t **net_p, IMAGE_t **img_ptr) { ELE_INFO_t *epi; if (edge_node->l) local_net_walk(ele_info, level, edge_node->l, net_p, img_ptr); /*if (edge_node->to_edge->type == 'p' || edge_node->to_edge->type == 's') {*/ epi = linked_ele(ele_info, edge_node->to_edge); if (!epi->ele) ele_read_in(epi, 1); if (!epi->ele->l_hold) build_local_network(epi, level, net_p, img_ptr); else if (epi->ele->l_hold == 2 && level < DEPTH) { epi->ele->l_hold = 1; clan_core_size ++; /*fprintf(log_file, " %d\n", epi->index); fflush(log_file);*/ if (epi->stat == 'z') edges_and_cps(epi, img_ptr); if (epi->ele->edges) local_net_walk(epi, level+1, epi->ele->edges, net_p, img_ptr); } /*}*/ if (edge_node->r) local_net_walk(ele_info, level, edge_node->r, net_p, img_ptr); } #endif void build_local_network(ELE_INFO_t *ele_info, ELE_DATA_t **net_p, ELE_DATA_t **net_tail_p, IMAGE_t **img_ptr) { ELEMENT_t *ele; ELE_DATA_t *que; /* seed the network with the first element */ que = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t)); que->ele_info = ele_info; que->next = NULL; *net_p = que; *net_tail_p = que; ele_info->ele->l_hold = 1; /* breadth first search */ while (que) { clan_size ++; if (que->ele_info->ele->l_hold <= DEPTH) { clan_core_size ++; if (que->ele_info->stat == 'z') edges_and_cps(que->ele_info, img_ptr); if (que->ele_info->ele->edges) recruit(que->ele_info, que->ele_info->ele->edges, net_tail_p, img_ptr); /* else { fprintf(log_file, "error: ele %d edge tree missing. Exit.\n", que->ele_info->index); fflush(log_file); exit(4); }*/ } que = que->next; } } void recruit(ELE_INFO_t *ele_info, EDGE_TREE_t *rt, ELE_DATA_t **net_tail_p, IMAGE_t **img_ptr) { ELE_INFO_t *epi; ELE_DATA_t *member; if (rt->l) recruit(ele_info, rt->l, net_tail_p, img_ptr); epi = linked_ele(ele_info, rt->to_edge); if (!epi->ele) ele_read_in(epi, 1); if (!epi->ele->l_hold) { epi->ele->l_hold = ele_info->ele->l_hold + 1; if (epi->stat == 'v' && epi->ele->l_hold < DEPTH) epi->ele->l_hold = DEPTH; member = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t)); member->ele_info = epi; member->next = NULL; (*net_tail_p)->next = member; *net_tail_p = member; } if (rt->r) recruit(ele_info, rt->r, net_tail_p, img_ptr); } void cruise_local_net(ELE_DATA_t *local_net, IMAGE_t **img_ptr) { ELE_DATA_t *que; int to_march = 1; while (to_march) { to_march = 0; que = local_net; while (que) { if (que->ele_info->ele->l_hold <= DEPTH) { local_ele_redef(que->ele_info, img_ptr, &to_march); } que = que->next; } } } void local_ele_redef(ELE_INFO_t *ele_info, IMAGE_t **img_ptr, int *march_p) { ELE_DATA_t *new_ele_data; ELEMENT_t *ele = ele_info->ele; if (ele->redef != NULL) { new_ele_data = ele->redef; while (new_ele_data != NULL) { local_ele_redef(new_ele_data->ele_info, img_ptr, march_p); new_ele_data = new_ele_data->next; } } else { if (ele_info->stat != 'v' && ele_info->stat != 'X') { if (ele->PCP) { *march_p = 1; ele_redef(ele_info, img_ptr); } else ele_info->stat = 'v'; } } } void dissolve_local_network(ELE_DATA_t **net_p) { ELE_DATA_t *que, *new_ele_data; int i, ele_left=0; char *command; /*MSP_DATA_t *md;*/ int j, in_clan; FILE *fp; ELE_INFO_t *cur_ele_info; /* output results to tmp2/clan, which holds results temporily and clean up memory */ que = *net_p; while (que) { dismiss_element(que->ele_info); que = que->next; } if (msp_in_mem) { err_no ++; fprintf(log_file, "error: error in bookkeeping: %d msps total, %d seen, %d left in memory\n", msp_index+1, msp_ct, msp_in_mem); fflush(log_file); msp_left += msp_in_mem; /*md = all_msps; while (md) { if (md->to_msp) { fprint_msp(log_file, md->to_msp); fflush(log_file); MSP_free(md->to_msp); } md = md->next; } if (msp_in_mem) { fprintf(log_file, "error: further discrepency: %d msps left\n", msp_in_mem); msp_in_mem = 0; }*/ } if (edge_in_mem) { err_no ++; fprintf(log_file, "error: error in bookkeeping: %d edges total, %d seen, %d left in memory\n", edge_index+1, edge_ct, edge_in_mem); fflush(log_file); edge_left += edge_in_mem; edge_in_mem = 0; } #if 0 for (i=0; iele) { ele_left ++; err_no ++; fprintf(log_file, "error: element %d not cleaned from memory. stat = %c\n", i+1, (*(all_ele+i))->stat); fflush(log_file); if ((*(all_ele+i))->stat != 'O' && (*(all_ele+i))->stat != 'X') ele_write_out(*(all_ele+i), 1); ele_cleanup(&(*(all_ele+i))->ele); } } if (ele_left) { err_no ++; fprintf(log_file, "error: %d elements left in memory\n", ele_left); fflush(log_file); /*system(command);*/ } #endif if (err_no) exit(3); #if 0 /* move files from tmp2/clan, i.e. finalize the result */ command = (char *) malloc(50*sizeof(char)); sprintf(command, "tmp2/clan/combos"); if (!emptyDir(command)) { sprintf(command, "mv -f tmp2/clan/combos combos/clan%d", clan_ct); if (system(command)) { fprintf(log_file, "error moving tmp2/clan/combos/\n"); fflush(log_file); stage_exit(6); } else { sprintf(command, "mkdir tmp2/clan/combos"); if (system(command)) { fprintf(log_file, "error generating dir tmp2/clan/combos/\n"); fflush(log_file); stage_exit(6); } } } sprintf(command, "tmp2/clan/obsolete"); if (!emptyDir(command)) { sprintf(command, "mv -f tmp2/clan/obsolete obsolete/clan%d", clan_ct); if (system(command)) { fprintf(log_file, "error moving tmp2/clan/obsolete/\n"); fflush(log_file); stage_exit(6); } else { sprintf(command, "mkdir tmp2/clan/obsolete"); if (system(command)) { fprintf(log_file, "error generating dir tmp2/clan/obsolete\n"); fflush(log_file); stage_exit(6); } } } sprintf(command, "mv -f tmp2/clan/e* tmp2/."); if (system(command)) { /*fprintf(log_file, "error moving files from tmp2/clan/\n"); fflush(log_file); stage_exit(6);*/ j = ele_ct < ele_array_size ? ele_ct : ele_array_size; for (i=0; i<=j; i++) { sprintf(command, "tmp2/clan/e%d", i+1); if (fp = fopen(command, "r")) in_clan = 1; else in_clan = 0; fclose(fp); if (in_clan) { sprintf(command, "mv -f tmp2/clan/e%d tmp2/.", i+1); if (system(command)) { fprintf(log_file, "error doing %s\n", command); fflush(log_file); stage_exit(6); } } } cur_ele_info = ele_info_data; while (cur_ele_info) { sprintf(command, "tmp2/clan/e%d", cur_ele_info->index); if (fp = fopen(command, "r")) in_clan = 1; else in_clan = 0; fclose(fp); if (in_clan) { sprintf(command, "mv -f tmp2/clan/e%d tmp2/.", cur_ele_info->index); if (system(command)) { fprintf(log_file, "error doing %s\n", command); fflush(log_file); stage_exit(6); } } cur_ele_info = cur_ele_info->next; } } free(command); #endif /* remove arkaine ele files, now done in main() que = *net_p; while (que) { if (que->ele_info->stat == 'X') remove_ele(que->ele_info); que = que->next; } */ ele_data_free(net_p); } #if 0 int emptyDir(char *dir_name) { int res = 1; DIR *cur_dir; struct dirent *dp; cur_dir = opendir(dir_name); while (cur_dir && res && (dp = readdir(cur_dir))) { if (strcmp(dp->d_name, ".") && strcmp(dp->d_name, "..")) res = 0; } closedir(cur_dir); return res; } void stage_exit(int code) { char *command = (char *) malloc(50*sizeof(char)); sprintf(command, "mv -f tmp2/redef_stat tmp2/redef_stat_prev"); if (system(command)) { fprintf(log_file, "error in moving tmp2/redef_stat\n"); fflush(log_file); exit(code); } sprintf(command, "mv -f tmp2/msp_no tmp2/msp_no_prev"); if (system(command)) { fprintf(log_file, "error in moving tmp2/msp_no\n"); fflush(log_file); exit(code); } sprintf(command, "mv -f tmp2/edge_no tmp2/edge_no_prev"); if (system(command)) { fprintf(log_file, "error in moving tmp2/edge_no\n"); fflush(log_file); exit(code); } report_redef_stat(); exit(code); } #endif void dismiss_element(ELE_INFO_t *ele_info) { ELE_DATA_t *new_ele_data; if (ele_info->ele->redef) { new_ele_data = ele_info->ele->redef; while (new_ele_data) { dismiss_element(new_ele_data->ele_info); new_ele_data = new_ele_data->next; } } /*printf("clearing ele %d\n", ele_info->index);*/ ele_info->ele->l_hold = 0; if (ele_info->stat != 'X') { if (!ele_info->ele->img_no) { ele_info->stat = 'X'; if (ele_info->ele->redef) combo_output(ele_info); else obs_output(ele_info); } else ele_write_out(ele_info, 1); } ele_cleanup(&ele_info->ele); } void remove_ele(ELE_INFO_t *ele_info) { char *command; command = (char *) malloc(50*sizeof(char)); sprintf(command, "rm -f tmp2/e%d", ele_info->index); if (system(command)) { fprintf(log_file, "error removing file tmp2/e%d\n", ele_info->index); fflush(log_file); exit(6); } free(command); } /****************************** * Redefining a given element * ******************************/ void ele_redef(ELE_INFO_t *ele_info, IMAGE_t **img_ptr) { ELE_DATA_t *new_ele_data; ELEMENT_t *cur_ele = ele_info->ele; BD_t *pbd; CP_t *cur; short to_dissect=0; IMG_DATA_t *cur_img_data; if (!cur_ele->to_img_data) listify(cur_ele->to_img_tree, &cur_ele->to_img_data); cur_ele->to_img_data = img_data_sort(cur_ele->to_img_data, cur_ele->img_no); /* find TBDs for the element */ if (cur_ele->PCP) { PCP_to_TBDs(cur_ele); } if (cur_ele->TBD) { TBD_merge(cur_ele); } if (cur_ele->TBD) { #if 0 to_dissect = 1; if (cur_ele->TBD->bd - cur_ele->frag.lb <= FLURRY || cur_ele->TBD->bd - cur_ele->frag.rb >= -FLURRY) { if (!cur_ele->TBD->next) { to_dissect = 0; if (cur_ele->TBD->bd - cur_ele->frag.lb <= FLURRY) cur_ele->frag.lb = cur_ele->TBD->bd; else cur_ele->frag.rb = cur_ele->TBD->bd; BD_free(&cur_ele->TBD); } else { if (cur_ele->TBD->next->bd - cur_ele->frag.rb >= -FLURRY) { if (!cur_ele->TBD->next->next) { to_dissect = 0; cur_ele->frag.lb = cur_ele->TBD->bd; cur_ele->frag.rb = cur_ele->TBD->next->bd; BD_free(&cur_ele->TBD); } } } } #endif pbd = cur_ele->TBD; while (pbd) { /*if (pbd->bd-cur_ele->frag.lb<-(FLURRY+5) || pbd->bd-cur_ele->frag.rb>(FLURRY+5)) { fprintf(log_file, "error: ele %d TBD outside ele bound\n", ele_info->index); fflush(log_file); exit(3); }*/ if (pbd->bd-cur_ele->frag.lb>FLURRY && pbd->bd-cur_ele->frag.rb<-FLURRY) { to_dissect ++; } pbd = pbd->next; } if (!to_dissect) { pbd = cur_ele->TBD; while (pbd) { if (/*pbd->bd-cur_ele->frag.lb>0 &&*/ pbd->bd-cur_ele->frag.lb<=FLURRY) { cur_ele->frag.lb = pbd->bd; } else if (/*pbd->bd-cur_ele->frag.rb<0 &&*/ pbd->bd-cur_ele->frag.rb>=-FLURRY) { cur_ele->frag.rb = pbd->bd; } pbd = pbd->next; } BD_free(&cur_ele->TBD); } else { /* dissect all images according to the TBDs */ dissect(ele_info); /* redefine elements according to the dissected images, if any left */ if (cur_ele->img_no) { cur_ele->to_img_data = img_data_sort(cur_ele->to_img_data, cur_ele->img_no); cur_ele->redef = ele_def(&cur_ele->to_img_data, CUTOFF1); } /* clear unnecessary memory, 'v'->'w' and update CPs for w's */ combo_update(ele_info); /* ele_redef() for offspring elements. we finish redefinition of all offsprings before pulling in partners, because the combo may have > 1 copy of the same family, which means other members' CPs won't be fully updated until all offsprings are processed */ new_ele_data = cur_ele->redef; while (new_ele_data != NULL) { new_ele_data->ele_info->ele->update = 1; new_ele_data->ele_info->ele->l_hold = cur_ele->l_hold; if (new_ele_data->ele_info->ele->to_img_tree) { edges_and_cps(new_ele_data->ele_info, img_ptr); if (new_ele_data->ele_info->ele->PCP) ele_redef(new_ele_data->ele_info, img_ptr); else new_ele_data->ele_info->stat = 'v'; } else { if (new_ele_data->ele_info->ele->img_no) { err_no ++; fprintf(log_file, "error: image tree missing in newly redefed offspring %d\n", new_ele_data->ele_info->index); fflush(log_file); exit(2); } else { combo_output(new_ele_data->ele_info); } } new_ele_data = new_ele_data->next; } } } if (cur_ele->img_no > 0) { ele_info->stat = 'v'; } else if (!to_dissect) combo_update(ele_info); /*img_data_free(&cur_ele->to_img_data);*/ } IMG_DATA_t *img_data_sort(IMG_DATA_t *img_data, int ct) { IMG_DATA_t **img_data_ptr; int i; if (!ct) return NULL; img_data_ptr = (IMG_DATA_t **) malloc(ct*sizeof(IMG_DATA_t *)); for (i=0; inext; } qsort(img_data_ptr, ct, sizeof(IMAGE_t *), frag_cmp); img_data = *img_data_ptr; ct --; for (i=0; inext = *(img_data_ptr+i+1); } (*(img_data_ptr+ct))->next = NULL; free(img_data_ptr); return img_data; } /*************************** * Determine possible TBDs * ***************************/ void PCP_to_TBDs(ELEMENT_t *ele) { int s = 0, left; BD_t *pbd_tmp, *pbd_prev, *pbd, *pbds; CP_t *cp; /* sort the PCP list according to cp */ CP_sort(&ele->PCP); /*clustering the PCPs into PBDs */ pbds = CP_cluster(ele->PCP); /* identify TBP from PBDs */ /* TBDs are removed from PBDs, what is left in PBDs are those unsuccessful ones */ pbd_tmp = pbds; pbd_prev = NULL; while (pbd_tmp != NULL) { /* s is the KEY! */ s = span(ele, pbd_tmp->bd); if (pbd_tmp->support >= s) { if (pbd_prev == NULL) { pbds = pbd_tmp->next; pbd_tmp->next = ele->TBD; ele->TBD = pbd_tmp; pbd_tmp = pbds; } else { pbd_prev->next = pbd_tmp->next; pbd_tmp->next = ele->TBD; ele->TBD = pbd_tmp; pbd_tmp = pbd_prev->next; } } else { pbd_prev = pbd_tmp; pbd_tmp = pbd_tmp->next; } } BD_free(&pbds); } #if 0 BD_t *CP_cluster(CP_t *cps) { int32_t first = cps->cp, last = cps->cp, sum = 0; int cpct = 0; BD_t *bds = NULL, *bd_tmp; while (cps != NULL) { if (cps->cp - last <= 10) { sum += cps->cp - first; cpct ++; } else { bd_tmp = (BD_t *) malloc(sizeof(BD_t)); bd_tmp->bd = sum/cpct + first; bd_tmp->support = cpct; bd_tmp->next = bds; bds = bd_tmp; first = cps->cp; sum = 0; cpct = 1; } if (cps->next == NULL) { bd_tmp = (BD_t *) malloc(sizeof(BD_t)); bd_tmp->bd = sum/cpct + first; bd_tmp->support = cpct; bd_tmp->next = bds; bds = bd_tmp; } last = cps->cp; cps = cps->next; } return bds; } #endif BD_t *CP_cluster(CP_t *cps) { int32_t first = cps->cp, last = cps->cp, sum = 0; CP_t *begin = cps; int cpct = 0; BD_t *bds = NULL, *bd_tmp; while (cps != NULL) { if (cps->cp - first <= 20 && cps->cp - last <= 10) { sum += cps->cp - first; cpct ++; last = cps->cp; cps = cps->next; } else { bd_tmp = (BD_t *) malloc(sizeof(BD_t)); bd_tmp->bd = sum/cpct + first; bd_tmp->support = cpct; bd_tmp->next = bds; bds = bd_tmp; if (cps->cp - last <= 10) begin = cps; else begin = begin->next; if (begin) { first = begin->cp; last = first; } sum = 0; cpct = 0; cps = begin; } } bd_tmp = (BD_t *) malloc(sizeof(BD_t)); bd_tmp->bd = sum/cpct + first; bd_tmp->support = cpct; bd_tmp->next = bds; bds = bd_tmp; return bds; } void CP_sort(CP_t **CP_ptr) { int i=0, j; CP_t *cur, **CPs; cur = *CP_ptr; while (cur != NULL) { i ++; cur = cur->next; } CPs = (CP_t **) malloc(i*sizeof(CP_t *)); i = 0; cur = *CP_ptr; while (cur != NULL) { *(CPs+i) = cur; i ++; cur = cur->next; } qsort(CPs, i, sizeof(CP_t *), CP_cmp); i --; for (j=0; jnext = *(CPs+j+1); } (*(CPs+i))->next = NULL; *CP_ptr = *CPs; free(CPs); } void BD_sort(BD_t **BD_ptr) { int i=0, j; BD_t *cur, **BDs; cur = *BD_ptr; while (cur != NULL) { i ++; cur = cur->next; } BDs = (BD_t **) malloc(i*sizeof(BD_t*)); i = 0; cur = *BD_ptr;; while (cur != NULL) { *(BDs+i) = cur; i ++; cur = cur->next; } qsort(BDs, i, sizeof(BD_t *), BD_cmp); i --; for (j=0; jnext = *(BDs+j+1); } (*(BDs+i))->next = NULL;; *BD_ptr = *BDs; free(BDs); } int span(ELEMENT_t *ele, int32_t cut) { /* span requires PCP sorted according to cp_cmp and images sorted according to frag_cmp */ int left=0, rite=0; IMG_DATA_t *id; id = ele->to_img_data; while (id && id->to_image->frag.lb <= cut-10) { left ++; if (id->to_image->frag.rb <= cut+10) rite ++; id = id->next; } return (left-rite)*FUDGE; } void TBD_merge(ELEMENT_t *ele) { BD_t *prev=NULL, *cur, *next; BD_sort(&ele->TBD); cur = ele->TBD; next = cur->next; while (next != NULL) { if (next->bd - cur->bd <= 10) { if (cur->support < next->support) { if (prev == NULL) { ele->TBD = next; } else { prev->next = next; } free(cur); cur = next; } else { cur->next = next->next; free(next); } if (cur) next = cur->next; else next = NULL; } else { prev = cur; cur = next; next = cur->next; } } } /************************** * Dissecting the element * **************************/ void dissect(ELE_INFO_t *ele_info) { IMG_DATA_t *cur_img_data, *img_data_tmp, *next; MSP_t *msp_tmp, *msp_ori; IMAGE_t *img_partner, *target_img, *target_partner; ELEMENT_t *ele_partner, *cur_ele = ele_info->ele; BD_t *tbd_tmp, *new_tbd; short dissected; cur_img_data = cur_ele->to_img_data; while (cur_img_data != NULL) { next = cur_img_data->next; dissected = 0; img_partner = partner(cur_img_data->to_image); ele_partner = img_partner->ele_info->ele; if (full_length(img_partner, CUTOFF2)){ ele_partner->flimg_no --; } tbd_tmp = cur_ele->TBD; while (tbd_tmp != NULL) { if (tbd_tmp->bd > cur_img_data->to_image->frag.lb || !tbd_tmp->next) { if (tbd_tmp->bd > cur_img_data->to_image->frag.lb && tbd_tmp->bd < cur_img_data->to_image->frag.rb) { if (tbd_tmp->bd - cur_img_data->to_image->frag.lb <= TOO_SHORT) { cur_img_data->to_image->to_msp->score = (int32_t) (cur_img_data->to_image->frag.rb-tbd_tmp->bd+1.)/(cur_img_data->to_image->frag.rb-cur_img_data->to_image->frag.lb+1.)*cur_img_data->to_image->to_msp->score; if (cur_img_data->to_image->to_msp->direction == 1) img_partner->frag.lb += tbd_tmp->bd - cur_img_data->to_image->frag.lb; else img_partner->frag.rb -= tbd_tmp->bd - cur_img_data->to_image->frag.lb; cur_img_data->to_image->frag.lb = tbd_tmp->bd; } else if (tbd_tmp->bd - cur_img_data->to_image->frag.rb >= -TOO_SHORT) { cur_img_data->to_image->to_msp->score = (int32_t) (tbd_tmp->bd-cur_img_data->to_image->frag.lb+1.)/(cur_img_data->to_image->frag.rb-cur_img_data->to_image->frag.lb+1.)*cur_img_data->to_image->to_msp->score; if (cur_img_data->to_image->to_msp->direction == 1) img_partner->frag.rb -= cur_img_data->to_image->frag.rb - tbd_tmp->bd; else img_partner->frag.lb += cur_img_data->to_image->frag.rb - tbd_tmp->bd; cur_img_data->to_image->frag.rb = tbd_tmp->bd; } else { dissected = 1; /* create a new MSP to hold the left products of the dissection */ msp_tmp = add_msp(cur_img_data->to_image->to_msp); /* upgrade the content of the new MSP */ if (cur_img_data->to_image == &cur_img_data->to_image->to_msp->query) { target_img = &msp_tmp->query; target_partner = &msp_tmp->sbjct; } else { target_img = &msp_tmp->sbjct; target_partner = &msp_tmp->query; } msp_tmp->score = (int32_t) (tbd_tmp->bd-target_img->frag.lb+1.)/(target_img->frag.rb-target_img->frag.lb+1.)*msp_tmp->score; if (msp_tmp->direction == 1) { // RMH: When tracking down the divide by zero problem I ended up signaling this // spot in the code as the likely place where things went initially wrong. // Explore further. target_partner->frag.rb -= target_img->frag.rb - tbd_tmp->bd; } else { target_partner->frag.lb += target_img->frag.rb - tbd_tmp->bd; } target_img->frag.rb = tbd_tmp->bd; fprint_msp(new_msps, msp_tmp); /* keep or ignore the new msp */ register_image(target_img, cur_ele); /* create the right product */ /* we cheat here. instead of generating a new MSP, we change the content of the original one, then output it into new_msp when finished. in the meantime, the index of the MSP is unchanged, which points to the oringinal MSP */ cur_img_data->to_image->to_msp->score -= msp_tmp->score; if (cur_img_data->to_image->to_msp->direction == 1) img_partner->frag.lb += tbd_tmp->bd - cur_img_data->to_image->frag.lb + 1; else img_partner->frag.rb -= tbd_tmp->bd - cur_img_data->to_image->frag.lb + 1; cur_img_data->to_image->frag.lb = tbd_tmp->bd +1; } } if (tbd_tmp->bd >= cur_img_data->to_image->frag.rb || !tbd_tmp->next) { /* end of this image */ if (dissected) { fprint_msp(new_msps, cur_img_data->to_image->to_msp); } if (too_short(&cur_img_data->to_image->frag) || too_short(&img_partner->frag)) { if (next && next->to_image->to_msp == cur_img_data->to_image->to_msp) next = next->next; dump_image(cur_img_data->to_image); } break; } } tbd_tmp = tbd_tmp->next; } cur_img_data = next; } /* the reason for not generating new elements according to the TBDs and then dissect and partition the images is that there's no gaining in time, it's virtually the same thing */ } int too_short(FRAG_t *f) { if (f->rb - f->lb <= TOO_SHORT) return 1; return 0; } MSP_t *add_msp(MSP_t *m) { MSP_t *msp_tmp; /*MSP_DATA_t *hanger;*/ msp_tmp = MSP_malloc(); /*hanger = msp_tmp->hanger;*/ *msp_tmp = *m; /*msp_tmp->hanger = hanger;*/ msp_index ++; msp_tmp->query.to_msp = msp_tmp; msp_tmp->query.index = 2*msp_index; msp_tmp->sbjct.to_msp = msp_tmp; msp_tmp->sbjct.index = 2*msp_index+1; msp_tmp->stat = 's'; /*msp_in_mem ++;*/ /*msp_ct ++;*/ return msp_tmp; } void register_image(IMAGE_t *i, ELEMENT_t *ele) { IMAGE_t *ip = partner(i); int ct; if (too_short(&i->frag)) { /* rec_image(&i->ele_info->ele->ignored, i); rec_image(&ip->ele_info->ele->ignored, ip); */ /* the msp here havn't been added to the corresponding elements, so we can simply free it */ MSP_free(i->to_msp); } else { /*ct = count_img_nodes(i->ele_info->ele->to_img_tree); if (ct != i->ele_info->ele->img_no) { err_no ++; fprintf(log_file, "error: image tree changed before inserting a new image: ele %d %d %d\n", i->ele_info->index, i->ele_info->ele->img_no, ct); fflush(log_file); exit(2); }*/ insert_image(&i->ele_info->ele->to_img_tree, i); i->ele_info->ele->img_no ++; /*ct = count_img_nodes(i->ele_info->ele->to_img_tree); if (ct != i->ele_info->ele->img_no) { err_no ++; fprintf(log_file, "error: trouble inserting a new image: ele %d %d %d\n", i->ele_info->index, i->ele_info->ele->img_no, ct); fflush(log_file); exit(2); }*/ if (i->ele_info->ele->to_img_data) put_image(&i->ele_info->ele->to_img_data, i); /*ct = count_img_nodes(ip->ele_info->ele->to_img_tree); if (ct != ip->ele_info->ele->img_no) { err_no ++; fprintf(log_file, "error: tree changed before inserting a new image: ele %d %d %d\n", ip->ele_info->index, ip->ele_info->ele->img_no, ct); fflush(log_file); exit(2); }*/ insert_image(&ip->ele_info->ele->to_img_tree, ip); ip->ele_info->ele->img_no ++; /*ct = count_img_nodes(ip->ele_info->ele->to_img_tree); if (ct != ip->ele_info->ele->img_no) { err_no ++; fprintf(log_file, "error: trouble inserting a new image: ele %d %d %d\n", ip->ele_info->index, ip->ele_info->ele->img_no, ct); fflush(log_file); exit(2); }*/ if (ip->ele_info->ele->to_img_data) put_image(&ip->ele_info->ele->to_img_data, ip); } } void put_image(IMG_DATA_t **idp, IMAGE_t *i) { IMG_DATA_t *img_data_tmp; img_data_tmp = (IMG_DATA_t *)malloc(sizeof(IMG_DATA_t)); img_data_tmp->to_image = i; img_data_tmp->next = *idp; *idp = img_data_tmp; } void dump_image(IMAGE_t *i) { IMAGE_t *ip = partner(i); int ct; if (i->ele_info->ele->to_img_data) remove_image(i); if (ip->ele_info->ele->to_img_data) remove_image(ip); /*ct = count_img_nodes(i->ele_info->ele->to_img_tree); if (ct != i->ele_info->ele->img_no) { err_no ++; fprintf(log_file, "error: image tree changed before deleting a node: ele %d %d %d\n", i->ele_info->index, i->ele_info->ele->img_no, ct); fflush(log_file); exit(2); }*/ delete_image(&i->ele_info->ele->to_img_tree, i); i->ele_info->ele->img_no --; /*ct = count_img_nodes(i->ele_info->ele->to_img_tree); if (ct != i->ele_info->ele->img_no) { err_no ++; fprintf(log_file, "error: trouble deleting an image node: ele %d %d %d\n", i->ele_info->index, i->ele_info->ele->img_no, ct); fflush(log_file); exit(2); }*/ /*ct = count_img_nodes(ip->ele_info->ele->to_img_tree); if (ct != ip->ele_info->ele->img_no) { err_no ++; fprintf(log_file, "error: image tree changed before deleting a node: ele %d %d %d\n", ip->ele_info->index, ip->ele_info->ele->img_no, ct); fflush(log_file); exit(2); }*/ delete_image(&ip->ele_info->ele->to_img_tree, ip); ip->ele_info->ele->img_no --; /*ct = count_img_nodes(ip->ele_info->ele->to_img_tree); if (ct != ip->ele_info->ele->img_no) { err_no ++; fprintf(log_file, "error: trouble deleting an image node: ele %d %d %d\n", ip->ele_info->index, ip->ele_info->ele->img_no, ct); fflush(log_file); exit(2); }*/ MSP_free(i->to_msp); } void remove_image(IMAGE_t *i) { IMG_DATA_t *prev_img_data=NULL, *cur_img_data; cur_img_data = i->ele_info->ele->to_img_data; while (cur_img_data != NULL) { if (cur_img_data->to_image == i) { if (prev_img_data != NULL) { prev_img_data->next = cur_img_data->next; } else { i->ele_info->ele->to_img_data = cur_img_data->next; } free(cur_img_data); break; } prev_img_data = cur_img_data; cur_img_data = cur_img_data->next; } } /***************************** *updating dissected element * *****************************/ void combo_update(ELE_INFO_t *ele_info) { if (ele_info->ele->img_no < 0) { err_no ++; fprintf(log_file, "error: combo ele %d has %d images\n", ele_info->index, ele_info->ele->img_no); fflush(log_file); exit(2); } ele_info->stat = 'X'; if (ele_info->ele->edges) combo_edge_update(ele_info, &ele_info->ele->edges); if (ele_info->ele->edge_no) { err_no ++; fprintf(log_file, "error: combo_ele %d, %d edge_node left\n", ele_info->index, ele_info->ele->edge_no); fflush(log_file); exit(4); } ele_info->ele->flimg_no = 0; if (ele_info->ele->PCP) CP_free(&ele_info->ele->PCP); if (ele_info->ele->redef) { if (ele_info->ele->to_img_data) { err_no ++; fprintf(log_file, "error re-defining ele %d, still images left\n", ele_info->index); fflush(log_file); exit(5); } /* all images and msps are relocated to offsprings, so img_tree_free() is enough */ if (ele_info->ele->to_img_tree) img_tree_free(&ele_info->ele->to_img_tree, ele_info); if (ele_info->ele->img_no) { err_no ++; fprintf(log_file, "error: combo_ele %d, %d img_node left\n", ele_info->index, ele_info->ele->img_no); fflush(log_file); ele_info->ele->img_no = 0; exit(2); } combo_output(ele_info); } else { if (ele_info->ele->img_no || ele_info->ele->to_img_data || ele_info->ele->to_img_tree) { err_no ++; fprintf(log_file, "error: images not cleaned in obs ele %d\n", ele_info->index); fflush(log_file); exit(2); } else obs_output(ele_info); } } void combo_edge_update(ELE_INFO_t *ele_info, EDGE_TREE_t **edge_node_p) { ELE_INFO_t *epi; EDGE_TREE_t *edge_node = *edge_node_p; ELEMENT_t *ele = ele_info->ele; if (edge_node->l) combo_edge_update(ele_info, &(*edge_node_p)->l); if (edge_node->r) combo_edge_update(ele_info, &(*edge_node_p)->r); epi = linked_ele(ele_info, edge_node->to_edge); if (epi->stat == 'v') epi->stat = 'w'; if (epi->ele->PCP) CP_clean(&epi->ele->PCP, ele_info); delete_edge(&epi->ele->edges, edge_node->to_edge); epi->ele->edge_no --; EDGE_free(edge_node->to_edge); ele_info->ele->edge_no --; free(edge_node); *edge_node_p = NULL; } void CP_clean(CP_t **cps_p, ELE_INFO_t *cont) { /*int res=0;*/ CP_t *cp_cur, *cp_prev; cp_cur = *cps_p; cp_prev = NULL; while (cp_cur != NULL) { if (cp_cur->contributor == cont) { if (cp_prev == NULL) { *cps_p = cp_cur->next; free(cp_cur); cp_cur = *cps_p; } else { cp_prev->next = cp_cur->next; free(cp_cur); cp_cur = cp_prev->next; } /*res ++;*/ } else { cp_prev = cp_cur; cp_cur = cp_cur->next; } } /*return res;*/ } /**************************************************** **************************************************** ** functions for finding PCPs and set up edges ** **************************************************** ****************************************************/ void edges_and_cps(ELE_INFO_t *ele_info, IMAGE_t **img_ptr) { /* the core function in this part, calls everything below */ int eff_img_ct, i, prim; int j, riteplace; short ritetime; MSP_t *prim_p; IMG_DATA_t *cur_img_data; ELEMENT_t *ele_partner, *cur_ele = ele_info->ele; ELE_INFO_t *epi; IMAGE_t *img_partner, *cur_img; IMAGE_t *token_image; int token_mark=0; IMG_NODE_t *consis_rt, *cur_consis_nd; ELE_DATA_t *ele_data_tmp; IMG_DATA_t *scovs; int32_t max_score=0; short dir; /* sort unprocessed images according to their partner element, and then their left bounds */ /* to allocate proper amount of memory */ /* when update is 1, it means the element is an offspring of a combo, in which case all the images need to be processed; when update is 0, those images whose partner is 'v' or 'w' should be omitted */ /* no self-images are accepted to generate pcps or edges, updating or not */ if (!cur_ele->to_img_data) listify(cur_ele->to_img_tree, &cur_ele->to_img_data); cur_img_data = cur_ele->to_img_data; eff_img_ct = 0; while(cur_img_data != NULL) { epi = partner(cur_img_data->to_image)->ele_info; if (epi->index != ele_info->index) { if (cur_ele->update || epi->stat == 'z') eff_img_ct ++; } cur_img_data = cur_img_data->next; } if (eff_img_ct) { token_image = (IMAGE_t *) malloc(sizeof(IMAGE_t)); token_image->frag.lb = 0; token_image->frag.rb = 0; token_image->to_msp = NULL; token_image->ele_info = NULL; consis_rt = (IMG_NODE_t *) malloc(sizeof(IMG_NODE_t)); consis_rt->to_image = token_image; consis_rt->children = NULL; consis_rt->sib = NULL; if (eff_img_ct > MAX_IMG) { img_ptr = (IMAGE_t **) malloc(eff_img_ct*sizeof(IMAGE_t *)); } cur_img_data = cur_ele->to_img_data; eff_img_ct = 0; while(cur_img_data != NULL) { epi = partner(cur_img_data->to_image)->ele_info; if (epi->index != ele_info->index) { if (cur_ele->update || epi->stat == 'z') { *(img_ptr+eff_img_ct) = cur_img_data->to_image; eff_img_ct ++; } } cur_img_data = cur_img_data->next; } qsort(img_ptr, eff_img_ct, sizeof(IMAGE_t *), partner_cmp); /* recognizing full-length images, and put partial and secondary images into a consistency tree, in which images connected are consistent with each other (look at the consis() function of definition of consistency) */ ritetime = 1; for (i=0; iele_info; ritetime = 0; if (!epi->ele) ele_read_in(epi, 1); ele_partner = epi->ele; riteplace = i; prim = 0; prim_p = NULL; max_score = 0; } if (img_partner->ele_info->index == epi->index) { /* still the same partner element */ /* full length */ if (full_length(cur_img, CUTOFF2)) { /*cur_img->to_msp->stat = 'p';*/ prim = 1; cur_ele->flimg_no ++; } if (full_length(img_partner, CUTOFF2)) { /*cur_img->to_msp->stat = 'p';*/ prim = 1; ele_partner->flimg_no ++; } /*if (cur_img->to_msp->stat == 'p') {*/ if (prim == 1) { prim = 0; if (cur_img->to_msp->iden > max_score) { max_score = cur_img->to_msp->iden; dir = cur_img->to_msp->direction; prim_p = cur_img->to_msp; } } if (!prim_p) { /* non-fl, and no fl found yet */ consis_tree_build(consis_rt, cur_img, 1); } } if (img_partner->ele_info->index != epi->index || i == eff_img_ct-1) { /* reached the end of the current ele_partner */ /* start a new ele_partner */ ritetime = 1; if (img_partner->ele_info->index != epi->index) i --; /* finish the current ele_partner */ if (prim_p) { prim_p->stat = 'p'; prim = 1; } else { /* if no fl, find partial primary images */ /*prim = find_prim(consis_rt, CUTOFF2, 0, 0, 0, &max_score, &dir);*/ prim = find_prim(consis_rt->children, CUTOFF2, ele_info->ele->frag.lb, -1, 0, 0, 0, 0, 0, &token_mark, &max_score, &dir); } /* build edge */ if (prim) { if (ele_info->index != epi->index) add_edge(ele_info, epi, 'p', max_score, dir); else { err_no ++; fprintf(log_file, "error: self edge seen: ele %d\n", ele_info->index); fflush(log_file); } for (j=riteplace; j<=i; j++) { if ((*(img_ptr+j))->to_msp->stat == 'p') { cur_img = *(img_ptr+j); img_partner = partner(cur_img); add_CP(&cur_ele->PCP, cur_img->frag.lb, epi); add_CP(&cur_ele->PCP, cur_img->frag.rb, epi); add_CP(&ele_partner->PCP, img_partner->frag.lb, ele_info); add_CP(&ele_partner->PCP, img_partner->frag.rb, ele_info); } } } else { /* no primary images, full-length or partial */ if (ele_info->index != epi->index) add_edge(ele_info, epi, 's', 0, 0); else { err_no ++; fprintf(log_file, "error: self edge seen: ele %d\n", ele_info->index); fflush(log_file); } } if (consis_rt->children != NULL) { consis_tree_free(consis_rt->children); consis_rt->children = NULL; } } } if (eff_img_ct > MAX_IMG) { free(img_ptr); } free(consis_rt); free(token_image); } if (ele_info->ele->edges) adjust_edge_tree(ele_info); cur_ele->update = 0; ele_info->stat = 't'; } /* NOTE: Due to the difference in computational precesion between 32bit * and 64 bit processors the following function may return differing * results. */ int full_length(IMAGE_t *i, float cutoff) { if (!i->ele_info->ele) { err_no ++; fprintf(log_file, "error: element %d not in memory\n", i->ele_info->index); fflush(log_file); exit(3); ele_read_in(i->ele_info, 1); } if (i->frag.lb-i->ele_info->ele->frag.lb < 10 && i->frag.rb-i->ele_info->ele->frag.rb > -10 && ((float) i->frag.rb-i->frag.lb)/(i->ele_info->ele->frag.rb-i->ele_info->ele->frag.lb) > cutoff) { return 1; } return 0; } void add_CP(CP_t **CP_ptr, int32_t cp, ELE_INFO_t *cont) { CP_t *new = (CP_t *) malloc(sizeof(CP_t)); new->cp = cp; new->contributor = cont; new->next = *CP_ptr; *CP_ptr = new; } void add_edge(ELE_INFO_t *ele1_info, ELE_INFO_t *ele2_info, char type, int32_t score, short dir) { EDGE_t *new = EDGE_malloc(); int ct; edge_index ++; new->index = edge_index; new->ele1_info = ele1_info; new->ele2_info = ele2_info; new->type = type; new->score = score; new->direction = dir; /*ct = count_edge_nodes(ele1_info->ele->edges); if (ct != ele1_info->ele->edge_no) { err_no ++; fprintf(log_file, "error: trouble before inserting edge\n"); fflush(log_file); exit(4); }*/ ele1_info->ele->edge_no ++; insert_edge(&ele1_info->ele->edges, new); /*ct = count_edge_nodes(ele1_info->ele->edges); if (ct != ele1_info->ele->edge_no) { err_no ++; fprintf(log_file, "error: trouble after inserting edge\n"); fflush(log_file); exit(4); }*/ if (ele1_info->index != ele2_info->index) { /*ct = count_edge_nodes(ele2_info->ele->edges); if (ct != ele2_info->ele->edge_no) { err_no ++; fprintf(log_file, "error: trouble before inserting edge\n"); fflush(log_file); exit(4); }*/ ele2_info->ele->edge_no ++; insert_edge(&ele2_info->ele->edges, new); /*ct = count_edge_nodes(ele2_info->ele->edges); if (ct != ele2_info->ele->edge_no) { err_no ++; fprintf(log_file, "error: trouble after inserting edge\n"); fflush(log_file); exit(4); }*/ } } void adjust_edge_tree(ELE_INFO_t *ele_info) { EDGE_t **edge_array; int ct, ct1; /*ct = count_edge_nodes(ele_info->ele->edges); if (ct != ele_info->ele->edge_no) { err_no ++; fprintf(log_file, "error: trouble before adjusting the edge tree: ele %d %d %d\n", ele_info->index, ele_info->ele->edge_no, ct); fflush(log_file); exit(4); } ct = count_total_edges(ele_info->ele->edges); if (ct != ele_info->ele->edge_no) { err_no ++; fprintf(log_file, "error: illegitimate edge in ele %d\n", ele_info->index); fflush(log_file); exit(5); }*/ ct = ele_info->ele->edge_no; edge_array = (EDGE_t **) malloc(ct*sizeof(EDGE_t *)); ct1 = charge_edge_array(edge_array, ele_info->ele->edges, 0); if (ct1 != ct) { err_no ++; fprintf(log_file, "error: trouble charging the edge array in ele %d: %d charged, %d expected\n", ele_info->index, ct1, ct); fflush(log_file); exit(4); } edge_tree_free(&ele_info->ele->edges); build_edge_tree(&ele_info->ele->edges, edge_array, 0, ct-1); /*ct = count_edge_nodes(ele_info->ele->edges); if (ct != ele_info->ele->edge_no) { err_no ++; fprintf(log_file, "error: trouble adjusting the edge tree: ele %d %d %d\n", ele_info->index, ele_info->ele->edge_no, ct); fflush(log_file); exit(4); }*/ free(edge_array); } int charge_edge_array(EDGE_t **edge_array, EDGE_TREE_t *rt, int pos) { if (rt->l) pos = charge_edge_array(edge_array, rt->l, pos); *(edge_array+pos) = rt->to_edge; pos ++; if (rt->r) pos = charge_edge_array(edge_array, rt->r, pos); return pos; } /****************************************** * functions for building the consis_tree * ******************************************/ int consis_tree_build(IMG_NODE_t *rt, IMAGE_t *im, int prequal) { int sum=0; IMG_NODE_t *nex_rt, *node; if (prequal || consis(rt->to_image, im, CUTOFF2)) { nex_rt = rt->children; while (nex_rt != NULL) { sum += consis_tree_build(nex_rt, im, 0); nex_rt = nex_rt->sib; } if (!sum) { node = (IMG_NODE_t *) malloc(sizeof(IMG_NODE_t)); node->recorded = 0; node->to_image = im; node->sib = NULL; node->children = NULL; *node_entry(&rt->children) = node; sum = 1; } } return sum; } int consis(IMAGE_t *i1, IMAGE_t *i2, float cutoff) { int res = 0; IMAGE_t *ip1 = partner(i1), *ip2 = partner(i2); if (i1->ele_info->index == i2->ele_info->index && ip1->ele_info->index == ip2->ele_info->index && i1->to_msp->direction == i2->to_msp->direction) { if (i1->to_msp->direction == 1) { if ((i1->frag.lb - i2->frag.lb)*(ip1->frag.lb - ip2->frag.lb) > 0) { if (!sing_cov(&i1->frag, &i2->frag, 1.0-cutoff) && !sing_cov(&ip1->frag, &ip2->frag, 1.0-cutoff)) { res = 1; } } } else { if ((i1->frag.lb - i2->frag.lb)*(ip1->frag.rb - ip2->frag.rb) < 0) { if (!sing_cov(&i1->frag, &i2->frag, 1.0-cutoff) && !sing_cov(&ip1->frag, &ip2->frag, 1.0-cutoff)) { res = 1; } } } } return res; } IMG_NODE_t ** node_entry(IMG_NODE_t **node_pp) { if (*node_pp != NULL) { return node_entry(&(*node_pp)->sib); } return node_pp; } void consis_tree_free(IMG_NODE_t *rt) { if (rt->sib != NULL) { consis_tree_free(rt->sib); } if (rt->children != NULL) { consis_tree_free(rt->children); } free(rt); } /***************************************** * functions for parsing the consis_tree * *****************************************/ /* I. function for finding primary images from the consis_tree */ #if 0 int find_prim(IMG_NODE_t *nd, float cutoff, int32_t score, int32_t hist, short which, int32_t *sc, short *d) { IMG_NODE_t *nex_node; int sum = 0; short level, further = 0; IMAGE_t *img_partner; if (!hist) level = 1; hist += nd->to_image->frag.rb - nd->to_image->frag.lb; if (level && hist) { /* if first image in a path isn't EOE, forget the path */ if (nd->to_image->frag.lb - nd->to_image->ele_info->ele->frag.lb < MARGIN) { which = 1; } img_partner = partner(nd->to_image); if (nd->to_image->to_msp->direction == 1) { if (img_partner->frag.lb - img_partner->ele_info->ele->frag.lb < MARGIN) { which += 2; } } else { if (img_partner->frag.rb - img_partner->ele_info->ele->frag.rb > -MARGIN) { which += 2; } } if (!which) return 0; } if (nd->children != NULL) { nex_node = nd->children; while (nex_node != NULL) { sum += find_prim(nex_node, cutoff, score, hist, which, sc, d); nex_node = nex_node->sib; } if (sum && hist) { nd->to_image->to_msp->stat = 'p'; /* p stands for primary, NOT partial */ } } else { /* the last image goes to EOE on the same element as the first image in the path */ if ((which == 1 || which == 3) && nd->to_image->frag.rb - nd->to_image->ele_info->ele->frag.rb > -MARGIN && (float) hist/(nd->to_image->ele_info->ele->frag.rb - nd->to_image->ele_info->ele->frag.lb) > cutoff) { further = 1; } else { img_partner = partner(nd->to_image); if ((which == 2 || which == 3) && (float) hist/(img_partner->ele_info->ele->frag.rb - img_partner->ele_info->ele->frag.lb) > cutoff) { if (nd->to_image->to_msp->direction == 1) { if (img_partner->frag.rb - img_partner->ele_info->ele->frag.rb > -MARGIN) further = 1; } else { if (img_partner->frag.lb - img_partner->ele_info->ele->frag.lb < MARGIN) further = 1; } } } if (further) { nd->to_image->to_msp->stat = 'p'; score += nd->to_image->to_msp->score; if (score > *sc) { *sc = score; *d = nd->to_image->to_msp->direction; } sum = 1; } else {sum = 0;} } return sum; } #endif int find_prim(IMG_NODE_t *nd, float cutoff, int32_t end1, int32_t end2, int32_t efl1, int32_t efl2, int32_t al1, int32_t al2, int32_t score, int *pmarkp, int32_t *sc, short *d) { int sum = 0, mark=0; int32_t skip1, skip2, len1, len2; IMAGE_t *ipt; if (nd->sib) sum += find_prim(nd->sib, cutoff, end1, end2, efl1, efl2, al1, al2, score, pmarkp, sc, d); ipt = partner(nd->to_image); if (end2 < 0) { /*first alignment in the group*/ if (nd->to_image->to_msp->direction == 1) end2 = ipt->ele_info->ele->frag.lb; else end2 = ipt->ele_info->ele->frag.rb; } skip1 = nd->to_image->frag.lb - end1; if (nd->to_image->to_msp->direction == 1) skip2 = ipt->frag.lb - end2; else skip2 = end2 - ipt->frag.rb; if (skip1>10 && skip2>10) { efl1 += skip1; efl2 += skip2; } len1 = nd->to_image->frag.rb - nd->to_image->frag.lb; len2 = ipt->frag.rb - ipt->frag.lb; efl1 += len1; efl2 += len2; al1 += len1; al2 += len2; score += ((int32_t) nd->to_image->to_msp->iden)*(len1+len2)/2; if (nd->children) { end1 = nd->to_image->frag.rb; if (nd->to_image->to_msp->direction == 1) end2 = ipt->frag.rb; else end2 = ipt->frag.lb; sum += find_prim(nd->children, cutoff, end1, end2, efl1, efl2, al1, al2, score, &mark, sc, d); } else { /*last alignment in group*/ skip1 = nd->to_image->ele_info->ele->frag.rb - nd->to_image->frag.rb; if (nd->to_image->to_msp->direction == 1) skip2 = ipt->ele_info->ele->frag.rb - ipt->frag.rb; else skip2 = ipt->frag.lb - ipt->ele_info->ele->frag.lb; if (skip1>10 && skip2>10) { efl1 += skip1; efl2 += skip2; } /*if (1.0*al1/efl1 > cutoff || 1.0*al2/efl2 > cutoff) {*/ if ( (1.0*al1/efl1 > cutoff || 1.0*al2/efl2 > cutoff) && (efl1-al1 < 30 || efl2-al2 < 30) ) { sum = 1; mark = 1; if ( (al1+al2) == 0 ) { // RMH: A divide by zero error has occured a few times at this point. // I looked extensively through the code and cannot determine what // is causing this -- although I have a reliable test case to // explore this further. For now this is the only workaround. // If al1 & al2 are zero then simply set them to 1. printf("eleredef warning: Divide by zero averted -- setting al1 to 1.\n"); al1 = 1; } score = score*2/(al1+al2); if (score > *sc) { *sc = score; *d = nd->to_image->to_msp->direction; } } } if (mark) { nd->to_image->to_msp->stat = 'p'; *pmarkp = 1; } return sum; } /************************ ************************ *** *** *** OUTPUT *** *** *** ************************ ************************/ void combo_output(ELE_INFO_t *ele_info) { char *ele_name; FILE *ele_fp; ELE_DATA_t *cur_ele_data; fprintf(combo, "%d %s %d %d \n", ele_info->index, ele_info->ele->frag.seq_name, ele_info->ele->frag.lb, ele_info->ele->frag.rb); fflush(combo); #if 0 /* no ele_read_in() needed, 'cuz where this function is called, both the combo and its offsprings are in the memory */ ele_name = (char *) malloc(30*sizeof(char)); sprintf(ele_name, "tmp2/clan/combos/e%d", ele_info->index); ele_fp = fopen(ele_name, "w"); fprintf(ele_fp, "ele %d\n", ele_info->index); fprintf(ele_fp, "offsprings \n"); cur_ele_data = ele_info->ele->redef; while (cur_ele_data != NULL) { if (cur_ele_data->ele_info->ele->direction == 1) fprintf(ele_fp, "%6d %10s %8d %8d\n", cur_ele_data->ele_info->index, cur_ele_data->ele_info->ele->frag.seq_name, cur_ele_data->ele_info->ele->frag.lb, cur_ele_data->ele_info->ele->frag.rb); else fprintf(ele_fp, "%6d %10s %8d %8d\n", cur_ele_data->ele_info->index, cur_ele_data->ele_info->ele->frag.seq_name, cur_ele_data->ele_info->ele->frag.rb, cur_ele_data->ele_info->ele->frag.lb); cur_ele_data = cur_ele_data->next; } fclose(ele_fp); free(ele_name); /* remove_ele(ele_info);*/ #endif } void obs_output(ELE_INFO_t *ele_info) { char *ele_name; FILE *ele_fp; fprintf(obs, "%d %s %d %d \n", ele_info->index, ele_info->ele->frag.seq_name, ele_info->ele->frag.lb, ele_info->ele->frag.rb); fflush(obs); #if 0 ele_name = (char *) malloc(30*sizeof(char)); sprintf(ele_name, "tmp2/clan/obsolete/e%d", ele_info->index); ele_fp = fopen(ele_name, "w"); fprint_ele_obs(ele_fp, ele_info); fclose(ele_fp); free(ele_name); /* remove_ele(ele_info);*/ #endif } void fprint_ele_obs(FILE *fp, ELE_INFO_t *ele_info) { int i; BD_t *cur_bd; ELEMENT_t *ele=ele_info->ele; fprintf(fp, "ele %d\n", ele_info->index); fprintf(fp, "%s %d %d \n", ele->frag.seq_name, ele->frag.lb, ele->frag.rb); if (ele->TBD != NULL) { fprintf(fp, "cutting points\n"); i = 0; cur_bd = ele->TBD; while (cur_bd != NULL) { fprintf(fp, "%d ", cur_bd->bd); i ++; if (i%10 == 0) fprintf(fp, "\n"); cur_bd = cur_bd->next; } } } /************************************** ************************************** * * * comparison fucntions for qsort() * * * ************************************** **************************************/ int frag_cmp(const void *i1, const void *i2) { int res = (*(IMG_DATA_t **)i1)->to_image->frag.seq_name - (*(IMG_DATA_t **)i2)->to_image->frag.seq_name; /*strncmp((*(IMG_DATA_t **)i1)->to_image->frag.seq_name, (*(IMG_DATA_t **)i2)->to_image->frag.seq_name, NAME_LEN)*/ if (res == 0) { res = (*(IMG_DATA_t **)i1)->to_image->frag.lb - (*(IMG_DATA_t **)i2)->to_image->frag.lb; if (res == 0) { res = (*(IMG_DATA_t **)i1)->to_image->frag.rb - (*(IMG_DATA_t **)i2)->to_image->frag.rb; } } return res; } int partner_cmp(const void *i1, const void *i2) { int res = partner(*((IMAGE_t **)i1))->ele_info->index - partner(*((IMAGE_t **)i2))->ele_info->index; if (res == 0) { res = (*((IMAGE_t **)i1))->to_msp->direction - (*((IMAGE_t **)i2))->to_msp->direction; } if (res == 0) { res = (*((IMAGE_t **)i1))->frag.lb - (*((IMAGE_t **)i2))->frag.lb; } if (res == 0) { res = (*((IMAGE_t **)i1))->frag.rb - (*((IMAGE_t **)i2))->frag.rb; } return res; } int CP_cmp(const void *cp1, const void *cp2) { return (*((CP_t **) cp1))->cp - (*((CP_t **) cp2))->cp; } int BD_cmp(const void *bd1, const void *bd2) { return (*((BD_t **) bd1))->bd - (*((BD_t **) bd2))->bd; } int fam_cmp(const void *fd1, const void *fd2) { return (*((FAM_DATA_t **) fd1))->to_family->index - (*((FAM_DATA_t **) fd2))->to_family->index; } RECON-1.08/src/bolts.h0000644000076400007640000000023212274532636014126 0ustar rhubleyrepeat/* standard stuff */ #include #include #include #define NAME_LEN 50 #define DEPTH 3 int32_t seq_no; char **seq_names; RECON-1.08/src/Makefile0000644000076400007640000000531312274532636014277 0ustar rhubleyrepeat# Makefile for ReCon # # VERSION = 1.08 ## where you want things installed BINDIR = ../bin MANDIR = $(HOME)/man ## sourcefiles #SRCDIR = . ## your compiler #CC = cc # for SGI Origin200 compiler# CC = gcc ## any special compiler flags you want # -pedantic clashes with -DMEMDEBUG?? # #CFLAGS = -g -Wall -pedantic CFLAGS = -O #CFLAGS = -g #CFLAGS = -TARG:exc_max -64 -Ofast=ip27 #specific SGI Origin200 compiler# ## machine specific definitions # None should be needed # # Development: # -DASSERT Diagnostics level 1. Assertions. # -DVERBOSE Diagnostics level 2. Verbosity. (unused at the moment) # -DMEMDEBUG Diagnostics level 3. Memory checking. (maybe slow!) # (must link w/ -ldbmalloc) # -DLINTING Suppress overzealous warnings from gcc -Wall and lint # #MDEFS = -DLINTING -DASSERT -DMEMDEBUG #MDEFS = -DASSERT ## how to install the man pages ## cp is fine INSTMAN = cp MANSUFFIX = 1 ## Your compression program COMPRESS = gzip # GNU compression (better, smaller) #COMPRESS = compress # generic UNIX compress (portable) ####### ## should not need to modify below this line ####### SHELL = /bin/sh LIBS = -lsquid -lm #LIBS = -ldbmalloc -lsquid -lm READMES = README #INSTALL COPYING DEMO GNULICENSE FILES PROGS = imagespread eledef eleredef edgeredef famdef MANSRC= DOCS = HDRS = bolts.h seqlist.h msps.h ele.h MAIN = SRC = imagespread.c eledef.c eleredef.c edgeredef.c famdef.c OBJ = DISTFILES = $(MAIN) $(SRC) $(HDRS) $(MANSRC) $(READMES) $(DOCS) TESTSUITE = DEMOS = $(HOME)/Demos all: $(PROGS) install: $(PROGS) cp $(PROGS) $(BINDIR)/ clean: -rm -f imagespread eledef eleredef edgeredef famdef *.o *~ *.Addrs *.Counts *.pixie Makefile.bak core $(PROGS) TAGS tags: etags -t $(DISTFILES) dist: @if test -d recon-$(VERSION); then rm -rf recon-$(VERSION); fi @if test -f recon-$(VERSION).tar.gz; then rm recon-$(VERSION).tar.gz; fi @if test -f recon-$(VERSION).tar.Z; then rm recon-$(VERSION).tar.Z; fi mkdir recon-$(VERSION)/ cp $(DISTFILES) recon-$(VERSION)/ cp Makefile.dist recon-$(VERSION)/Makefile mkdir recon-$(VERSION)/Testsuite for testfile in $(TESTSUITE); do \ cp Testsuite/$$testfile recon-$(VERSION)/Testsuite/;\ done mkdir recon-$(VERSION)/Demos for demofile in $(DEMOS); do\ cp Demos/$$demofile recon-$(VERSION)/Demos/;\ done tar cvf recon-$(VERSION).tar recon-$(VERSION) $(COMPRESS) recon-$(VERSION).tar test: (cd Testsuite; testsuite.sh) lint: lint -h -I$(SQUIDDIR) $(RFLAGS) $(MAIN) $(SRC) $(SQUIDDIR)/llib-lsquid.ln /usr/lib/lint/llib-lm.ln .c.o: $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< .m.o: $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< RECON-1.08/LICENSE0000640000076400007640000004307612274532636013061 0ustar rhubleyrepeat GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 675 Mass Ave, Cambridge, MA 02139, USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. 8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS Appendix: How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) 19yy This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) 19yy name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Library General Public License instead of this License. RECON-1.08/bin/0000755000076400007640000000000012274532636012616 5ustar rhubleyrepeat