debian/0000755000000000000000000000000011725447234007177 5ustar debian/watch0000644000000000000000000000016711717554365010241 0ustar version=3 opts="pasv" \ ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blimps/blimps-([0-9.]+)\.tar\.gz debian uupdate debian/blimps-utils.docs0000644000000000000000000000001711725370641012470 0ustar README UPDATES debian/copyright0000644000000000000000000001436611725370065011141 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Blimps Upstream-Contact: J. Henikoff Source: http://blocks.fhcrc.org/blocks/uploads/blimps Files: * Copyright: 1993-2007, Fred Hutchinson Cancer Research Center License: FHCRC LICENSE -- License and copyright information for BLOCKS and BLIMPS . --------------------------------------------------------------------------- FHCRC NONCOMMERCIAL LICENSE Fred Hutchinson Cancer Research Center 1100 Fairview AV N Seattle, WA 98109-1024 . . This license may be copied and distributed but may not be modified in any way. . RECITALS: . A. Fred Hutchinson Cancer Research Center is a nonprofit corporation dedicated to investigating the nature and causes of cancer and methods of cancer prevention and treatment and for conducting education in all phases of cancer research. . B. This license is designed to permit certain activities with respect to any computer programs to which it applies on the terms stated in this license. . TERMS AND CONDITIONS: . 1. Definitions. . "Program" means the computer software and associated documentation in whatever form or format including source and object code. . "Derivative Work" means any modification, addition, upgrade, update or improvement of the Program and any other work constituting a derivative work under the copyright laws. . "Licensee" means licensee of the Program under this license. . "FHCRC" means Fred Hutchinson Cancer Research Center. . 2. License, Copy, Distribute and Create Derivative Work. FHCRC hereby grants Licensee and Licensee accepts, subject to the terms and conditions of this Agreement, a nonexclusive, royalty-free license to use, copy and sublicense the Program and prepare and sublicense Derivative Works. This license is expressly limited as follows: . a. All copies of the Program must conspicuously show an appropriate copyright notice and disclaimer of warranty and must expressly refer to this license. In addition, Derivative Works must conspicuously state that the Program has been modified and the date of any modification. . b. Licensee may not charge any fee or royalty for copies of the Program or Derivative Work. Licensee is authorized to sublicense the Program and any Derivative Work to third parties on a royalty-free basis subject to the terms of this license but may not otherwise distribute the Program or any Derivative Work. Notwithstanding the foregoing, Licensee may be reimbursed for any actual expenses it incurs in reproducing or delivering a copy of the Program or any Derivative Work. . c. This license does not apply to a work written entirely by Licensee. . d. Licensee agrees to make available to any person to whom it sublicenses this Program or a Derivative Work source code and object code for the Program or Derivative Work. . e. Licensee may not impose any terms in addition to the terms of this license on any third party to whom it distributes the Program, any Derivative Work or any copy thereof. . 3. Reservation of Rights to FHCRC. FHCRC hereby reserves to itself all rights of any nature whatsoever with respect to the Program. Any Derivative Work created by FHCRC or its employees or agents is not subject to the terms of this license. . 4. Termination of license. This license precludes any copying, modification, sublicensing or other distribution of any Program or Derivative Work except as expressly permitted under this license. Violation of the terms of this license by Licensee will be deemed an automatic termination of Licensee's rights under this license; provided, however, that sublicenses derived from Licensee will remain in full force and effect provided that any such sublicensees do not breach the terms of this license. . 5. Acceptance of Terms of License. Licensee agrees that by copying or distributing this Program or by creating, copying or distributing any Derivative Work, Licensee has agreed to the terms of this license. . 6. Limitation of Remedies and Indemnity. Because this Program is licensed on a royalty-free basis, FHCRC and any person distributing this Program or any Derivative Work expressly disclaim all warranties express or implied including, without limitation, any implied warranty of merchantability or fitness for a particular purpose. Neither FHCRC nor any other party distributing the Program or any Derivative Work will be liable for any damages arising from or related to the use of the Program or such Derivative Work, including, without limitation, incidental or consequential damages caused by the use or inability to use the Program or loss or damage to data. . Licensee agrees to indemnify, defend and hold FHCRC harmless from and against any claims, causes of action, damages, liabilities and expenses, including without limitation attorney's fees, arising from or related to Licensee's use, copying or distribution of the Program or any Derivative Work. . 7. Severability. If any provision of this license is held invalid under any applicable law or for any other reason, such invalidity shall not effect any other provision of this license that can be given effect without the invalid provision. . 8. Notice. Persons wishing to communicate with FHCRC concerning this license or the Program should address their communications as follows: . Fred Hutchinson Cancer Research Center Attn: Dr. Steven Henikoff 1100 Fairview AV N, A1-162 PO Box 19024 Seattle, WA 98109-1024 Files: debian/* Copyright: 2009-2012 Laszlo Kajan , 2012 Andreas Tille License: GPL Packaging is licensed under the GPL, see `/usr/share/common-licenses/GPL'. debian/changelog0000644000000000000000000000022311725447234011046 0ustar blimps (3.9-1) unstable; urgency=low * Initial release (Closes: #657897) -- Andreas Tille Tue, 06 Mar 2012 18:51:08 +0100 debian/blimps-examples.examples0000644000000000000000000000001311725363153014030 0ustar examples/* debian/README.Debian0000644000000000000000000000076611723512510011235 0ustar blimps for Debian ----------------- Blimps is no longer maintained upstream. Out of the many binaries from the upstream blimps package only fastaseqs is included in blimps-utils. The reason for this is that only that utility is needed by packages that depend on blimps and no new packages are expected to depend on blimps. If you need something and you can not find it in this package, please contact the package maintaner(s). -- Laszlo Kajan Wed, 25 Nov 2009 12:26:22 +0100 debian/blimps-utils.manpages0000644000000000000000000000001711725370276013337 0ustar fastaseqs.1.gz debian/README.source0000644000000000000000000000131511723512510011342 0ustar blimps for Debian ----------------- blimps is no longer maintained upstream, see http://blocks.fhcrc.org/blocks/uploads/blimps/. Therefore fixes to source can not be communicated to upstream. Since no new software is expected to require blimps, packaging focuses only on features required by packages that already depend on blimps (such as sift). If you need something and you can not find it in this package, please contact the package maintaner(s). Patches ....... Patches are documented in their headers. Autobuilding ............ The FHCRC NONCOMMERCIAL LICENSE does not prohibit building the source. It also does not prohibit the distribution of the binary software on a royalty-free basis. # vim:et:ts=2: debian/libblimps3.install0000644000000000000000000000002211712214531012605 0ustar usr/lib/lib*.so.* debian/source/0000755000000000000000000000000011721776167010505 5ustar debian/source/format0000644000000000000000000000001411712214530011670 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000211721776647010406 0ustar 8 debian/patches/0000755000000000000000000000000011721776167010634 5ustar debian/patches/patch0010000644000000000000000000042256111723512510012067 0ustar * replaced gets() with fgets() * fixes to blimps/Makefile.Linux Index: blimps-3.9/blimps/addseqs.c =================================================================== --- blimps-3.9.orig/blimps/addseqs.c 2012-02-03 21:58:55.968242949 +0100 +++ blimps-3.9/blimps/addseqs.c 2012-02-03 22:01:33.780367907 +0100 @@ -150,7 +150,7 @@ else { printf("\nEnter name of file containing blocks: "); - gets(infile); + fgets(infile, MAXNAME, stdin); } if ( (fblk=fopen(infile, "r")) == NULL) { @@ -164,7 +164,7 @@ else { printf("\nEnter name of sequence file: "); - gets(seqsfile); + fgets(seqsfile, MAXNAME, stdin); } if ( (fseq=fopen(seqsfile, "r")) == NULL) { @@ -177,7 +177,7 @@ else { printf("\nEnter name of output seqs file: "); - gets(outfile); + fgets(outfile, MAXNAME, stdin); } if ( (fout=fopen(outfile, "w")) == NULL) { Index: blimps-3.9/blimps/biassed_blocks_finder.c =================================================================== --- blimps-3.9.orig/blimps/biassed_blocks_finder.c 2012-02-03 21:58:55.992242645 +0100 +++ blimps-3.9/blimps/biassed_blocks_finder.c 2012-02-03 22:02:36.760368069 +0100 @@ -25,6 +25,11 @@ void unescape_url(char *url); void plustospace(char *str); */ +// lkajan: very nice but util.c does not have an interface defined +// lkajan: can't figure out where this came from but it certainly picked up the wrong fmakeword +char *fmakeword(FILE *f, char stop, int *cl); +char *makeword(char *line, char stop); + entry entries[10000]; @@ -124,7 +129,7 @@ /* check that a block was specified */ - if (BLOCK_Ptr->val[0] == NULL) + if (BLOCK_Ptr->val[0] == 0) { printf("

Error

\n"); printf("You need to enter a block by writing or pasting a block in the window.

\n"); @@ -139,7 +144,7 @@ /* if block was pasted/written - */ - if (BLOCK_Ptr->val[0] != NULL) + if (BLOCK_Ptr->val[0] != 0) { /* open up the block file to write to */ @@ -264,7 +269,7 @@ /**********************************************************************/ -void main(int argc, char *argv[]) { +int main(int argc, char *argv[]) { printf("Content-type: text/html\n\n\n"); @@ -301,6 +306,6 @@ clean_temp_files() ; - exit(0) ; + return(0) ; } Index: blimps-3.9/blimps/blalign.c =================================================================== --- blimps-3.9.orig/blimps/blalign.c 2012-02-03 21:58:56.016242628 +0100 +++ blimps-3.9/blimps/blalign.c 2012-02-03 22:01:33.800368017 +0100 @@ -119,7 +119,7 @@ else { printf("\nEnter name of file of blocks: "); - gets(bdbname); + fgets(bdbname, MAXNAME, stdin); } if ( (bfp=fopen(bdbname, "r")) == NULL) { Index: blimps-3.9/blimps/bldist.c =================================================================== --- blimps-3.9.orig/blimps/bldist.c 2012-02-03 21:58:56.040242492 +0100 +++ blimps-3.9/blimps/bldist.c 2012-02-03 22:01:33.808368122 +0100 @@ -70,7 +70,7 @@ else { printf("\nEnter name of file of fasta multiple alignments: "); - gets(bdbname); + fgets(bdbname, MAXNAME, stdin); } if ( (ifp=fopen(bdbname, "r")) == NULL) { @@ -94,7 +94,7 @@ else { printf("\nEnter name of file containing substitution matrix: "); - gets(sijname); + fgets(sijname, MAXNAME, stdin); } if ( (sfp=fopen(sijname, "r")) == NULL) { @@ -127,7 +127,7 @@ else { printf("\nEnter name of output file: "); - gets(outname); + fgets(outname, MAXNAME, stdin); } if ( (ofp=fopen(outname, "w")) == NULL) { @@ -140,7 +140,7 @@ else { printf("\nEnter type (S=similarity, D=dissimilarity, C=correlation): "); - gets(ctemp); + fgets(ctemp, MAXNAME, stdin); } OutType = 1; /* similarity is default */ if (ctemp[0] == 'd' || ctemp[0] == 'D' || ctemp[0] == '2') OutType = 2; Index: blimps-3.9/blimps/blDR.c =================================================================== --- blimps-3.9.orig/blimps/blDR.c 2012-02-03 21:58:56.064244662 +0100 +++ blimps-3.9/blimps/blDR.c 2012-02-03 22:01:33.812367892 +0100 @@ -56,7 +56,7 @@ else { printf("\nEnter name of blocks database: "); - gets(bdbname); + fgets(bdbname, MAXNAME, stdin); } if ( (bfp=fopen(bdbname, "r")) == NULL) { @@ -69,7 +69,7 @@ { printf("\nSequence database must be in fasta format:"); printf("\nEnter name of sequence database: "); - gets(sdbname); + fgets(sdbname, MAXNAME, stdin); } if ( (sfp=fopen(sdbname, "r")) == NULL) { @@ -81,7 +81,7 @@ else { printf("\nEnter name of new blocks database: "); - gets(outname); + fgets(outname, MAXNAME, stdin); } if ( (ofp=fopen(outname, "w")) == NULL) { Index: blimps-3.9/blimps/blexplode.c =================================================================== --- blimps-3.9.orig/blimps/blexplode.c 2012-02-03 21:58:56.088245006 +0100 +++ blimps-3.9/blimps/blexplode.c 2012-02-03 22:01:33.816367915 +0100 @@ -29,7 +29,7 @@ else { printf("\nEnter name of blocks database: "); - gets(bdbname); + fgets(bdbname, MAXNAME, stdin); } if ( (bfp=fopen(bdbname, "r")) == NULL) { Index: blimps-3.9/blimps/blk2DR.c =================================================================== --- blimps-3.9.orig/blimps/blk2DR.c 2012-02-03 21:58:56.112246115 +0100 +++ blimps-3.9/blimps/blk2DR.c 2012-02-03 22:01:33.824367868 +0100 @@ -31,7 +31,7 @@ else { printf("\nEnter name of blocks database: "); - gets(bdbname); + fgets(bdbname, MAXNAME, stdin); } if ( (bfp=fopen(bdbname, "r")) == NULL) { Index: blimps-3.9/blimps/blk2GC.c =================================================================== --- blimps-3.9.orig/blimps/blk2GC.c 2012-02-03 21:58:56.136242506 +0100 +++ blimps-3.9/blimps/blk2GC.c 2012-02-03 22:01:33.828368154 +0100 @@ -30,7 +30,7 @@ else { printf("\nEnter name of blocks database: "); - gets(bdbname); + fgets(bdbname, MAXNAME, stdin); } if ( (bfp=fopen(bdbname, "r")) == NULL) { Index: blimps-3.9/blimps/blk2lis.c =================================================================== --- blimps-3.9.orig/blimps/blk2lis.c 2012-02-03 21:58:56.160242554 +0100 +++ blimps-3.9/blimps/blk2lis.c 2012-02-03 22:01:33.836367894 +0100 @@ -30,7 +30,7 @@ else { printf("\nEnter name of blocks database: "); - gets(bdbname); + fgets(bdbname, MAXNAME, stdin); } if ( (bfp=fopen(bdbname, "r")) == NULL) { Index: blimps-3.9/blimps/blk2mot.c =================================================================== --- blimps-3.9.orig/blimps/blk2mot.c 2012-02-03 21:58:56.184244654 +0100 +++ blimps-3.9/blimps/blk2mot.c 2012-02-03 22:01:33.844367867 +0100 @@ -43,7 +43,7 @@ char Seqname[MAXSEQS][SNAMELEN]; /*=======================================================================*/ -void main(argc, argv) +int main(argc, argv) int argc; char *argv[]; { @@ -71,7 +71,7 @@ else { printf("\nEnter name of file containing sequences: "); - gets(seqfile); + fgets(seqfile, FNAMELEN, stdin); } if ( (fseq=fopen(seqfile, "r")) == NULL) { @@ -92,7 +92,7 @@ else { printf("\nEnter name of blocks file: "); - gets(blkfile); + fgets(blkfile, FNAMELEN, stdin); } if ( (fblk=fopen(blkfile, "r")) == NULL) { @@ -126,7 +126,7 @@ else { printf("\nEnter name of new motomat file: "); - gets(motfile); + fgets(motfile, FNAMELEN, stdin); } if ( (fmot=fopen(motfile, "wb")) == NULL) { @@ -135,7 +135,7 @@ } write_motifs(fmot, info, motif); fclose(fmot); - exit(0); + return(0); } /* end of main */ /*====================================================================== Index: blimps-3.9/blimps/blk2pssm.c =================================================================== --- blimps-3.9.orig/blimps/blk2pssm.c 2012-02-03 21:58:56.208243132 +0100 +++ blimps-3.9/blimps/blk2pssm.c 2012-02-03 22:01:33.848367783 +0100 @@ -67,7 +67,8 @@ Block *block; Matrix *matrix, *logodds; char bdbname[MAXNAME], conname[MAXNAME]; - char ctemp[10]; +#define BLK2PSSM_CTEMPLEN 10 + char ctemp[BLK2PSSM_CTEMPLEN]; int format, type, itemp; ErrorLevelReport = 5; /* No blimps errors reported */ @@ -87,7 +88,7 @@ else { printf("\nEnter name of BLOCKS input file: "); - gets(bdbname); + fgets(bdbname, MAXNAME, stdin); } if ( (bfp=fopen(bdbname, "r")) == NULL) { @@ -100,7 +101,7 @@ else { printf("\nEnter name of PSSM output file: "); - gets(conname); + fgets(conname, MAXNAME, stdin); } if ( (ofp=fopen(conname, "w")) == NULL) { @@ -115,7 +116,7 @@ else { printf("\nEnter PSSM format type (B=blimps, M=mast, G=Gribskov, P=Psi-Blast) [B]: "); - gets(ctemp); + fgets(ctemp, BLK2PSSM_CTEMPLEN, stdin ); } if (strlen(ctemp) && (ctemp[0] == 'm' || ctemp[0] == 'M')) { format = 1; type = 6; } Index: blimps-3.9/blimps/blk2slx.c =================================================================== --- blimps-3.9.orig/blimps/blk2slx.c 2012-02-03 21:58:56.228242420 +0100 +++ blimps-3.9/blimps/blk2slx.c 2012-02-03 22:01:33.856367897 +0100 @@ -35,7 +35,7 @@ else { printf("\nEnter name of blocks database: "); - gets(bdbname); + fgets(bdbname, MAXNAME, stdin); } if ( (bfp=fopen(bdbname, "r")) == NULL) { @@ -48,7 +48,7 @@ else { printf("\nEnter name of new slx database: "); - gets(conname); + fgets(conname, MAXNAME, stdin); } if ( (ofp=fopen(conname, "w")) == NULL) { Index: blimps-3.9/blimps/blklis.c =================================================================== --- blimps-3.9.orig/blimps/blklis.c 2012-02-03 21:58:56.252244950 +0100 +++ blimps-3.9/blimps/blklis.c 2012-02-03 22:01:33.860301362 +0100 @@ -34,7 +34,7 @@ else { printf("\nEnter name of file of blocks: "); - gets(infile); + fgets(infile, 80, stdin); } if ( (fin=fopen(infile, "r")) == NULL) { @@ -46,7 +46,7 @@ else { printf("\nEnter name of output file: "); - gets(outfile); + fgets(outfile, 80, stdin ); } if ( (fout=fopen(outfile, "w+")) == NULL) { Index: blimps-3.9/blimps/blkprob.c =================================================================== --- blimps-3.9.orig/blimps/blkprob.c 2012-02-03 21:58:56.276243207 +0100 +++ blimps-3.9/blimps/blkprob.c 2012-02-03 22:01:33.872367951 +0100 @@ -325,7 +325,7 @@ { printf("\nEnter number of hits to report or "); printf("blimps configuration file name [%d]: ", MaxHit); - gets(ctemp); + fgets(ctemp, FNAMELEN, stdin); } if (!strlen(ctemp)) strcpy(ctemp, "0"); for (i=0; iclusters[i].sequences[j].length; k++) { printf("%c", aa_btoa[block->clusters[i].sequences[j].sequence[k]]); } Index: blimps-3.9/blimps/blocks_search.c =================================================================== --- blimps-3.9.orig/blimps/blocks_search.c 2012-02-03 21:58:56.324242665 +0100 +++ blimps-3.9/blimps/blocks_search.c 2012-02-03 22:03:02.608242149 +0100 @@ -302,8 +302,9 @@ else if (!strncmp(entries[i].val, "pfam", 9)) { Pfam_Flag = TRUE; } } - else if (!strncmp(entries[i].name, "bias", 4)) - { strcpy(Minus_Flag, entries[i].val); } +// lkajan: what was the intention here? Looks like this would copy entries[i].val to the value of boolean Minus_Flag interpreted as a pointer - trigger to segfault? +// else if (!strncmp(entries[i].name, "bias", 4)) +// { strcpy(Minus_Flag, entries[i].val); } else if (!strncmp(entries[i].name, "ty", 2)) { strcpy(type, entries[i].val); } else if (!strncmp(entries[i].name, "st", 2)) @@ -379,7 +380,7 @@ cshp = fopen(csh_file, "w"); - fprintf(cshp, "\#\!/bin/csh\n"); + fprintf(cshp, "#!/bin/csh\n"); fprintf(cshp, "unalias mv\n"); fprintf(cshp, "%s %s >& /dev/null\n", blimps, cs_file); if (Title_Ptr != NULL) @@ -419,7 +420,7 @@ mailprog, email_addr, buf, Address_Ptr->val, blksort_output); } } - fprintf(cshp, "exit\(0\)\n"); + fprintf(cshp, "exit(0)\n"); fclose(cshp); sprintf(buf, "chmod a+x %s", csh_file); system(buf); @@ -433,7 +434,7 @@ Boolean loop = TRUE; int tot, sum; - if (Sequence_Ptr->val[0] == NULL) { + if (Sequence_Ptr->val[0] == 0) { printf("

Search Error

\n"); printf("You need to enter a sequence to search with.

\n"); exit(0); @@ -590,7 +591,7 @@ /*=======================================================================*/ -void main(int argc, char *argv[]) { +int main(int argc, char *argv[]) { /* @@ -655,5 +656,5 @@ /* fclose(jgh); */ - exit(0); + return(0); } /* end of main */ Index: blimps-3.9/blimps/block_vis.c =================================================================== --- blimps-3.9.orig/blimps/block_vis.c 2012-02-03 21:58:56.348242549 +0100 +++ blimps-3.9/blimps/block_vis.c 2012-02-03 22:01:33.896367700 +0100 @@ -868,7 +868,7 @@ * each input file. The only actual work done here is interpreting * '*' in the output filename. */ -void main(int argc, char *argv[]) +int main(int argc, char *argv[]) { int i1, i2, i3, i4; char out_filename[80]; @@ -910,5 +910,7 @@ /* No arguments? Give the user some help (and skip the warning above) */ if (argc == 1) do_help(); + + return(0); } Index: blimps-3.9/blimps/blpssm.c =================================================================== --- blimps-3.9.orig/blimps/blpssm.c 2012-02-03 21:58:56.372242140 +0100 +++ blimps-3.9/blimps/blpssm.c 2012-02-03 22:01:33.904367947 +0100 @@ -241,7 +241,7 @@ else { printf("\nEnter name of configuration file: "); - gets(cfname); + fgets(cfname, FNAMELEN, stdin); } if ( (cfp=fopen(cfname, "r")) == NULL) { Index: blimps-3.9/blimps/blweight.c =================================================================== --- blimps-3.9.orig/blimps/blweight.c 2012-02-03 21:58:56.396242171 +0100 +++ blimps-3.9/blimps/blweight.c 2012-02-03 22:01:33.916367894 +0100 @@ -92,7 +92,8 @@ FILE *bfp, *ofp; Block *block, *cblock; int wtype, clus, stype; - char bdbname[MAXNAME], conname[MAXNAME], ctemp[10]; +#define BLWEIGHT_CTEMPLEN 10 + char bdbname[MAXNAME], conname[MAXNAME], ctemp[BLWEIGHT_CTEMPLEN]; struct timeval tv; ErrorLevelReport = 5; /* don't want to see them */ @@ -119,7 +120,7 @@ else { printf("\nEnter name of blocks database: "); - gets(bdbname); + fgets( bdbname, MAXNAME, stdin ); } if ( (bfp=fopen(bdbname, "r")) == NULL) { @@ -132,7 +133,7 @@ else { printf("\nEnter name of new weighted blocks database: "); - gets(conname); + fgets( conname, MAXNAME, stdin ); } if ( (ofp=fopen(conname, "w")) == NULL) { @@ -149,7 +150,7 @@ { printf("\nEnter weighting scheme (P=position-based, V=Voronoi, "); printf("\n A=Vingron & Argos, Cn = n-percent cluster [P]: "); - gets(ctemp); + fgets( ctemp, BLWEIGHT_CTEMPLEN, stdin ); } if (strlen(ctemp)) { @@ -187,7 +188,7 @@ else { printf("\nEnter scale (M=>max=100, N=>sum=#seq, ###=>sum=###) [M]: "); - gets(ctemp); + fgets( ctemp, BLWEIGHT_CTEMPLEN, stdin ); } if (strlen(ctemp)) { Index: blimps-3.9/blimps/cobbler.c =================================================================== --- blimps-3.9.orig/blimps/cobbler.c 2012-02-03 21:58:56.436242699 +0100 +++ blimps-3.9/blimps/cobbler.c 2012-02-03 22:01:33.928367965 +0100 @@ -256,7 +256,7 @@ else { printf("\nEnter name of configuration file: "); - gets(cfname); + fgets(cfname, MAXNAME, stdin); } if ( (cfp=fopen(cfname, "r")) == NULL) { Index: blimps-3.9/blimps/coduse.c =================================================================== --- blimps-3.9.orig/blimps/coduse.c 2012-02-03 21:58:56.460292853 +0100 +++ blimps-3.9/blimps/coduse.c 2012-02-03 22:01:33.932368014 +0100 @@ -65,7 +65,7 @@ else { printf("\nEnter name of CUTG spsum file: "); - gets(infile); + fgets(infile, MAXNAME, stdin ); } if ( (fin=fopen(infile, "r")) == NULL) { @@ -78,7 +78,7 @@ else { printf("Enter organism name (leave blank for first organism in file): "); - gets(organism); + fgets(organism, MAXNAME, stdin); } if (strlen(organism)) { @@ -95,7 +95,7 @@ else { printf("\nEnter name of Blimps codon usage output file: "); - gets(outfile); + fgets(outfile, MAXNAME, stdin); } if ( (fout=fopen(outfile, "w")) == NULL) { Index: blimps-3.9/blimps/email.c =================================================================== --- blimps-3.9.orig/blimps/email.c 2012-02-03 21:58:56.484242590 +0100 +++ blimps-3.9/blimps/email.c 2012-02-03 22:01:33.940368038 +0100 @@ -35,7 +35,7 @@ else { printf("\nEnter name of sequence file: "); - gets(filename); + fgets(filename, MAXNAME, stdin); } if ( (bfp=fopen(filename, "r")) == NULL) { Index: blimps-3.9/blimps/fastaseqs.c =================================================================== --- blimps-3.9.orig/blimps/fastaseqs.c 2012-02-03 21:58:56.508245227 +0100 +++ blimps-3.9/blimps/fastaseqs.c 2012-02-03 22:01:33.944367858 +0100 @@ -39,7 +39,7 @@ else { printf("\nEnter name of input sequence file: "); - gets(infile); + fgets(infile, MAXNAME, stdin); } if ( (fin=fopen(infile, "r")) == NULL) { @@ -52,7 +52,7 @@ else { printf("\nEnter name of output file: "); - gets(outfile); + fgets(outfile, MAXNAME, stdin); } if ( (fout=fopen(outfile, "w")) == NULL) { Index: blimps-3.9/blimps/find_biassed_blocks.c =================================================================== --- blimps-3.9.orig/blimps/find_biassed_blocks.c 2012-02-03 21:58:56.532242527 +0100 +++ blimps-3.9/blimps/find_biassed_blocks.c 2012-02-03 22:01:33.952367787 +0100 @@ -290,7 +290,7 @@ else /* get input file interactively */ { printf("\nEnter name of a file with blocks or block matrices: "); - gets(bdbname); + fgets(bdbname, MAXNAME, stdin); } if ( (*bfp=fopen(bdbname, "r")) == NULL) Index: blimps-3.9/blimps/format_block.c =================================================================== --- blimps-3.9.orig/blimps/format_block.c 2012-02-03 21:58:56.552242598 +0100 +++ blimps-3.9/blimps/format_block.c 2012-02-03 22:04:33.268242693 +0100 @@ -242,14 +242,14 @@ } /* - * resize_block_sequences + * fb_resize_block_sequences * Increases the memory for the storage of the sequences of a block. * Parameter: * Block *block: the block to resize * Error codes: none */ -static void resize_block_sequences(block) +static void fb_resize_block_sequences(block) Block *block; { int i; @@ -315,13 +315,13 @@ /* check that obligatory fields have something */ /* Note if sequence names and start positions not supplied */ - if (SEQ_NAMES_Ptr->val[0] == NULL) no_seq_names = 1 ; + if (SEQ_NAMES_Ptr->val[0] == 0) no_seq_names = 1 ; else no_seq_names = 0 ; - if (SEQ_POS_Ptr->val[0] == NULL) no_seq_pos = 1 ; + if (SEQ_POS_Ptr->val[0] == 0) no_seq_pos = 1 ; else no_seq_pos = 0 ; - if (SEQS_Ptr->val[0] == NULL) + if (SEQS_Ptr->val[0] == 0) { printf("

Error

\n"); printf("No sequences specified.

\n"); @@ -403,7 +403,7 @@ exit(0); } - if (MA_WIDTH_Ptr->val[0] != NULL && + if (MA_WIDTH_Ptr->val[0] != 0 && block->width != atoi (MA_WIDTH_Ptr->val)) { printf("

Warning

\n"); @@ -470,15 +470,15 @@ if (seq_header) { /* skip blanks */ - for(; isspace(SEQS_Ptr->val[i]) && SEQS_Ptr->val[i] != '/n' && - SEQS_Ptr->val[i] != '/0'; i++) ; - if (SEQS_Ptr->val[i] == '/n') /* no name is found in line */ + for(; isspace(SEQS_Ptr->val[i]) && SEQS_Ptr->val[i] != '\n' && + SEQS_Ptr->val[i] != '\0'; i++) ; + if (SEQS_Ptr->val[i] == '\n') /* no name is found in line */ sprintf(block->sequences[block->num_sequences].name, "%s%d", UNKNOWN_SEQ_NAME, block->num_sequences+1) ; else /* copy first 20 chars or until a space is reached */ for(k=0; !(isspace(SEQS_Ptr->val[i])) && k<20 && - SEQS_Ptr->val[i] != '/n' ; i++, k++) + SEQS_Ptr->val[i] != '\n' ; i++, k++) block->sequences[block->num_sequences].name[k] = SEQS_Ptr->val[i]; /* end string */ @@ -520,7 +520,7 @@ string[j] = '\0' ; if (block->max_sequences <= block->num_sequences+1) - resize_block_sequences(block) ; + fb_resize_block_sequences(block) ; /* process the sequence */ @@ -623,7 +623,7 @@ string[j] = '\0' ; if (block->max_sequences <= k) - resize_block_sequences(block) ; + fb_resize_block_sequences(block) ; /* copy up to first 20 chars of name */ strncpy(block->sequences[k].name,string,20) ; @@ -681,7 +681,7 @@ } string[j] = '\0' ; - if (block->max_sequences <= k+1) resize_block_sequences(block) ; + if (block->max_sequences <= k+1) fb_resize_block_sequences(block) ; block->sequences[k].position = atoi(string) ; @@ -703,7 +703,7 @@ /* check that actual number of sequences is equal to what the user gave */ - if (MA_SEQS_Ptr->val[0] != NULL && + if (MA_SEQS_Ptr->val[0] != 0 && block->num_sequences != atoi (MA_SEQS_Ptr->val)) { printf("

Warning

\n"); @@ -719,7 +719,7 @@ /* get block header data */ - if (ID_Ptr->val[0] == NULL) + if (ID_Ptr->val[0] == 0) strcpy(block->id, "None") ; else strncpy(block->id,ID_Ptr->val, SMALL_BUFF_LENGTH) ; @@ -727,7 +727,7 @@ strcat(block->id, "; BLOCK") ; - if (AC_Ptr->val[0] == NULL) + if (AC_Ptr->val[0] == 0) { strncpy(block->number, block->sequences[0].name, MAXAC) ; } @@ -746,7 +746,7 @@ strcpy(block->ac,block->number) ; - if (MIN_DIST_Ptr->val[0] == NULL) + if (MIN_DIST_Ptr->val[0] == 0) { j = 10000 ; for(i=0; inum_sequences; i++) @@ -758,7 +758,7 @@ block->ac, j) ; - if (MAX_DIST_Ptr->val[0] == NULL) + if (MAX_DIST_Ptr->val[0] == 0) { j = 0 ; for(i=0; inum_sequences; i++) @@ -769,12 +769,12 @@ sprintf(block->ac, "%s,%d)", block->ac, j) ; - if (DE_Ptr->val[0] == NULL) + if (DE_Ptr->val[0] == 0) strcpy(block->de, "None") ; else strncpy(block->de,DE_Ptr->val, SMALL_BUFF_LENGTH) ; - if (MA_METH_Ptr->val[0] != NULL) + if (MA_METH_Ptr->val[0] != 0) strncpy(block->bl,MA_METH_Ptr->val, SMALL_BUFF_LENGTH-25) ; else strcpy(block->bl,"Method unspecified") ; @@ -881,7 +881,7 @@ } -void main(int argc, char *argv[]) { +int main(int argc, char *argv[]) { printf("Content-type: text/html\n\n\n"); @@ -918,6 +918,6 @@ clean_temp_files() ; - exit(0) ; + return(0) ; } Index: blimps-3.9/blimps/htmlize-codehop.c =================================================================== --- blimps-3.9.orig/blimps/htmlize-codehop.c 2012-02-03 21:58:56.576245371 +0100 +++ blimps-3.9/blimps/htmlize-codehop.c 2012-02-03 22:01:33.964368000 +0100 @@ -47,7 +47,7 @@ void condense(); /*======================================================================*/ -void main(argc, argv) +int main(argc, argv) int argc; char *argv[]; { @@ -250,7 +250,7 @@ printf("\n%d blocks, %d oligos processed\n", nblock, noligo); */ - exit(0); + return(0); } /* end of main */ /*=========================================================================*/ struct olist *make_olist() Index: blimps-3.9/blimps/htmlize-LAMA.c =================================================================== --- blimps-3.9.orig/blimps/htmlize-LAMA.c 2012-02-03 21:58:56.600245084 +0100 +++ blimps-3.9/blimps/htmlize-LAMA.c 2012-02-03 22:01:33.972368017 +0100 @@ -13,6 +13,7 @@ #include #include +#include #define TRUE 1 Index: blimps-3.9/blimps/interpro.c =================================================================== --- blimps-3.9.orig/blimps/interpro.c 2012-02-03 21:58:56.624245384 +0100 +++ blimps-3.9/blimps/interpro.c 2012-02-03 22:01:33.976367852 +0100 @@ -94,7 +94,7 @@ else { printf("\nEnter name of interpro xml file: "); - gets(iprfile); + fgets(iprfile, MAXNAME, stdin); } if ( (fip=fopen(iprfile, "r")) == NULL) { @@ -108,7 +108,7 @@ else { printf("\nEnter name of interpro entry or all : "); - gets(iprname); + fgets(iprname, MAXAC, stdin); } if (!strlen(iprname)) strcpy(iprname, "all"); All = NO; Index: blimps-3.9/blimps/LAMA.c =================================================================== --- blimps-3.9.orig/blimps/LAMA.c 2012-02-03 21:58:56.648243282 +0100 +++ blimps-3.9/blimps/LAMA.c 2012-02-03 22:01:33.984368213 +0100 @@ -400,12 +400,12 @@ else /* get input file(s) interactively */ { printf("\nEnter name of a file with blocks or block matrices: "); - gets(bdbname[0]); + fgets(bdbname[0], MAXNAME, stdin); printf("\nThe blocks/matrices in this file will be intercompared.\n"); printf("If you wish to compare them against blocks/matrices in\n"); printf("another file enter that file name (else just hit ).\n"); - gets(bdbname[1]); + fgets(bdbname[1], MAXNAME, stdin); if (bdbname[1][0] == '\0') *inpfiles = 1 ; else *inpfiles = 2 ; @@ -426,7 +426,7 @@ else { printf("\nEnter name of output file: "); - gets(outname); + fgets(outname, MAXNAME, stdin); } if ( (*out=fopen(outname, "w")) == NULL) Index: blimps-3.9/blimps/LAMA_search.c =================================================================== --- blimps-3.9.orig/blimps/LAMA_search.c 2012-02-03 21:58:56.672242748 +0100 +++ blimps-3.9/blimps/LAMA_search.c 2012-02-03 22:02:47.176242818 +0100 @@ -281,7 +281,7 @@ /* check that a block was specified */ - if (Qblock_Ptr->val[0] == NULL) + if (Qblock_Ptr->val[0] == 0) { printf("

Search Error

\n"); printf("You need to enter a block to search with by writing or pasting a block in the query block window.

\n"); @@ -296,7 +296,7 @@ /* if block was pasted/written - */ - if (Qblock_Ptr->val[0] != NULL) + if (Qblock_Ptr->val[0] != 0) { /* open up the block file to write to */ @@ -579,7 +579,7 @@ /* mail the person the results */ /* NOTE: need to echo the header lines for the LAMA output :P */ /* NOTE: all this should need to do is to cat the ouput file. */ - sprintf(buf, "%s %s '(cat %s) | /usr/bin/mailx -s \"LAMA Results\" -r \"blocks\@fhcrc.org\" %s'", add_queue_entry, LAMA_queue, LAMA_output, Address_Ptr->val); + sprintf(buf, "%s %s '(cat %s) | /usr/bin/mailx -s \"LAMA Results\" -r \"blocks@fhcrc.org\" %s'", add_queue_entry, LAMA_queue, LAMA_output, Address_Ptr->val); system(buf); @@ -666,7 +666,7 @@ } /* end of run Cyrca */ -void main(int argc, char *argv[]) { +int main(int argc, char *argv[]) { printf("Content-type: text/html\n\n\n"); @@ -715,5 +715,5 @@ clean_temp_files() ; - exit(0) ; + return(0) ; } Index: blimps-3.9/blimps/lisblk.c =================================================================== --- blimps-3.9.orig/blimps/lisblk.c 2012-02-03 21:58:56.856367328 +0100 +++ blimps-3.9/blimps/lisblk.c 2012-02-03 22:01:34.028368291 +0100 @@ -33,7 +33,7 @@ char Title[MAXLINE]; /*======================================================================*/ -void main(argc, argv) +int main(argc, argv) int argc; char *argv[]; { @@ -53,7 +53,7 @@ else { printf("\nEnter name of file containing list of sequences: "); - gets(lisfile); + fgets(lisfile, FNAMELEN, stdin); } if ( (flis=fopen(lisfile, "r")) == NULL) { @@ -69,7 +69,7 @@ else { printf("\nEnter name of block file: "); - gets(blkfile); + fgets(blkfile, FNAMELEN, stdin); } if ((fblk=fopen(blkfile, "r")) == NULL) @@ -85,7 +85,7 @@ if ((fblk=fopen(blkfile, "r")) == NULL) { printf("\nEnter name of block file: "); - gets(blkfile); + fgets(blkfile, FNAMELEN, stdin); } } if (fblk == NULL) @@ -147,7 +147,7 @@ fclose(fout); printf("\n"); - exit(0); + return(0); } /* end of main */ /*================================================================*/ int flag_ids(block, ids) Index: blimps-3.9/blimps/mablock.c =================================================================== --- blimps-3.9.orig/blimps/mablock.c 2012-02-03 21:58:56.880439022 +0100 +++ blimps-3.9/blimps/mablock.c 2012-02-03 22:01:34.040367995 +0100 @@ -102,7 +102,8 @@ { FILE *ifp, *bfp, *sfp; Sequence *seqs[MAXSEQ]; - char ctemp[MAXNAME], bdbname[MAXNAME], outtype[10], *ptr; +#define MABLOCK_OUTTYPELEN 10 + char ctemp[MAXNAME], bdbname[MAXNAME], outtype[MABLOCK_OUTTYPELEN], *ptr; int db_type, seq_type, nseq, i, bflag, ftype; struct blocks_list *blocks; Block *block; @@ -127,7 +128,7 @@ else { printf("\nEnter name of blocks database: "); - gets(bdbname); + fgets( bdbname, MAXNAME, stdin ); } if ( (ifp=fopen(bdbname, "r")) == NULL) { @@ -157,7 +158,7 @@ else { printf("\nEnter name of output file: "); - gets(OutName); + fgets( OutName, MAXNAME, stdin ); } strcpy(ctemp, OutName); strcat(ctemp, ".blks"); if ( (bfp=fopen(ctemp, "w")) == NULL) @@ -177,7 +178,7 @@ else { printf("\nEnter type of output file [B=blocks|F=fasta]: "); - gets(outtype); + fgets( outtype, MABLOCK_OUTTYPELEN, stdin ); } if (outtype[0] == 'F' || outtype[0] == 'f') ftype = 1; /* ------------4th arg = optional min trimming size--------------------*/ Index: blimps-3.9/blimps/Makefile.Linux =================================================================== --- blimps-3.9.orig/blimps/Makefile.Linux 2012-02-03 21:58:56.904242649 +0100 +++ blimps-3.9/blimps/Makefile.Linux 2012-02-03 22:01:34.264242740 +0100 @@ -44,19 +44,25 @@ # so the Makefile continues to work. # Linux +VERSION := 3.9 +SOVERSION := 3.0.0 +SHORTSOVERSION := 3 + DEFINES = SYSTEM = -OPTIMIZ = -Wall -O2 +#OPTIMIZ = -Wall -O2 +OPTIMIZ = -Wuninitialized -O2 +#OPTIMIZ = -Werror -O2 RANLIB = ls MAKE = make -DEPEND = makedepend +DEPEND = $(CC) # ar -t libpssm.a for table of contents AR = ar RM = rm -f MV = mv -f -CP = cp +CP = cp -af # C compiler @@ -106,12 +112,12 @@ # C Flags to compiler #CFLAGS = `getconf LFS_CFLAGS` $(OPTIMIZ) $(DEFINES) $(INCLUDES) -CFLAGS = $(OPTIMIZ) $(DEFINES) $(INCLUDES) +CFLAGS = $(OPTIMIZ) $(DEFINES) $(INCLUDES) -fpic # Linker Flags LDFLAGS = $(CFLAGS) -LDLIBS = -lblimps -ly -lm +LDLIBS = -lblimps -lm LDOPTIONS = $(LDFLAGS) $(LDDIR) # cc ld options @@ -120,6 +126,9 @@ LIBRARY_DIR = ./ LDDIR = -L$(LIBRARY_DIR) +#SHARED_LIB_DIR := ./.libs +SHARED_LIB_DIR := . + # source files SRCS = blimps-mem.c \ @@ -197,34 +206,36 @@ OTHER_OBJS_DEBUG = /usr/lib/debug/malloc.o \ /usr/lib/debug/mallocmap.o -LIBOBJS = pattern.o \ - files.o \ - frequency.o \ - convert.o \ +LIBOBJS = \ + blimps.o \ + blimps-mem.o \ blocks.o \ + config.o \ + convert.o \ errors.o \ + files.o \ + frequency.o \ gcode.o \ + lists.o \ matrix.o \ memory.o \ - sequences.o \ - strutil.o \ - sl.o \ - version.o \ options.o \ - blimps-mem.o \ - config.o \ - lists.o \ + p2clib.o \ + pattern.o \ + protomat.o \ scores.o \ scoring.o \ - p2clib.o \ + sequences.o \ + sl.o \ + strutil.o \ util.o \ - protomat.o + version.o # need malloc.o for malloc_debug() which will have free() raise SIGABRT # if it is unable to free the space. -LIBRARIES = libblimps.a +LIBRARIES = libblimps.a $(SHARED_LIB_DIR)/libblimps.so.$(SOVERSION) ######################################################################## @@ -235,10 +246,10 @@ ######################################################################## ######################################################################## -install: clean all move-lib move-bin - all: lib blimps blweight blalign bldist blk2pssm rank_matrix retblock codehop htmlize-codehop oligo_melt mablock cobbler addseqs fastaseqs LAMA find_biassed_blocks makeblockmap prints2blocks lisblk coduse narrow blk2slx blkprob interpro pssmdist pssmBL papssm matrix_logob makelogob blocks_search LAMA_search block_vis format_block biassed_blocks_finder htmlize-LAMA show_aligned_blocks makelis blk2mot +install: clean all move-lib move-bin + blimps: $(LIBRARIES) blimps.o $(LIBOBJS) $(RM) $@ $(CC) -o $@ blimps.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) @@ -427,7 +438,15 @@ # libblimps.a: $(LIBOBJS) - $(AR) cr $@ $(LIBOBJS) ; $(RANLIB) $@ + $(AR) cr $@ $(LIBOBJS) + +$(SHARED_LIB_DIR): + mkdir -p $@ + +$(SHARED_LIB_DIR)/libblimps.so.$(SOVERSION): $(LIBOBJS) | $(SHARED_LIB_DIR) + $(CC) $(LDFLAGS) -shared -Wl,-soname,libblimps.so.$(SHORTSOVERSION) -o $@ -lm $(LIBOBJS) + /sbin/ldconfig -n $(SHARED_LIB_DIR) + rm -f $(SHARED_LIB_DIR)/libblimps.so && ln -sf libblimps.so.$(SOVERSION) $(SHARED_LIB_DIR)/libblimps.so ######################################################################## ######################################################################## @@ -480,57 +499,61 @@ etags ./*.[ch] $(INCLUDE_DIR)/*.[ch] -depend: - $(DEPEND) -- $(CFLAGS) -- -s "# DO NOT DELETE" -- $(SRCS) +depend: deps.mk -clean:: +clean: $(RM) blimps blweight blalign bldist blk2pssm rank_matrix retblock codehop htmlize-codehop oligo_melt mablock makeblockmap prints2blocks lisblk coduse narrow blkprob blk2slx LAMA find_biassed_blocks fastaseqs addseqs cobbler interpro pssmdist pssmBL papssm matrix_logob makelogob blocks_search LAMA_search block_vis format_block biassed_blocks_finder htmlize-LAMA show_aligned_blocks makelis blk2mot $(RM) *.a *.o *~ + if [ "$(SHARED_LIB_DIR)" != "." ]; then $(RM) -r $(SHARED_LIB_DIR); fi + rm -f $(SHARED_LIB_DIR)/libblimps.so* @echo " " +distclean: clean + $(RM) deps.mk + move-lib: - $(MV) lib*.a ../lib + $(CP) lib*.a $(SHARED_LIB_DIR)/*.so ../lib move-bin: - $(MV) blimps ../bin - $(MV) blweight ../bin - $(MV) blalign ../bin - $(MV) bldist ../bin - $(MV) blk2pssm ../bin - $(MV) rank_matrix ../bin - $(MV) retblock ../bin - $(MV) codehop ../bin - $(MV) htmlize-codehop ../bin - $(MV) oligo_melt ../bin - $(MV) mablock ../bin - $(MV) makeblockmap ../bin - $(MV) prints2blocks ../bin - $(MV) lisblk ../bin - $(MV) coduse ../bin - $(MV) narrow ../bin - $(MV) blkprob ../bin - $(MV) blk2slx ../bin - $(MV) LAMA ../bin - $(MV) find_biassed_blocks ../bin - $(MV) fastaseqs ../bin - $(MV) addseqs ../bin - $(MV) cobbler ../bin - $(MV) interpro ../bin - $(MV) pssmdist ../bin - $(MV) pssmBL ../bin - $(MV) papssm ../bin - $(MV) matrix_logob ../bin - $(MV) makelogob ../bin - $(MV) blocks_search ../bin - $(MV) LAMA_search ../bin - $(MV) block_vis ../bin - $(MV) format_block ../bin - $(MV) biassed_blocks_finder ../bin - $(MV) htmlize-LAMA ../bin - $(MV) show_aligned_blocks ../bin - $(MV) makelis ../bin - $(MV) blk2mot ../bin + $(CP) blimps ../bin + $(CP) blweight ../bin + $(CP) blalign ../bin + $(CP) bldist ../bin + $(CP) blk2pssm ../bin + $(CP) rank_matrix ../bin + $(CP) retblock ../bin + $(CP) codehop ../bin + $(CP) htmlize-codehop ../bin + $(CP) oligo_melt ../bin + $(CP) mablock ../bin + $(CP) makeblockmap ../bin + $(CP) prints2blocks ../bin + $(CP) lisblk ../bin + $(CP) coduse ../bin + $(CP) narrow ../bin + $(CP) blkprob ../bin + $(CP) blk2slx ../bin + $(CP) LAMA ../bin + $(CP) find_biassed_blocks ../bin + $(CP) fastaseqs ../bin + $(CP) addseqs ../bin + $(CP) cobbler ../bin + $(CP) interpro ../bin + $(CP) pssmdist ../bin + $(CP) pssmBL ../bin + $(CP) papssm ../bin + $(CP) matrix_logob ../bin + $(CP) makelogob ../bin + $(CP) blocks_search ../bin + $(CP) LAMA_search ../bin + $(CP) block_vis ../bin + $(CP) format_block ../bin + $(CP) biassed_blocks_finder ../bin + $(CP) htmlize-LAMA ../bin + $(CP) show_aligned_blocks ../bin + $(CP) makelis ../bin + $(CP) blk2mot ../bin ########## @@ -687,1272 +710,14 @@ $(VERSIONDISTRIB)/blimps.$(TXTVER)/docs/INSTALL $(FTPDIR) @echo " " - +deps.mk: + $(DEPEND) -MM $(CFLAGS) $(SRCS) > $@ ########################################################################### +.PHONY: depend all clean distclean dist ########################################################################### -# dependencies generated by makedepend - -# DO NOT DELETE +# dependencies +include deps.mk -blimps-mem.o: ../include/global.h /usr/include/stdlib.h -blimps-mem.o: /usr/include/features.h /usr/include/sys/cdefs.h -blimps-mem.o: /usr/include/gnu/stubs.h -blimps-mem.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -blimps-mem.o: /usr/include/stdio.h /usr/include/bits/types.h -blimps-mem.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -blimps-mem.o: /usr/include/libio.h /usr/include/_G_config.h -blimps-mem.o: /usr/include/wchar.h /usr/include/bits/wchar.h -blimps-mem.o: /usr/include/gconv.h -blimps-mem.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -blimps-mem.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -blimps-mem.o: /usr/include/string.h /usr/include/ctype.h -blimps-mem.o: /usr/include/endian.h /usr/include/bits/endian.h -blimps-mem.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -blimps-mem.o: ../include/errors.h ../include/memory.h blimps-mem.h blimps.h -blimps-mem.o: lists.h ../include/skiplist.h -blimps.o: /usr/include/math.h /usr/include/features.h -blimps.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -blimps.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -blimps.o: /usr/include/bits/mathcalls.h /usr/include/signal.h -blimps.o: /usr/include/bits/sigset.h /usr/include/bits/types.h -blimps.o: /usr/include/bits/wordsize.h -blimps.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -blimps.o: /usr/include/bits/typesizes.h /usr/include/bits/signum.h -blimps.o: ../include/global.h /usr/include/stdlib.h /usr/include/stdio.h -blimps.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -blimps.o: /usr/include/bits/wchar.h /usr/include/gconv.h -blimps.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -blimps.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -blimps.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -blimps.o: /usr/include/bits/endian.h /usr/include/malloc.h -blimps.o: ../include/license.h ../include/strutil.h ../include/errors.h -blimps.o: ../include/memory.h ../include/version.h ../include/residues.h -blimps.o: ../include/blastapp.h /usr/include/limits.h -blimps.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -blimps.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -blimps.o: ../include/gcode.h ../include/files.h ../include/blocks.h -blimps.o: ../include/output.h ../include/sequences.h ../include/matrix.h -blimps.o: ../include/pattern.h ../include/convert.h ../include/frequency.h -blimps.o: ../include/options.h blimps.h blimps-mem.h config.h scores.h -blimps.o: scoring.h lists.h ../include/skiplist.h -blweight.o: ../include/blocksprogs.h /usr/include/stdlib.h -blweight.o: /usr/include/features.h /usr/include/sys/cdefs.h -blweight.o: /usr/include/gnu/stubs.h -blweight.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -blweight.o: /usr/include/stdio.h /usr/include/bits/types.h -blweight.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -blweight.o: /usr/include/libio.h /usr/include/_G_config.h -blweight.o: /usr/include/wchar.h /usr/include/bits/wchar.h -blweight.o: /usr/include/gconv.h -blweight.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -blweight.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -blweight.o: /usr/include/string.h /usr/include/math.h -blweight.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -blweight.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -blweight.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -blweight.o: /usr/include/ctype.h /usr/include/endian.h -blweight.o: /usr/include/bits/endian.h ../include/global.h -blweight.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -blweight.o: ../include/errors.h ../include/memory.h ../include/residues.h -blweight.o: ../include/blastapp.h /usr/include/limits.h -blweight.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -blweight.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -blweight.o: ../include/gcode.h ../include/blocks.h ../include/output.h -blweight.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -blweight.o: ../include/convert.h ../include/frequency.h ../include/files.h -blweight.o: ../include/protomat.h /usr/include/sys/time.h /usr/include/time.h -blweight.o: /usr/include/bits/time.h /usr/include/sys/select.h -blweight.o: /usr/include/bits/select.h /usr/include/bits/sigset.h -blalign.o: ../include/blocksprogs.h /usr/include/stdlib.h -blalign.o: /usr/include/features.h /usr/include/sys/cdefs.h -blalign.o: /usr/include/gnu/stubs.h -blalign.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -blalign.o: /usr/include/stdio.h /usr/include/bits/types.h -blalign.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -blalign.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -blalign.o: /usr/include/bits/wchar.h /usr/include/gconv.h -blalign.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -blalign.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -blalign.o: /usr/include/string.h /usr/include/math.h -blalign.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -blalign.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -blalign.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -blalign.o: /usr/include/ctype.h /usr/include/endian.h -blalign.o: /usr/include/bits/endian.h ../include/global.h -blalign.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -blalign.o: ../include/errors.h ../include/memory.h ../include/residues.h -blalign.o: ../include/blastapp.h /usr/include/limits.h -blalign.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -blalign.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -blalign.o: ../include/gcode.h ../include/blocks.h ../include/output.h -blalign.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -blalign.o: ../include/convert.h ../include/frequency.h ../include/files.h -blalign.o: ../include/protomat.h -bldist.o: ../include/blocksprogs.h /usr/include/stdlib.h -bldist.o: /usr/include/features.h /usr/include/sys/cdefs.h -bldist.o: /usr/include/gnu/stubs.h -bldist.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -bldist.o: /usr/include/stdio.h /usr/include/bits/types.h -bldist.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -bldist.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -bldist.o: /usr/include/bits/wchar.h /usr/include/gconv.h -bldist.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -bldist.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -bldist.o: /usr/include/string.h /usr/include/math.h -bldist.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -bldist.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -bldist.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -bldist.o: /usr/include/ctype.h /usr/include/endian.h -bldist.o: /usr/include/bits/endian.h ../include/global.h -bldist.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -bldist.o: ../include/errors.h ../include/memory.h ../include/residues.h -bldist.o: ../include/blastapp.h /usr/include/limits.h -bldist.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -bldist.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -bldist.o: ../include/gcode.h ../include/blocks.h ../include/output.h -bldist.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -bldist.o: ../include/convert.h ../include/frequency.h ../include/files.h -bldist.o: ../include/protomat.h -blk2pssm.o: ../include/blocksprogs.h /usr/include/stdlib.h -blk2pssm.o: /usr/include/features.h /usr/include/sys/cdefs.h -blk2pssm.o: /usr/include/gnu/stubs.h -blk2pssm.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -blk2pssm.o: /usr/include/stdio.h /usr/include/bits/types.h -blk2pssm.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -blk2pssm.o: /usr/include/libio.h /usr/include/_G_config.h -blk2pssm.o: /usr/include/wchar.h /usr/include/bits/wchar.h -blk2pssm.o: /usr/include/gconv.h -blk2pssm.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -blk2pssm.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -blk2pssm.o: /usr/include/string.h /usr/include/math.h -blk2pssm.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -blk2pssm.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -blk2pssm.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -blk2pssm.o: /usr/include/ctype.h /usr/include/endian.h -blk2pssm.o: /usr/include/bits/endian.h ../include/global.h -blk2pssm.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -blk2pssm.o: ../include/errors.h ../include/memory.h ../include/residues.h -blk2pssm.o: ../include/blastapp.h /usr/include/limits.h -blk2pssm.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -blk2pssm.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -blk2pssm.o: ../include/gcode.h ../include/blocks.h ../include/output.h -blk2pssm.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -blk2pssm.o: ../include/convert.h ../include/frequency.h ../include/files.h -blk2pssm.o: ../include/protomat.h -rank_matrix.o: ../include/blocksprogs.h /usr/include/stdlib.h -rank_matrix.o: /usr/include/features.h /usr/include/sys/cdefs.h -rank_matrix.o: /usr/include/gnu/stubs.h -rank_matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -rank_matrix.o: /usr/include/stdio.h /usr/include/bits/types.h -rank_matrix.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -rank_matrix.o: /usr/include/libio.h /usr/include/_G_config.h -rank_matrix.o: /usr/include/wchar.h /usr/include/bits/wchar.h -rank_matrix.o: /usr/include/gconv.h -rank_matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -rank_matrix.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -rank_matrix.o: /usr/include/string.h /usr/include/math.h -rank_matrix.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -rank_matrix.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -rank_matrix.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -rank_matrix.o: /usr/include/ctype.h /usr/include/endian.h -rank_matrix.o: /usr/include/bits/endian.h ../include/global.h -rank_matrix.o: /usr/include/malloc.h ../include/license.h -rank_matrix.o: ../include/strutil.h ../include/errors.h ../include/memory.h -rank_matrix.o: ../include/residues.h ../include/blastapp.h -rank_matrix.o: /usr/include/limits.h -rank_matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -rank_matrix.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -rank_matrix.o: ../include/gcode.h ../include/blocks.h ../include/output.h -rank_matrix.o: ../include/sequences.h ../include/matrix.h -rank_matrix.o: ../include/pattern.h ../include/convert.h -rank_matrix.o: ../include/frequency.h ../include/files.h -rank_matrix.o: ../include/protomat.h -retblock.o: ../include/blocksprogs.h /usr/include/stdlib.h -retblock.o: /usr/include/features.h /usr/include/sys/cdefs.h -retblock.o: /usr/include/gnu/stubs.h -retblock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -retblock.o: /usr/include/stdio.h /usr/include/bits/types.h -retblock.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -retblock.o: /usr/include/libio.h /usr/include/_G_config.h -retblock.o: /usr/include/wchar.h /usr/include/bits/wchar.h -retblock.o: /usr/include/gconv.h -retblock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -retblock.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -retblock.o: /usr/include/string.h /usr/include/math.h -retblock.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -retblock.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -retblock.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -retblock.o: /usr/include/ctype.h /usr/include/endian.h -retblock.o: /usr/include/bits/endian.h ../include/global.h -retblock.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -retblock.o: ../include/errors.h ../include/memory.h ../include/residues.h -retblock.o: ../include/blastapp.h /usr/include/limits.h -retblock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -retblock.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -retblock.o: ../include/gcode.h ../include/blocks.h ../include/output.h -retblock.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -retblock.o: ../include/convert.h ../include/frequency.h ../include/files.h -retblock.o: ../include/protomat.h -codehop.o: ../include/blocksprogs.h /usr/include/stdlib.h -codehop.o: /usr/include/features.h /usr/include/sys/cdefs.h -codehop.o: /usr/include/gnu/stubs.h -codehop.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -codehop.o: /usr/include/stdio.h /usr/include/bits/types.h -codehop.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -codehop.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -codehop.o: /usr/include/bits/wchar.h /usr/include/gconv.h -codehop.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -codehop.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -codehop.o: /usr/include/string.h /usr/include/math.h -codehop.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -codehop.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -codehop.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -codehop.o: /usr/include/ctype.h /usr/include/endian.h -codehop.o: /usr/include/bits/endian.h ../include/global.h -codehop.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -codehop.o: ../include/errors.h ../include/memory.h ../include/residues.h -codehop.o: ../include/blastapp.h /usr/include/limits.h -codehop.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -codehop.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -codehop.o: ../include/gcode.h ../include/blocks.h ../include/output.h -codehop.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -codehop.o: ../include/convert.h ../include/frequency.h ../include/files.h -codehop.o: ../include/protomat.h codehop.h /usr/include/sys/time.h -codehop.o: /usr/include/time.h /usr/include/bits/time.h -codehop.o: /usr/include/sys/select.h /usr/include/bits/select.h -codehop.o: /usr/include/bits/sigset.h -htmlize-codehop.o: /usr/include/stdio.h /usr/include/features.h -htmlize-codehop.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -htmlize-codehop.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -htmlize-codehop.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -htmlize-codehop.o: /usr/include/bits/typesizes.h /usr/include/libio.h -htmlize-codehop.o: /usr/include/_G_config.h /usr/include/wchar.h -htmlize-codehop.o: /usr/include/bits/wchar.h /usr/include/gconv.h -htmlize-codehop.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -htmlize-codehop.o: /usr/include/bits/stdio_lim.h -htmlize-codehop.o: /usr/include/bits/sys_errlist.h /usr/include/string.h -htmlize-codehop.o: /usr/include/stdlib.h -oligo_melt.o: ../include/blocksprogs.h /usr/include/stdlib.h -oligo_melt.o: /usr/include/features.h /usr/include/sys/cdefs.h -oligo_melt.o: /usr/include/gnu/stubs.h -oligo_melt.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -oligo_melt.o: /usr/include/stdio.h /usr/include/bits/types.h -oligo_melt.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -oligo_melt.o: /usr/include/libio.h /usr/include/_G_config.h -oligo_melt.o: /usr/include/wchar.h /usr/include/bits/wchar.h -oligo_melt.o: /usr/include/gconv.h -oligo_melt.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -oligo_melt.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -oligo_melt.o: /usr/include/string.h /usr/include/math.h -oligo_melt.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -oligo_melt.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -oligo_melt.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -oligo_melt.o: /usr/include/ctype.h /usr/include/endian.h -oligo_melt.o: /usr/include/bits/endian.h ../include/global.h -oligo_melt.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -oligo_melt.o: ../include/errors.h ../include/memory.h ../include/residues.h -oligo_melt.o: ../include/blastapp.h /usr/include/limits.h -oligo_melt.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -oligo_melt.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -oligo_melt.o: ../include/gcode.h ../include/blocks.h ../include/output.h -oligo_melt.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -oligo_melt.o: ../include/convert.h ../include/frequency.h ../include/files.h -oligo_melt.o: ../include/protomat.h -mablock.o: ../include/blocksprogs.h /usr/include/stdlib.h -mablock.o: /usr/include/features.h /usr/include/sys/cdefs.h -mablock.o: /usr/include/gnu/stubs.h -mablock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -mablock.o: /usr/include/stdio.h /usr/include/bits/types.h -mablock.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -mablock.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -mablock.o: /usr/include/bits/wchar.h /usr/include/gconv.h -mablock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -mablock.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -mablock.o: /usr/include/string.h /usr/include/math.h -mablock.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -mablock.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -mablock.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -mablock.o: /usr/include/ctype.h /usr/include/endian.h -mablock.o: /usr/include/bits/endian.h ../include/global.h -mablock.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -mablock.o: ../include/errors.h ../include/memory.h ../include/residues.h -mablock.o: ../include/blastapp.h /usr/include/limits.h -mablock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -mablock.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -mablock.o: ../include/gcode.h ../include/blocks.h ../include/output.h -mablock.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -mablock.o: ../include/convert.h ../include/frequency.h ../include/files.h -mablock.o: ../include/protomat.h -cobbler.o: ../include/blocksprogs.h /usr/include/stdlib.h -cobbler.o: /usr/include/features.h /usr/include/sys/cdefs.h -cobbler.o: /usr/include/gnu/stubs.h -cobbler.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -cobbler.o: /usr/include/stdio.h /usr/include/bits/types.h -cobbler.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -cobbler.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -cobbler.o: /usr/include/bits/wchar.h /usr/include/gconv.h -cobbler.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -cobbler.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -cobbler.o: /usr/include/string.h /usr/include/math.h -cobbler.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -cobbler.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -cobbler.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -cobbler.o: /usr/include/ctype.h /usr/include/endian.h -cobbler.o: /usr/include/bits/endian.h ../include/global.h -cobbler.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -cobbler.o: ../include/errors.h ../include/memory.h ../include/residues.h -cobbler.o: ../include/blastapp.h /usr/include/limits.h -cobbler.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -cobbler.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -cobbler.o: ../include/gcode.h ../include/blocks.h ../include/output.h -cobbler.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -cobbler.o: ../include/convert.h ../include/frequency.h ../include/files.h -cobbler.o: ../include/protomat.h /usr/include/sys/time.h /usr/include/time.h -cobbler.o: /usr/include/bits/time.h /usr/include/sys/select.h -cobbler.o: /usr/include/bits/select.h /usr/include/bits/sigset.h -addseqs.o: ../include/blocksprogs.h /usr/include/stdlib.h -addseqs.o: /usr/include/features.h /usr/include/sys/cdefs.h -addseqs.o: /usr/include/gnu/stubs.h -addseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -addseqs.o: /usr/include/stdio.h /usr/include/bits/types.h -addseqs.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -addseqs.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -addseqs.o: /usr/include/bits/wchar.h /usr/include/gconv.h -addseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -addseqs.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -addseqs.o: /usr/include/string.h /usr/include/math.h -addseqs.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -addseqs.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -addseqs.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -addseqs.o: /usr/include/ctype.h /usr/include/endian.h -addseqs.o: /usr/include/bits/endian.h ../include/global.h -addseqs.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -addseqs.o: ../include/errors.h ../include/memory.h ../include/residues.h -addseqs.o: ../include/blastapp.h /usr/include/limits.h -addseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -addseqs.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -addseqs.o: ../include/gcode.h ../include/blocks.h ../include/output.h -addseqs.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -addseqs.o: ../include/convert.h ../include/frequency.h ../include/files.h -addseqs.o: ../include/protomat.h -fastaseqs.o: ../include/blocksprogs.h /usr/include/stdlib.h -fastaseqs.o: /usr/include/features.h /usr/include/sys/cdefs.h -fastaseqs.o: /usr/include/gnu/stubs.h -fastaseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -fastaseqs.o: /usr/include/stdio.h /usr/include/bits/types.h -fastaseqs.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -fastaseqs.o: /usr/include/libio.h /usr/include/_G_config.h -fastaseqs.o: /usr/include/wchar.h /usr/include/bits/wchar.h -fastaseqs.o: /usr/include/gconv.h -fastaseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -fastaseqs.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -fastaseqs.o: /usr/include/string.h /usr/include/math.h -fastaseqs.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -fastaseqs.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -fastaseqs.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -fastaseqs.o: /usr/include/ctype.h /usr/include/endian.h -fastaseqs.o: /usr/include/bits/endian.h ../include/global.h -fastaseqs.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -fastaseqs.o: ../include/errors.h ../include/memory.h ../include/residues.h -fastaseqs.o: ../include/blastapp.h /usr/include/limits.h -fastaseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -fastaseqs.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -fastaseqs.o: ../include/gcode.h ../include/blocks.h ../include/output.h -fastaseqs.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -fastaseqs.o: ../include/convert.h ../include/frequency.h ../include/files.h -fastaseqs.o: ../include/protomat.h -LAMA.o: ../include/blocksprogs.h /usr/include/stdlib.h -LAMA.o: /usr/include/features.h /usr/include/sys/cdefs.h -LAMA.o: /usr/include/gnu/stubs.h -LAMA.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -LAMA.o: /usr/include/stdio.h /usr/include/bits/types.h -LAMA.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -LAMA.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -LAMA.o: /usr/include/bits/wchar.h /usr/include/gconv.h -LAMA.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -LAMA.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -LAMA.o: /usr/include/string.h /usr/include/math.h -LAMA.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -LAMA.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -LAMA.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -LAMA.o: /usr/include/ctype.h /usr/include/endian.h /usr/include/bits/endian.h -LAMA.o: ../include/global.h /usr/include/malloc.h ../include/license.h -LAMA.o: ../include/strutil.h ../include/errors.h ../include/memory.h -LAMA.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h -LAMA.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -LAMA.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -LAMA.o: ../include/gcode.h ../include/blocks.h ../include/output.h -LAMA.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -LAMA.o: ../include/convert.h ../include/frequency.h ../include/files.h -LAMA.o: ../include/protomat.h LAMA.h -find_biassed_blocks.o: ../include/blocksprogs.h /usr/include/stdlib.h -find_biassed_blocks.o: /usr/include/features.h /usr/include/sys/cdefs.h -find_biassed_blocks.o: /usr/include/gnu/stubs.h -find_biassed_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -find_biassed_blocks.o: /usr/include/stdio.h /usr/include/bits/types.h -find_biassed_blocks.o: /usr/include/bits/wordsize.h -find_biassed_blocks.o: /usr/include/bits/typesizes.h /usr/include/libio.h -find_biassed_blocks.o: /usr/include/_G_config.h /usr/include/wchar.h -find_biassed_blocks.o: /usr/include/bits/wchar.h /usr/include/gconv.h -find_biassed_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -find_biassed_blocks.o: /usr/include/bits/stdio_lim.h -find_biassed_blocks.o: /usr/include/bits/sys_errlist.h /usr/include/string.h -find_biassed_blocks.o: /usr/include/math.h /usr/include/bits/huge_val.h -find_biassed_blocks.o: /usr/include/bits/mathdef.h -find_biassed_blocks.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -find_biassed_blocks.o: /usr/include/bits/posix_opt.h -find_biassed_blocks.o: /usr/include/bits/confname.h /usr/include/ctype.h -find_biassed_blocks.o: /usr/include/endian.h /usr/include/bits/endian.h -find_biassed_blocks.o: ../include/global.h /usr/include/malloc.h -find_biassed_blocks.o: ../include/license.h ../include/strutil.h -find_biassed_blocks.o: ../include/errors.h ../include/memory.h -find_biassed_blocks.o: ../include/residues.h ../include/blastapp.h -find_biassed_blocks.o: /usr/include/limits.h -find_biassed_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -find_biassed_blocks.o: ../include/alphabet.h ../include/aabet.h -find_biassed_blocks.o: ../include/ntbet.h ../include/gcode.h -find_biassed_blocks.o: ../include/blocks.h ../include/output.h -find_biassed_blocks.o: ../include/sequences.h ../include/matrix.h -find_biassed_blocks.o: ../include/pattern.h ../include/convert.h -find_biassed_blocks.o: ../include/frequency.h ../include/files.h -find_biassed_blocks.o: ../include/protomat.h blkvblk.h -makeblockmap.o: ../include/blocksprogs.h /usr/include/stdlib.h -makeblockmap.o: /usr/include/features.h /usr/include/sys/cdefs.h -makeblockmap.o: /usr/include/gnu/stubs.h -makeblockmap.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -makeblockmap.o: /usr/include/stdio.h /usr/include/bits/types.h -makeblockmap.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -makeblockmap.o: /usr/include/libio.h /usr/include/_G_config.h -makeblockmap.o: /usr/include/wchar.h /usr/include/bits/wchar.h -makeblockmap.o: /usr/include/gconv.h -makeblockmap.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -makeblockmap.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -makeblockmap.o: /usr/include/string.h /usr/include/math.h -makeblockmap.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -makeblockmap.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -makeblockmap.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -makeblockmap.o: /usr/include/ctype.h /usr/include/endian.h -makeblockmap.o: /usr/include/bits/endian.h ../include/global.h -makeblockmap.o: /usr/include/malloc.h ../include/license.h -makeblockmap.o: ../include/strutil.h ../include/errors.h ../include/memory.h -makeblockmap.o: ../include/residues.h ../include/blastapp.h -makeblockmap.o: /usr/include/limits.h -makeblockmap.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -makeblockmap.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -makeblockmap.o: ../include/gcode.h ../include/blocks.h ../include/output.h -makeblockmap.o: ../include/sequences.h ../include/matrix.h -makeblockmap.o: ../include/pattern.h ../include/convert.h -makeblockmap.o: ../include/frequency.h ../include/files.h -makeblockmap.o: ../include/protomat.h blockmap.h -prints2blocks.o: ../include/blocksprogs.h /usr/include/stdlib.h -prints2blocks.o: /usr/include/features.h /usr/include/sys/cdefs.h -prints2blocks.o: /usr/include/gnu/stubs.h -prints2blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -prints2blocks.o: /usr/include/stdio.h /usr/include/bits/types.h -prints2blocks.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -prints2blocks.o: /usr/include/libio.h /usr/include/_G_config.h -prints2blocks.o: /usr/include/wchar.h /usr/include/bits/wchar.h -prints2blocks.o: /usr/include/gconv.h -prints2blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -prints2blocks.o: /usr/include/bits/stdio_lim.h -prints2blocks.o: /usr/include/bits/sys_errlist.h /usr/include/string.h -prints2blocks.o: /usr/include/math.h /usr/include/bits/huge_val.h -prints2blocks.o: /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h -prints2blocks.o: /usr/include/unistd.h /usr/include/bits/posix_opt.h -prints2blocks.o: /usr/include/bits/confname.h /usr/include/ctype.h -prints2blocks.o: /usr/include/endian.h /usr/include/bits/endian.h -prints2blocks.o: ../include/global.h /usr/include/malloc.h -prints2blocks.o: ../include/license.h ../include/strutil.h -prints2blocks.o: ../include/errors.h ../include/memory.h -prints2blocks.o: ../include/residues.h ../include/blastapp.h -prints2blocks.o: /usr/include/limits.h -prints2blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -prints2blocks.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -prints2blocks.o: ../include/gcode.h ../include/blocks.h ../include/output.h -prints2blocks.o: ../include/sequences.h ../include/matrix.h -prints2blocks.o: ../include/pattern.h ../include/convert.h -prints2blocks.o: ../include/frequency.h ../include/files.h -prints2blocks.o: ../include/protomat.h -lisblk.o: ../include/blocksprogs.h /usr/include/stdlib.h -lisblk.o: /usr/include/features.h /usr/include/sys/cdefs.h -lisblk.o: /usr/include/gnu/stubs.h -lisblk.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -lisblk.o: /usr/include/stdio.h /usr/include/bits/types.h -lisblk.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -lisblk.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -lisblk.o: /usr/include/bits/wchar.h /usr/include/gconv.h -lisblk.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -lisblk.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -lisblk.o: /usr/include/string.h /usr/include/math.h -lisblk.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -lisblk.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -lisblk.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -lisblk.o: /usr/include/ctype.h /usr/include/endian.h -lisblk.o: /usr/include/bits/endian.h ../include/global.h -lisblk.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -lisblk.o: ../include/errors.h ../include/memory.h ../include/residues.h -lisblk.o: ../include/blastapp.h /usr/include/limits.h -lisblk.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -lisblk.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -lisblk.o: ../include/gcode.h ../include/blocks.h ../include/output.h -lisblk.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -lisblk.o: ../include/convert.h ../include/frequency.h ../include/files.h -lisblk.o: ../include/protomat.h -coduse.o: ../include/blocksprogs.h /usr/include/stdlib.h -coduse.o: /usr/include/features.h /usr/include/sys/cdefs.h -coduse.o: /usr/include/gnu/stubs.h -coduse.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -coduse.o: /usr/include/stdio.h /usr/include/bits/types.h -coduse.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -coduse.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -coduse.o: /usr/include/bits/wchar.h /usr/include/gconv.h -coduse.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -coduse.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -coduse.o: /usr/include/string.h /usr/include/math.h -coduse.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -coduse.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -coduse.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -coduse.o: /usr/include/ctype.h /usr/include/endian.h -coduse.o: /usr/include/bits/endian.h ../include/global.h -coduse.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -coduse.o: ../include/errors.h ../include/memory.h ../include/residues.h -coduse.o: ../include/blastapp.h /usr/include/limits.h -coduse.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -coduse.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -coduse.o: ../include/gcode.h ../include/blocks.h ../include/output.h -coduse.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -coduse.o: ../include/convert.h ../include/frequency.h ../include/files.h -coduse.o: ../include/protomat.h -narrow.o: ../include/blocksprogs.h /usr/include/stdlib.h -narrow.o: /usr/include/features.h /usr/include/sys/cdefs.h -narrow.o: /usr/include/gnu/stubs.h -narrow.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -narrow.o: /usr/include/stdio.h /usr/include/bits/types.h -narrow.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -narrow.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -narrow.o: /usr/include/bits/wchar.h /usr/include/gconv.h -narrow.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -narrow.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -narrow.o: /usr/include/string.h /usr/include/math.h -narrow.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -narrow.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -narrow.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -narrow.o: /usr/include/ctype.h /usr/include/endian.h -narrow.o: /usr/include/bits/endian.h ../include/global.h -narrow.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -narrow.o: ../include/errors.h ../include/memory.h ../include/residues.h -narrow.o: ../include/blastapp.h /usr/include/limits.h -narrow.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -narrow.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -narrow.o: ../include/gcode.h ../include/blocks.h ../include/output.h -narrow.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -narrow.o: ../include/convert.h ../include/frequency.h ../include/files.h -narrow.o: ../include/protomat.h -blk2slx.o: ../include/blocksprogs.h /usr/include/stdlib.h -blk2slx.o: /usr/include/features.h /usr/include/sys/cdefs.h -blk2slx.o: /usr/include/gnu/stubs.h -blk2slx.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -blk2slx.o: /usr/include/stdio.h /usr/include/bits/types.h -blk2slx.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -blk2slx.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -blk2slx.o: /usr/include/bits/wchar.h /usr/include/gconv.h -blk2slx.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -blk2slx.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -blk2slx.o: /usr/include/string.h /usr/include/math.h -blk2slx.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -blk2slx.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -blk2slx.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -blk2slx.o: /usr/include/ctype.h /usr/include/endian.h -blk2slx.o: /usr/include/bits/endian.h ../include/global.h -blk2slx.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -blk2slx.o: ../include/errors.h ../include/memory.h ../include/residues.h -blk2slx.o: ../include/blastapp.h /usr/include/limits.h -blk2slx.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -blk2slx.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -blk2slx.o: ../include/gcode.h ../include/blocks.h ../include/output.h -blk2slx.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -blk2slx.o: ../include/convert.h ../include/frequency.h ../include/files.h -blk2slx.o: ../include/protomat.h -blkprob.o: ../include/blocksprogs.h /usr/include/stdlib.h -blkprob.o: /usr/include/features.h /usr/include/sys/cdefs.h -blkprob.o: /usr/include/gnu/stubs.h -blkprob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -blkprob.o: /usr/include/stdio.h /usr/include/bits/types.h -blkprob.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -blkprob.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -blkprob.o: /usr/include/bits/wchar.h /usr/include/gconv.h -blkprob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -blkprob.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -blkprob.o: /usr/include/string.h /usr/include/math.h -blkprob.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -blkprob.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -blkprob.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -blkprob.o: /usr/include/ctype.h /usr/include/endian.h -blkprob.o: /usr/include/bits/endian.h ../include/global.h -blkprob.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -blkprob.o: ../include/errors.h ../include/memory.h ../include/residues.h -blkprob.o: ../include/blastapp.h /usr/include/limits.h -blkprob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -blkprob.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -blkprob.o: ../include/gcode.h ../include/blocks.h ../include/output.h -blkprob.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -blkprob.o: ../include/convert.h ../include/frequency.h ../include/files.h -blkprob.o: ../include/protomat.h -blocks.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h -blocks.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -blocks.o: /usr/include/stdio.h /usr/include/bits/types.h -blocks.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -blocks.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -blocks.o: /usr/include/bits/wchar.h /usr/include/gconv.h -blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -blocks.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -blocks.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -blocks.o: /usr/include/bits/endian.h /usr/include/malloc.h -blocks.o: ../include/license.h ../include/strutil.h ../include/errors.h -blocks.o: ../include/memory.h ../include/blocks.h ../include/output.h -blocks.o: ../include/sequences.h ../include/residues.h ../include/blastapp.h -blocks.o: /usr/include/limits.h -blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -blocks.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -blocks.o: ../include/gcode.h -config.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h -config.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -config.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -config.o: /usr/include/stdio.h /usr/include/bits/types.h -config.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -config.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -config.o: /usr/include/bits/wchar.h /usr/include/gconv.h -config.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -config.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -config.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -config.o: /usr/include/bits/endian.h /usr/include/malloc.h -config.o: ../include/license.h ../include/strutil.h ../include/errors.h -config.o: ../include/memory.h ../include/files.h ../include/sequences.h -config.o: ../include/pattern.h ../include/options.h config.h blimps.h -config.o: scoring.h lists.h ../include/skiplist.h -convert.o: /usr/include/assert.h /usr/include/features.h -convert.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -convert.o: /usr/include/math.h /usr/include/bits/huge_val.h -convert.o: /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h -convert.o: ../include/global.h /usr/include/stdlib.h -convert.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -convert.o: /usr/include/stdio.h /usr/include/bits/types.h -convert.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -convert.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -convert.o: /usr/include/bits/wchar.h /usr/include/gconv.h -convert.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -convert.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -convert.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -convert.o: /usr/include/bits/endian.h /usr/include/malloc.h -convert.o: ../include/license.h ../include/strutil.h ../include/errors.h -convert.o: ../include/memory.h ../include/options.h ../include/blocks.h -convert.o: ../include/output.h ../include/sequences.h ../include/matrix.h -convert.o: ../include/pattern.h ../include/residues.h ../include/blastapp.h -convert.o: /usr/include/limits.h -convert.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -convert.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -convert.o: ../include/gcode.h ../include/frequency.h ../include/protomat.h -convert.o: ../include/convert.h blimps.h -errors.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h -errors.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -errors.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -errors.o: /usr/include/stdio.h /usr/include/bits/types.h -errors.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -errors.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -errors.o: /usr/include/bits/wchar.h /usr/include/gconv.h -errors.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -errors.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -errors.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -errors.o: /usr/include/bits/endian.h /usr/include/malloc.h -errors.o: ../include/license.h ../include/strutil.h ../include/errors.h -errors.o: ../include/memory.h -files.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h -files.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -files.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -files.o: /usr/include/stdio.h /usr/include/bits/types.h -files.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -files.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -files.o: /usr/include/bits/wchar.h /usr/include/gconv.h -files.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -files.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -files.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -files.o: /usr/include/bits/endian.h /usr/include/malloc.h -files.o: ../include/license.h ../include/strutil.h ../include/errors.h -files.o: ../include/memory.h ../include/files.h ../include/sequences.h -frequency.o: ../include/global.h /usr/include/stdlib.h -frequency.o: /usr/include/features.h /usr/include/sys/cdefs.h -frequency.o: /usr/include/gnu/stubs.h -frequency.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -frequency.o: /usr/include/stdio.h /usr/include/bits/types.h -frequency.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -frequency.o: /usr/include/libio.h /usr/include/_G_config.h -frequency.o: /usr/include/wchar.h /usr/include/bits/wchar.h -frequency.o: /usr/include/gconv.h -frequency.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -frequency.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -frequency.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -frequency.o: /usr/include/bits/endian.h /usr/include/malloc.h -frequency.o: ../include/license.h ../include/strutil.h ../include/errors.h -frequency.o: ../include/memory.h ../include/blocks.h ../include/output.h -frequency.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -frequency.o: ../include/frequency.h ../include/convert.h ../include/files.h -frequency.o: ../include/residues.h ../include/blastapp.h -frequency.o: /usr/include/limits.h -frequency.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -frequency.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -frequency.o: ../include/gcode.h -gcode.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h -gcode.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -gcode.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -gcode.o: /usr/include/stdio.h /usr/include/bits/types.h -gcode.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -gcode.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -gcode.o: /usr/include/bits/wchar.h /usr/include/gconv.h -gcode.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -gcode.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -gcode.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -gcode.o: /usr/include/bits/endian.h /usr/include/malloc.h -gcode.o: ../include/license.h ../include/strutil.h ../include/errors.h -gcode.o: ../include/memory.h ../include/residues.h ../include/blastapp.h -gcode.o: /usr/include/limits.h -gcode.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -gcode.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -gcode.o: ../include/gcode.h ../include/sequences.h -lists.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h -lists.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -lists.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -lists.o: /usr/include/stdio.h /usr/include/bits/types.h -lists.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -lists.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -lists.o: /usr/include/bits/wchar.h /usr/include/gconv.h -lists.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -lists.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -lists.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -lists.o: /usr/include/bits/endian.h /usr/include/malloc.h -lists.o: ../include/license.h ../include/strutil.h ../include/errors.h -lists.o: ../include/memory.h ../include/blocks.h ../include/output.h -lists.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -lists.o: lists.h ../include/skiplist.h blimps.h scores.h -matrix.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h -matrix.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -matrix.o: /usr/include/stdio.h /usr/include/bits/types.h -matrix.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -matrix.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -matrix.o: /usr/include/bits/wchar.h /usr/include/gconv.h -matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -matrix.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -matrix.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -matrix.o: /usr/include/bits/endian.h /usr/include/malloc.h -matrix.o: ../include/license.h ../include/strutil.h ../include/errors.h -matrix.o: ../include/memory.h ../include/blocks.h ../include/output.h -matrix.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -matrix.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h -matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -matrix.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -matrix.o: ../include/gcode.h -memory.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h -memory.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -memory.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -memory.o: /usr/include/stdio.h /usr/include/bits/types.h -memory.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -memory.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -memory.o: /usr/include/bits/wchar.h /usr/include/gconv.h -memory.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -memory.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -memory.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -memory.o: /usr/include/bits/endian.h /usr/include/malloc.h -memory.o: ../include/license.h ../include/strutil.h ../include/errors.h -memory.o: ../include/memory.h -pattern.o: /usr/include/assert.h /usr/include/features.h -pattern.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -pattern.o: ../include/global.h /usr/include/stdlib.h -pattern.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -pattern.o: /usr/include/stdio.h /usr/include/bits/types.h -pattern.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -pattern.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -pattern.o: /usr/include/bits/wchar.h /usr/include/gconv.h -pattern.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -pattern.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -pattern.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -pattern.o: /usr/include/bits/endian.h /usr/include/malloc.h -pattern.o: ../include/license.h ../include/strutil.h ../include/errors.h -pattern.o: ../include/memory.h ../include/files.h ../include/blocks.h -pattern.o: ../include/output.h ../include/sequences.h ../include/matrix.h -pattern.o: ../include/pattern.h ../include/residues.h ../include/blastapp.h -pattern.o: /usr/include/limits.h -pattern.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -pattern.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -pattern.o: ../include/gcode.h ../include/skiplist.h -scores.o: /usr/include/math.h /usr/include/features.h -scores.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -scores.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -scores.o: /usr/include/bits/mathcalls.h ../include/global.h -scores.o: /usr/include/stdlib.h -scores.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -scores.o: /usr/include/stdio.h /usr/include/bits/types.h -scores.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -scores.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -scores.o: /usr/include/bits/wchar.h /usr/include/gconv.h -scores.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -scores.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -scores.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -scores.o: /usr/include/bits/endian.h /usr/include/malloc.h -scores.o: ../include/license.h ../include/strutil.h ../include/errors.h -scores.o: ../include/memory.h ../include/blocks.h ../include/output.h -scores.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -scores.o: scores.h blimps.h scoring.h lists.h ../include/skiplist.h -scoring.o: /usr/include/math.h /usr/include/features.h -scoring.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -scoring.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -scoring.o: /usr/include/bits/mathcalls.h ../include/global.h -scoring.o: /usr/include/stdlib.h -scoring.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -scoring.o: /usr/include/stdio.h /usr/include/bits/types.h -scoring.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -scoring.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -scoring.o: /usr/include/bits/wchar.h /usr/include/gconv.h -scoring.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -scoring.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -scoring.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -scoring.o: /usr/include/bits/endian.h /usr/include/malloc.h -scoring.o: ../include/license.h ../include/strutil.h ../include/errors.h -scoring.o: ../include/memory.h ../include/blocks.h ../include/output.h -scoring.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -scoring.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h -scoring.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -scoring.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -scoring.o: ../include/gcode.h scoring.h blimps.h scores.h lists.h -scoring.o: ../include/skiplist.h -sequences.o: ../include/global.h /usr/include/stdlib.h -sequences.o: /usr/include/features.h /usr/include/sys/cdefs.h -sequences.o: /usr/include/gnu/stubs.h -sequences.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -sequences.o: /usr/include/stdio.h /usr/include/bits/types.h -sequences.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -sequences.o: /usr/include/libio.h /usr/include/_G_config.h -sequences.o: /usr/include/wchar.h /usr/include/bits/wchar.h -sequences.o: /usr/include/gconv.h -sequences.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -sequences.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -sequences.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -sequences.o: /usr/include/bits/endian.h /usr/include/malloc.h -sequences.o: ../include/license.h ../include/strutil.h ../include/errors.h -sequences.o: ../include/memory.h ../include/sequences.h ../include/residues.h -sequences.o: ../include/blastapp.h /usr/include/limits.h -sequences.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -sequences.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -sequences.o: ../include/gcode.h -sl.o: /usr/include/assert.h /usr/include/features.h /usr/include/sys/cdefs.h -sl.o: /usr/include/gnu/stubs.h /usr/include/time.h /usr/include/bits/types.h -sl.o: /usr/include/bits/wordsize.h -sl.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -sl.o: /usr/include/bits/typesizes.h ../include/global.h /usr/include/stdlib.h -sl.o: /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h -sl.o: /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h -sl.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -sl.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -sl.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -sl.o: /usr/include/bits/endian.h /usr/include/malloc.h ../include/license.h -sl.o: ../include/strutil.h ../include/errors.h ../include/memory.h -sl.o: ../include/skiplist.h -strutil.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h -strutil.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -strutil.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -strutil.o: /usr/include/stdio.h /usr/include/bits/types.h -strutil.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -strutil.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -strutil.o: /usr/include/bits/wchar.h /usr/include/gconv.h -strutil.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -strutil.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -strutil.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -strutil.o: /usr/include/bits/endian.h /usr/include/malloc.h -strutil.o: ../include/license.h ../include/strutil.h ../include/errors.h -strutil.o: ../include/memory.h -version.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h -version.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -version.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -version.o: /usr/include/stdio.h /usr/include/bits/types.h -version.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -version.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -version.o: /usr/include/bits/wchar.h /usr/include/gconv.h -version.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -version.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -version.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -version.o: /usr/include/bits/endian.h /usr/include/malloc.h -version.o: ../include/license.h ../include/strutil.h ../include/errors.h -version.o: ../include/memory.h ../include/version.h -options.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h -options.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -options.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -options.o: /usr/include/stdio.h /usr/include/bits/types.h -options.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -options.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -options.o: /usr/include/bits/wchar.h /usr/include/gconv.h -options.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -options.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -options.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h -options.o: /usr/include/bits/endian.h /usr/include/malloc.h -options.o: ../include/license.h ../include/strutil.h ../include/errors.h -options.o: ../include/memory.h ../include/options.h -protomat.o: /usr/include/sys/types.h /usr/include/features.h -protomat.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -protomat.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -protomat.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -protomat.o: /usr/include/bits/typesizes.h /usr/include/time.h -protomat.o: /usr/include/dirent.h /usr/include/bits/dirent.h -protomat.o: /usr/include/ctype.h /usr/include/endian.h -protomat.o: /usr/include/bits/endian.h ../include/protomat.h -protomat.o: /usr/include/stdlib.h /usr/include/stdio.h /usr/include/libio.h -protomat.o: /usr/include/_G_config.h /usr/include/wchar.h -protomat.o: /usr/include/bits/wchar.h /usr/include/gconv.h -protomat.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -protomat.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -protomat.o: /usr/include/string.h -interpro.o: ../include/blocksprogs.h /usr/include/stdlib.h -interpro.o: /usr/include/features.h /usr/include/sys/cdefs.h -interpro.o: /usr/include/gnu/stubs.h -interpro.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -interpro.o: /usr/include/stdio.h /usr/include/bits/types.h -interpro.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -interpro.o: /usr/include/libio.h /usr/include/_G_config.h -interpro.o: /usr/include/wchar.h /usr/include/bits/wchar.h -interpro.o: /usr/include/gconv.h -interpro.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -interpro.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -interpro.o: /usr/include/string.h /usr/include/math.h -interpro.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -interpro.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -interpro.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -interpro.o: /usr/include/ctype.h /usr/include/endian.h -interpro.o: /usr/include/bits/endian.h ../include/global.h -interpro.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -interpro.o: ../include/errors.h ../include/memory.h ../include/residues.h -interpro.o: ../include/blastapp.h /usr/include/limits.h -interpro.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -interpro.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -interpro.o: ../include/gcode.h ../include/blocks.h ../include/output.h -interpro.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -interpro.o: ../include/convert.h ../include/frequency.h ../include/files.h -interpro.o: ../include/protomat.h -pssmdist.o: ../include/blocksprogs.h /usr/include/stdlib.h -pssmdist.o: /usr/include/features.h /usr/include/sys/cdefs.h -pssmdist.o: /usr/include/gnu/stubs.h -pssmdist.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -pssmdist.o: /usr/include/stdio.h /usr/include/bits/types.h -pssmdist.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -pssmdist.o: /usr/include/libio.h /usr/include/_G_config.h -pssmdist.o: /usr/include/wchar.h /usr/include/bits/wchar.h -pssmdist.o: /usr/include/gconv.h -pssmdist.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -pssmdist.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -pssmdist.o: /usr/include/string.h /usr/include/math.h -pssmdist.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -pssmdist.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -pssmdist.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -pssmdist.o: /usr/include/ctype.h /usr/include/endian.h -pssmdist.o: /usr/include/bits/endian.h ../include/global.h -pssmdist.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -pssmdist.o: ../include/errors.h ../include/memory.h ../include/residues.h -pssmdist.o: ../include/blastapp.h /usr/include/limits.h -pssmdist.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -pssmdist.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -pssmdist.o: ../include/gcode.h ../include/blocks.h ../include/output.h -pssmdist.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -pssmdist.o: ../include/convert.h ../include/frequency.h ../include/files.h -pssmdist.o: ../include/protomat.h -pssmBL.o: ../include/blocksprogs.h /usr/include/stdlib.h -pssmBL.o: /usr/include/features.h /usr/include/sys/cdefs.h -pssmBL.o: /usr/include/gnu/stubs.h -pssmBL.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -pssmBL.o: /usr/include/stdio.h /usr/include/bits/types.h -pssmBL.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -pssmBL.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -pssmBL.o: /usr/include/bits/wchar.h /usr/include/gconv.h -pssmBL.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -pssmBL.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -pssmBL.o: /usr/include/string.h /usr/include/math.h -pssmBL.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -pssmBL.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -pssmBL.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -pssmBL.o: /usr/include/ctype.h /usr/include/endian.h -pssmBL.o: /usr/include/bits/endian.h ../include/global.h -pssmBL.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -pssmBL.o: ../include/errors.h ../include/memory.h ../include/residues.h -pssmBL.o: ../include/blastapp.h /usr/include/limits.h -pssmBL.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -pssmBL.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -pssmBL.o: ../include/gcode.h ../include/blocks.h ../include/output.h -pssmBL.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -pssmBL.o: ../include/convert.h ../include/frequency.h ../include/files.h -pssmBL.o: ../include/protomat.h -papssm.o: ../include/blocksprogs.h /usr/include/stdlib.h -papssm.o: /usr/include/features.h /usr/include/sys/cdefs.h -papssm.o: /usr/include/gnu/stubs.h -papssm.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -papssm.o: /usr/include/stdio.h /usr/include/bits/types.h -papssm.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -papssm.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -papssm.o: /usr/include/bits/wchar.h /usr/include/gconv.h -papssm.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -papssm.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -papssm.o: /usr/include/string.h /usr/include/math.h -papssm.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -papssm.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -papssm.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -papssm.o: /usr/include/ctype.h /usr/include/endian.h -papssm.o: /usr/include/bits/endian.h ../include/global.h -papssm.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -papssm.o: ../include/errors.h ../include/memory.h ../include/residues.h -papssm.o: ../include/blastapp.h /usr/include/limits.h -papssm.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -papssm.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -papssm.o: ../include/gcode.h ../include/blocks.h ../include/output.h -papssm.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -papssm.o: ../include/convert.h ../include/frequency.h ../include/files.h -papssm.o: ../include/protomat.h blimps.h -matrix_logob.o: /usr/include/sys/types.h /usr/include/features.h -matrix_logob.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -matrix_logob.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -matrix_logob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -matrix_logob.o: /usr/include/bits/typesizes.h /usr/include/time.h -matrix_logob.o: /usr/include/sys/stat.h /usr/include/bits/stat.h -matrix_logob.o: ../include/blocksprogs.h /usr/include/stdlib.h -matrix_logob.o: /usr/include/stdio.h /usr/include/libio.h -matrix_logob.o: /usr/include/_G_config.h /usr/include/wchar.h -matrix_logob.o: /usr/include/bits/wchar.h /usr/include/gconv.h -matrix_logob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -matrix_logob.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -matrix_logob.o: /usr/include/string.h /usr/include/math.h -matrix_logob.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -matrix_logob.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -matrix_logob.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -matrix_logob.o: /usr/include/ctype.h /usr/include/endian.h -matrix_logob.o: /usr/include/bits/endian.h ../include/global.h -matrix_logob.o: /usr/include/malloc.h ../include/license.h -matrix_logob.o: ../include/strutil.h ../include/errors.h ../include/memory.h -matrix_logob.o: ../include/residues.h ../include/blastapp.h -matrix_logob.o: /usr/include/limits.h -matrix_logob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -matrix_logob.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -matrix_logob.o: ../include/gcode.h ../include/blocks.h ../include/output.h -matrix_logob.o: ../include/sequences.h ../include/matrix.h -matrix_logob.o: ../include/pattern.h ../include/convert.h -matrix_logob.o: ../include/frequency.h ../include/files.h -matrix_logob.o: ../include/protomat.h -makelogob.o: p2c.h /usr/include/stdio.h /usr/include/features.h -makelogob.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -makelogob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -makelogob.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -makelogob.o: /usr/include/bits/typesizes.h /usr/include/libio.h -makelogob.o: /usr/include/_G_config.h /usr/include/wchar.h -makelogob.o: /usr/include/bits/wchar.h /usr/include/gconv.h -makelogob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -makelogob.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -makelogob.o: /usr/include/stdlib.h /usr/include/string.h /usr/include/ctype.h -makelogob.o: /usr/include/endian.h /usr/include/bits/endian.h -makelogob.o: /usr/include/math.h /usr/include/bits/huge_val.h -makelogob.o: /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h -makelogob.o: /usr/include/setjmp.h /usr/include/bits/setjmp.h -makelogob.o: /usr/include/bits/sigset.h /usr/include/assert.h -blocks_search.o: /usr/include/stdio.h /usr/include/features.h -blocks_search.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -blocks_search.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -blocks_search.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h -blocks_search.o: /usr/include/bits/typesizes.h /usr/include/libio.h -blocks_search.o: /usr/include/_G_config.h /usr/include/wchar.h -blocks_search.o: /usr/include/bits/wchar.h /usr/include/gconv.h -blocks_search.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -blocks_search.o: /usr/include/bits/stdio_lim.h -blocks_search.o: /usr/include/bits/sys_errlist.h /usr/include/stdlib.h -blocks_search.o: ../include/global.h /usr/include/string.h -blocks_search.o: /usr/include/ctype.h /usr/include/endian.h -blocks_search.o: /usr/include/bits/endian.h /usr/include/malloc.h -blocks_search.o: ../include/license.h ../include/strutil.h -blocks_search.o: ../include/errors.h ../include/memory.h -blocks_search.o: /usr/include/unistd.h /usr/include/bits/posix_opt.h -blocks_search.o: /usr/include/bits/confname.h -LAMA_search.o: ../include/blocksprogs.h /usr/include/stdlib.h -LAMA_search.o: /usr/include/features.h /usr/include/sys/cdefs.h -LAMA_search.o: /usr/include/gnu/stubs.h -LAMA_search.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -LAMA_search.o: /usr/include/stdio.h /usr/include/bits/types.h -LAMA_search.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -LAMA_search.o: /usr/include/libio.h /usr/include/_G_config.h -LAMA_search.o: /usr/include/wchar.h /usr/include/bits/wchar.h -LAMA_search.o: /usr/include/gconv.h -LAMA_search.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -LAMA_search.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -LAMA_search.o: /usr/include/string.h /usr/include/math.h -LAMA_search.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -LAMA_search.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -LAMA_search.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -LAMA_search.o: /usr/include/ctype.h /usr/include/endian.h -LAMA_search.o: /usr/include/bits/endian.h ../include/global.h -LAMA_search.o: /usr/include/malloc.h ../include/license.h -LAMA_search.o: ../include/strutil.h ../include/errors.h ../include/memory.h -LAMA_search.o: ../include/residues.h ../include/blastapp.h -LAMA_search.o: /usr/include/limits.h -LAMA_search.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -LAMA_search.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -LAMA_search.o: ../include/gcode.h ../include/blocks.h ../include/output.h -LAMA_search.o: ../include/sequences.h ../include/matrix.h -LAMA_search.o: ../include/pattern.h ../include/convert.h -LAMA_search.o: ../include/frequency.h ../include/files.h -LAMA_search.o: ../include/protomat.h -block_vis.o: ../include/blocksprogs.h /usr/include/stdlib.h -block_vis.o: /usr/include/features.h /usr/include/sys/cdefs.h -block_vis.o: /usr/include/gnu/stubs.h -block_vis.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -block_vis.o: /usr/include/stdio.h /usr/include/bits/types.h -block_vis.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -block_vis.o: /usr/include/libio.h /usr/include/_G_config.h -block_vis.o: /usr/include/wchar.h /usr/include/bits/wchar.h -block_vis.o: /usr/include/gconv.h -block_vis.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -block_vis.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -block_vis.o: /usr/include/string.h /usr/include/math.h -block_vis.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -block_vis.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -block_vis.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -block_vis.o: /usr/include/ctype.h /usr/include/endian.h -block_vis.o: /usr/include/bits/endian.h ../include/global.h -block_vis.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -block_vis.o: ../include/errors.h ../include/memory.h ../include/residues.h -block_vis.o: ../include/blastapp.h /usr/include/limits.h -block_vis.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -block_vis.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -block_vis.o: ../include/gcode.h ../include/blocks.h ../include/output.h -block_vis.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -block_vis.o: ../include/convert.h ../include/frequency.h ../include/files.h -block_vis.o: ../include/protomat.h blockmap.h -format_block.o: ../include/blocksprogs.h /usr/include/stdlib.h -format_block.o: /usr/include/features.h /usr/include/sys/cdefs.h -format_block.o: /usr/include/gnu/stubs.h -format_block.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -format_block.o: /usr/include/stdio.h /usr/include/bits/types.h -format_block.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -format_block.o: /usr/include/libio.h /usr/include/_G_config.h -format_block.o: /usr/include/wchar.h /usr/include/bits/wchar.h -format_block.o: /usr/include/gconv.h -format_block.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -format_block.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -format_block.o: /usr/include/string.h /usr/include/math.h -format_block.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -format_block.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -format_block.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -format_block.o: /usr/include/ctype.h /usr/include/endian.h -format_block.o: /usr/include/bits/endian.h ../include/global.h -format_block.o: /usr/include/malloc.h ../include/license.h -format_block.o: ../include/strutil.h ../include/errors.h ../include/memory.h -format_block.o: ../include/residues.h ../include/blastapp.h -format_block.o: /usr/include/limits.h -format_block.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -format_block.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -format_block.o: ../include/gcode.h ../include/blocks.h ../include/output.h -format_block.o: ../include/sequences.h ../include/matrix.h -format_block.o: ../include/pattern.h ../include/convert.h -format_block.o: ../include/frequency.h ../include/files.h -format_block.o: ../include/protomat.h -biassed_blocks_finder.o: ../include/blocksprogs.h /usr/include/stdlib.h -biassed_blocks_finder.o: /usr/include/features.h /usr/include/sys/cdefs.h -biassed_blocks_finder.o: /usr/include/gnu/stubs.h -biassed_blocks_finder.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -biassed_blocks_finder.o: /usr/include/stdio.h /usr/include/bits/types.h -biassed_blocks_finder.o: /usr/include/bits/wordsize.h -biassed_blocks_finder.o: /usr/include/bits/typesizes.h /usr/include/libio.h -biassed_blocks_finder.o: /usr/include/_G_config.h /usr/include/wchar.h -biassed_blocks_finder.o: /usr/include/bits/wchar.h /usr/include/gconv.h -biassed_blocks_finder.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -biassed_blocks_finder.o: /usr/include/bits/stdio_lim.h -biassed_blocks_finder.o: /usr/include/bits/sys_errlist.h -biassed_blocks_finder.o: /usr/include/string.h /usr/include/math.h -biassed_blocks_finder.o: /usr/include/bits/huge_val.h -biassed_blocks_finder.o: /usr/include/bits/mathdef.h -biassed_blocks_finder.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -biassed_blocks_finder.o: /usr/include/bits/posix_opt.h -biassed_blocks_finder.o: /usr/include/bits/confname.h /usr/include/ctype.h -biassed_blocks_finder.o: /usr/include/endian.h /usr/include/bits/endian.h -biassed_blocks_finder.o: ../include/global.h /usr/include/malloc.h -biassed_blocks_finder.o: ../include/license.h ../include/strutil.h -biassed_blocks_finder.o: ../include/errors.h ../include/memory.h -biassed_blocks_finder.o: ../include/residues.h ../include/blastapp.h -biassed_blocks_finder.o: /usr/include/limits.h -biassed_blocks_finder.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -biassed_blocks_finder.o: ../include/alphabet.h ../include/aabet.h -biassed_blocks_finder.o: ../include/ntbet.h ../include/gcode.h -biassed_blocks_finder.o: ../include/blocks.h ../include/output.h -biassed_blocks_finder.o: ../include/sequences.h ../include/matrix.h -biassed_blocks_finder.o: ../include/pattern.h ../include/convert.h -biassed_blocks_finder.o: ../include/frequency.h ../include/files.h -biassed_blocks_finder.o: ../include/protomat.h -htmlize-LAMA.o: /usr/include/stdlib.h /usr/include/features.h -htmlize-LAMA.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h -htmlize-LAMA.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -htmlize-LAMA.o: /usr/include/stdio.h /usr/include/bits/types.h -htmlize-LAMA.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -htmlize-LAMA.o: /usr/include/libio.h /usr/include/_G_config.h -htmlize-LAMA.o: /usr/include/wchar.h /usr/include/bits/wchar.h -htmlize-LAMA.o: /usr/include/gconv.h -htmlize-LAMA.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -htmlize-LAMA.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -show_aligned_blocks.o: ../include/blocksprogs.h /usr/include/stdlib.h -show_aligned_blocks.o: /usr/include/features.h /usr/include/sys/cdefs.h -show_aligned_blocks.o: /usr/include/gnu/stubs.h -show_aligned_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -show_aligned_blocks.o: /usr/include/stdio.h /usr/include/bits/types.h -show_aligned_blocks.o: /usr/include/bits/wordsize.h -show_aligned_blocks.o: /usr/include/bits/typesizes.h /usr/include/libio.h -show_aligned_blocks.o: /usr/include/_G_config.h /usr/include/wchar.h -show_aligned_blocks.o: /usr/include/bits/wchar.h /usr/include/gconv.h -show_aligned_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -show_aligned_blocks.o: /usr/include/bits/stdio_lim.h -show_aligned_blocks.o: /usr/include/bits/sys_errlist.h /usr/include/string.h -show_aligned_blocks.o: /usr/include/math.h /usr/include/bits/huge_val.h -show_aligned_blocks.o: /usr/include/bits/mathdef.h -show_aligned_blocks.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -show_aligned_blocks.o: /usr/include/bits/posix_opt.h -show_aligned_blocks.o: /usr/include/bits/confname.h /usr/include/ctype.h -show_aligned_blocks.o: /usr/include/endian.h /usr/include/bits/endian.h -show_aligned_blocks.o: ../include/global.h /usr/include/malloc.h -show_aligned_blocks.o: ../include/license.h ../include/strutil.h -show_aligned_blocks.o: ../include/errors.h ../include/memory.h -show_aligned_blocks.o: ../include/residues.h ../include/blastapp.h -show_aligned_blocks.o: /usr/include/limits.h -show_aligned_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -show_aligned_blocks.o: ../include/alphabet.h ../include/aabet.h -show_aligned_blocks.o: ../include/ntbet.h ../include/gcode.h -show_aligned_blocks.o: ../include/blocks.h ../include/output.h -show_aligned_blocks.o: ../include/sequences.h ../include/matrix.h -show_aligned_blocks.o: ../include/pattern.h ../include/convert.h -show_aligned_blocks.o: ../include/frequency.h ../include/files.h -show_aligned_blocks.o: ../include/protomat.h -blk2mot.o: ../include/blocksprogs.h /usr/include/stdlib.h -blk2mot.o: /usr/include/features.h /usr/include/sys/cdefs.h -blk2mot.o: /usr/include/gnu/stubs.h -blk2mot.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h -blk2mot.o: /usr/include/stdio.h /usr/include/bits/types.h -blk2mot.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h -blk2mot.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h -blk2mot.o: /usr/include/bits/wchar.h /usr/include/gconv.h -blk2mot.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h -blk2mot.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h -blk2mot.o: /usr/include/string.h /usr/include/math.h -blk2mot.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h -blk2mot.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h -blk2mot.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h -blk2mot.o: /usr/include/ctype.h /usr/include/endian.h -blk2mot.o: /usr/include/bits/endian.h ../include/global.h -blk2mot.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h -blk2mot.o: ../include/errors.h ../include/memory.h ../include/residues.h -blk2mot.o: ../include/blastapp.h /usr/include/limits.h -blk2mot.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h -blk2mot.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h -blk2mot.o: ../include/gcode.h ../include/blocks.h ../include/output.h -blk2mot.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h -blk2mot.o: ../include/convert.h ../include/frequency.h ../include/files.h -blk2mot.o: ../include/protomat.h Index: blimps-3.9/blimps/makelogob.c =================================================================== --- blimps-3.9.orig/blimps/makelogob.c 2012-02-03 21:58:56.928242561 +0100 +++ blimps-3.9/blimps/makelogob.c 2012-02-03 22:01:34.060367844 +0100 @@ -797,7 +797,7 @@ *w = NULL; return; } - *w = (waveparam *)Malloc(sizeof(waveparam)); + *w = (waveparam *)malloc(sizeof(waveparam)); p = *w; while (!BUFEOF(afile->f)) { fscanf(afile->f, "%c%*[^\n]", &p->extreme); @@ -831,7 +831,7 @@ } } if (!BUFEOF(afile->f)) { - p->next = (waveparam *)Malloc(sizeof(waveparam)); + p->next = (waveparam *)malloc(sizeof(waveparam)); p = p->next; } else p->next = NULL; @@ -2007,7 +2007,7 @@ return; } - *thestrings = (strings *)Malloc(sizeof(strings)); + *thestrings = (strings *)malloc(sizeof(strings)); stringspot = *thestrings; for (n = 1; n <= numberstrings; n++) { if (BUFEOF(theplace->f)) { @@ -2023,7 +2023,7 @@ halt(); } if (n < numberstrings) { - stringspot->next = (strings *)Malloc(sizeof(strings)); + stringspot->next = (strings *)malloc(sizeof(strings)); stringspot = stringspot->next; } else stringspot->next = NULL; Index: blimps-3.9/blimps/matrix_logob.c =================================================================== --- blimps-3.9.orig/blimps/matrix_logob.c 2012-02-03 21:58:56.952242669 +0100 +++ blimps-3.9/blimps/matrix_logob.c 2012-02-03 22:01:34.068367778 +0100 @@ -331,7 +331,7 @@ else { printf("\nEnter name of BLOCK or MATRIX file: "); - gets(bdbname); + fgets(bdbname, MAXNAME, stdin); } /* Read stdin if the filename starts with '-' */ @@ -347,7 +347,7 @@ else /* get input file(s) interactively */ { printf("\nEnter AC in %s or - to make logos for all: ", bdbname); - gets(blockAC); + fgets(blockAC, MAXNAME, stdin); } /* ------------3rd arg = file name suffix ------------------------------JGH*/ @@ -356,7 +356,7 @@ else { printf("\nEnter file name suffix: "); - gets(suffix); + fgets(suffix, MAXNAME, stdin); printf("Logos will be written to logo.%s\n", suffix); } @@ -588,7 +588,7 @@ printf(" after viewing you can also choose to print,\n") ; printf(" P to print logo (%s %s).)\n", PSprint, outname) ; - gets(ans) ; + fgets(ans, 2, stdin) ; switch (toupper(ans[0])) { Index: blimps-3.9/blimps/narrow.c =================================================================== --- blimps-3.9.orig/blimps/narrow.c 2012-02-03 21:58:56.992242661 +0100 +++ blimps-3.9/blimps/narrow.c 2012-02-03 22:01:34.080368098 +0100 @@ -93,7 +93,7 @@ else { printf("\nEnter type of input file (Block|Frequencies|Weights): "); - gets(ctemp); + fgets(ctemp, 80, stdin); } if (ctemp[0] == 'F' || ctemp[0] == 'f') type = 1; else if (ctemp[0] == 'W' || ctemp[0] == 'w') type = 2; @@ -104,7 +104,7 @@ else { printf("\nEnter name of input file: "); - gets(chkname); + fgets(chkname, 80, stdin); } if ( (chk=fopen(chkname, "r")) == NULL) { Index: blimps-3.9/blimps/oligo_melt.c =================================================================== --- blimps-3.9.orig/blimps/oligo_melt.c 2012-02-03 21:58:57.016242811 +0100 +++ blimps-3.9/blimps/oligo_melt.c 2012-02-03 22:01:34.084367826 +0100 @@ -75,7 +75,7 @@ else { printf("Enter name of file containing oligos: "); - gets(fname); + fgets(fname, 80, stdin); } if (!strlen(fname) ) inpf = stdin; else if ((inpf=fopen(fname, "r")) == NULL) Index: blimps-3.9/blimps/papssm.c =================================================================== --- blimps-3.9.orig/blimps/papssm.c 2012-02-03 21:58:57.040242995 +0100 +++ blimps-3.9/blimps/papssm.c 2012-02-03 22:01:34.096367794 +0100 @@ -163,7 +163,7 @@ int read_cf(); int load_frequencies(); -double read_freq(); +static double read_freq(); void load_subst(); double nrgamma(); double addlogs(); @@ -250,7 +250,7 @@ else { printf("\nEnter name of configuration file: "); - gets(cfname); + fgets(cfname, FNAMELEN, stdin); } if ( (cfp=fopen(cfname, "r")) == NULL) { Index: blimps-3.9/blimps/prints2blocks.c =================================================================== --- blimps-3.9.orig/blimps/prints2blocks.c 2012-02-03 21:58:57.064243161 +0100 +++ blimps-3.9/blimps/prints2blocks.c 2012-02-03 22:01:34.112370260 +0100 @@ -63,7 +63,7 @@ { printf( "\nEnter name of input file (Prints protein motifs database): "); - gets(inpfname); + fgets(inpfname, MAXNAME, stdin); } if ( (inpf=fopen(inpfname, "r")) == NULL) Index: blimps-3.9/blimps/protomat.c =================================================================== --- blimps-3.9.orig/blimps/protomat.c 2012-02-03 21:58:57.088242308 +0100 +++ blimps-3.9/blimps/protomat.c 2012-02-03 22:01:34.120367726 +0100 @@ -438,7 +438,8 @@ char *dir_unix(line) char *line; { - char tname[FNAMELEN], mem[MAXLINE], pros[FNAMELEN], *ptr; + char tname[FNAMELEN], mem[MAXLINE], *ptr; + static char pros[FNAMELEN]; int test; DIR *dp; Index: blimps-3.9/blimps/protxblk.c =================================================================== --- blimps-3.9.orig/blimps/protxblk.c 2012-02-03 21:58:57.112250471 +0100 +++ blimps-3.9/blimps/protxblk.c 2012-02-03 22:01:34.124367836 +0100 @@ -37,7 +37,7 @@ else { printf("\nEnter name of blocks database: "); - gets(bdbname); + fgets(bdbname, MAXNAME, stdin); } if ( (bfp=fopen(bdbname, "r")) == NULL) { @@ -50,7 +50,7 @@ else { printf("\nEnter name of output file: "); - gets(conname); + fgets(conname, MAXNAME, stdin); } if ( (ofp=fopen(conname, "w")) == NULL) { Index: blimps-3.9/blimps/pssmBL.c =================================================================== --- blimps-3.9.orig/blimps/pssmBL.c 2012-02-03 21:58:57.136245051 +0100 +++ blimps-3.9/blimps/pssmBL.c 2012-02-03 22:01:34.128368059 +0100 @@ -29,7 +29,7 @@ else { printf("\nEnter name of pssmdist.dat file: "); - gets(pssmname); + fgets(pssmname, MAXNAME, stdin); } if ( (pfp=fopen(pssmname, "r")) == NULL) { @@ -42,7 +42,7 @@ else { printf("\nEnter name of blocks database: "); - gets(bdbname); + fgets(bdbname, MAXNAME, stdin); } if ( (bfp=fopen(bdbname, "r")) == NULL) { @@ -55,7 +55,7 @@ else { printf("\nEnter name of new blocks database: "); - gets(conname); + fgets(conname, MAXNAME, stdin); } if ( (ofp=fopen(conname, "a")) == NULL) { Index: blimps-3.9/blimps/pssmdist.c =================================================================== --- blimps-3.9.orig/blimps/pssmdist.c 2012-02-03 21:58:57.160242689 +0100 +++ blimps-3.9/blimps/pssmdist.c 2012-02-03 22:01:34.136422451 +0100 @@ -81,7 +81,7 @@ int compute(); int load_freqs(); -double read_a_freq(); +static double read_a_freq(); void fix_freqs(); int count_tps(); @@ -113,7 +113,7 @@ else { printf("\nEnter name of matrix database: "); - gets(mname); + fgets(mname, MAXNAME, stdin); } if ( (mfp=fopen(mname, "r")) == NULL) { @@ -126,7 +126,7 @@ else { printf("\nEnter name of observed frequencies database: "); - gets(oname); + fgets(oname, MAXNAME, stdin); } if ( (ofp=fopen(oname, "r")) == NULL) { @@ -138,7 +138,7 @@ else { printf("\nEnter name of frequency file: "); - gets(fname); + fgets(fname, MAXNAME,stdin); } if ( (ffp=fopen(fname, "r")) == NULL) { @@ -155,7 +155,7 @@ { printf("\nEnter number of sequences in a typical search [%.0f]: ", Search); - gets(ctemp); + fgets(ctemp, MAXNAME, stdin); } if (strlen(ctemp)) Search = atof(ctemp); /* ------------5th arg = #aas in a search--------------------*/ @@ -166,7 +166,7 @@ { printf("\nEnter number of amino acids in a typical database [%.0f]: ", SearchAA); - gets(ctemp); + fgets(ctemp, MAXNAME, stdin); } if (strlen(ctemp)) SearchAA = atof(ctemp); printf ("Assuming %.0f sequences, %.0f amino acids in a search\n", Index: blimps-3.9/blimps/rank_matrix.c =================================================================== --- blimps-3.9.orig/blimps/rank_matrix.c 2012-02-03 21:58:57.184242671 +0100 +++ blimps-3.9/blimps/rank_matrix.c 2012-02-03 22:01:34.140418430 +0100 @@ -39,7 +39,7 @@ else { printf("\nEnter name of scoring matrix: "); - gets(matname); + fgets(matname, MAXNAME, stdin); } if ( (fmat=fopen(matname, "r")) == NULL) { Index: blimps-3.9/blimps/readchk.c =================================================================== --- blimps-3.9.orig/blimps/readchk.c 2012-02-03 21:58:57.208242554 +0100 +++ blimps-3.9/blimps/readchk.c 2012-02-03 22:01:34.148318588 +0100 @@ -20,7 +20,7 @@ else { printf("\nEnter name of configuration file: "); - gets(chkname); + fgets(chkname, 80, stdin); } if ( (chk=fopen(chkname, "r")) == NULL) { Index: blimps-3.9/blimps/readmast.c =================================================================== --- blimps-3.9.orig/blimps/readmast.c 2012-02-03 21:58:57.232242646 +0100 +++ blimps-3.9/blimps/readmast.c 2012-02-03 22:01:34.160367725 +0100 @@ -26,7 +26,7 @@ else { printf("\nEnter name of configuration file: "); - gets(chkname); + fgets(chkname, 80, stdin); } if ( (chk=fopen(chkname, "r")) == NULL) { Index: blimps-3.9/blimps/retblock.c =================================================================== --- blimps-3.9.orig/blimps/retblock.c 2012-02-03 21:58:57.256245156 +0100 +++ blimps-3.9/blimps/retblock.c 2012-02-03 22:01:34.164367729 +0100 @@ -50,7 +50,7 @@ else { printf("\nEnter name of blocks database: "); - gets(bdbname); + fgets(bdbname, MAXNAME, stdin); } if ( (bfp=fopen(bdbname, "r")) == NULL) { @@ -66,7 +66,7 @@ { strcpy(acname, "all"); printf("\nEnter AC of blocks to extract, or all [%s]: ", acname); - gets(acname); + fgets(acname, MAXNAME, stdin); } if (strcasecmp(acname, "all") == 0) allflag = TRUE; Index: blimps-3.9/blimps/sequences.c =================================================================== --- blimps-3.9.orig/blimps/sequences.c 2012-02-03 21:58:57.280242598 +0100 +++ blimps-3.9/blimps/sequences.c 2012-02-03 22:01:34.172367940 +0100 @@ -665,7 +665,7 @@ stemp is a huge negative number ... */ if (seq_type == AA_SEQ) { - while ( (c != NULL) && (c != '\0') && (num_seen < room_left) ) { + while ( (c != 0) && (c != '\0') && (num_seen < room_left) ) { stemp = aa_atob[c]; if (stemp < 0 || stemp > AAID_MAX) stemp = AAID_MAX + 1; if ( stemp <= AAID_MAX ) { @@ -1201,7 +1201,7 @@ } } else { - printf("??) \t"); + printf("??"") \t"); printf("\n"); for(k=0; klength; k++) { printf("%c", aa_btoa[seq->sequence[k]]); Index: blimps-3.9/blimps/sortblk.c =================================================================== --- blimps-3.9.orig/blimps/sortblk.c 2012-02-03 21:58:57.304243124 +0100 +++ blimps-3.9/blimps/sortblk.c 2012-02-03 22:01:34.176367755 +0100 @@ -58,7 +58,7 @@ else { printf("\nEnter name of blocks database: "); - gets(bdbname); + fgets(bdbname, MAXNAME, stdin); } if ( (bfp=fopen(bdbname, "r")) == NULL) { @@ -71,7 +71,7 @@ else { printf("\nEnter name of new sorted blocks database: "); - gets(conname); + fgets(conname, MAXNAME, stdin); } if ( (ofp=fopen(conname, "w")) == NULL) { Index: blimps-3.9/blimps/translate.c =================================================================== --- blimps-3.9.orig/blimps/translate.c 2012-02-03 21:58:57.344242740 +0100 +++ blimps-3.9/blimps/translate.c 2012-02-03 22:01:34.184367687 +0100 @@ -29,7 +29,7 @@ else { printf("\nEnter name of sequence database: "); - gets(sname); + fgets(sname, MAXNAME, stdin); } if ( (bfp=fopen(sname, "r")) == NULL) { @@ -50,7 +50,7 @@ else { printf("\nEnter name of new translated sequence database: "); - gets(outname); + fgets(outname, MAXNAME, stdin); } if ( (ofp=fopen(outname, "w")) == NULL) { @@ -62,7 +62,7 @@ else { printf("\nEnter translation frame: "); - gets(ctemp); + fgets(ctemp, MAXNAME, stdin); frame = atoi(ctemp); } if (frame == 0 || frame < -3 || frame > 3) frame = 1; @@ -74,7 +74,7 @@ for (code = 0; code < NUMBER_OF_GENETIC_CODES; code++) printf("\n %d %s", code, gcodes[code].name); printf("\nEnter genetic code: "); - gets(ctemp); + fgets(ctemp, MAXNAME, stdin); code = atoi(ctemp); } if (code < 0 || code > 8) code = 0; Index: blimps-3.9/blimps/util.c =================================================================== --- blimps-3.9.orig/blimps/util.c 2012-02-03 21:58:57.368242612 +0100 +++ blimps-3.9/blimps/util.c 2012-02-03 22:01:34.192367708 +0100 @@ -1,5 +1,6 @@ #include #include +#include #define LF 10 #define CR 13 @@ -92,7 +93,7 @@ return -1; } -int getline(char *s, int n, FILE *f) { +int blimps_getline(char *s, int n, FILE *f) { register int i=0; while(1) { Index: blimps-3.9/protomat/Makefile.Linux =================================================================== --- blimps-3.9.orig/protomat/Makefile.Linux 2012-02-03 21:58:57.400242558 +0100 +++ blimps-3.9/protomat/Makefile.Linux 2012-02-03 22:02:24.588297986 +0100 @@ -3,52 +3,65 @@ # Type "make blksort" to compile blksort program CC = gcc CFLAGS = -Wall -O2 -c -CL = gcc -LFLAGS = -lm -o +LDFLAGS = -lm -o RM = /bin/rm -f MV = /bin/mv -f +CP = cp -af + +BIN := blksort getblock getseq multimat motifj motomat uextract blosum blastdat # -install: clean all -clean: - $(RM) *.o blksort getblock getseq multimat motifj motomat uextract blosum blastdat -all: blksort getblock getseq multimat motifj motomat uextract blosum blastdat +all: $(BIN) # +install: $(BIN) + $(CP) blksort ../bin + $(CP) getblock ../bin + $(CP) getseq ../bin + $(CP) multimat ../bin + $(CP) motifj ../bin + $(CP) motomat ../bin + $(CP) uextract ../bin + $(CP) blosum ../bin + $(CP) blastdat ../bin + +clean: + $(RM) *.o $(BIN) + # blksort: Analyze results of a BLOCKS search blksort: blksort.o motmisc.o - $(CL) blksort.o motmisc.o $(LFLAGS) blksort - mv blksort ../bin + $(CC) blksort.o motmisc.o $(LDFLAGS) blksort + # getblock: Retrieve BLOCKs getblock: getblock.o motmisc.o - $(CL) getblock.o motmisc.o $(LFLAGS) getblock - mv getblock ../bin + $(CC) getblock.o motmisc.o $(LDFLAGS) getblock + # getseq: Retrieve a sequence getseq: getseq.o motmisc.o - $(CL) getseq.o motmisc.o $(LFLAGS) getseq - mv getseq ../bin + $(CC) getseq.o motmisc.o $(LDFLAGS) getseq + # multimat: Analyze results of a MATRIX search multimat: multimat.o motmisc.o - $(CL) multimat.o motmisc.o $(LFLAGS) multimat - mv multimat ../bin + $(CC) multimat.o motmisc.o $(LDFLAGS) multimat + # motifj: Make blocks using Ham Smith's motif algorithm motifj: motifj.o motmisc.o - $(CL) motifj.o motmisc.o $(LFLAGS) motifj - mv motifj ../bin + $(CC) motifj.o motmisc.o $(LDFLAGS) motifj + # motomat: Assemble blocks from motifj motomat: motomat.o motmisc.o - $(CL) motomat.o motmisc.o $(LFLAGS) motomat - mv motomat ../bin + $(CC) motomat.o motmisc.o $(LDFLAGS) motomat + # uextract: Extract protein families from prosite.dat uextract: uextract.o motmisc.o - $(CL) uextract.o motmisc.o $(LFLAGS) uextract - mv uextract ../bin + $(CC) uextract.o motmisc.o $(LDFLAGS) uextract + # blosum: Make substitution matrices from blocks blosum: blosum.o motmisc.o - $(CL) blosum.o motmisc.o $(LFLAGS) blosum - mv blosum ../bin + $(CC) blosum.o motmisc.o $(LDFLAGS) blosum + # blastdat: Read blast output blastdat: blastdat.o motmisc.o - $(CL) blastdat.o motmisc.o $(LFLAGS) blastdat - mv blastdat ../bin + $(CC) blastdat.o motmisc.o $(LDFLAGS) blastdat + # blksort.o: blksort.c motifj.h $(CC) $(CFLAGS) blksort.c Index: blimps-3.9/Makefile =================================================================== --- /dev/null 1970-01-01 00:00:00.000000000 +0000 +++ blimps-3.9/Makefile 2012-02-03 22:01:34.208367543 +0100 @@ -0,0 +1,117 @@ +PACKAGE := blimps +VERSION := 3.9 +DISTDIR := $(PACKAGE)-$(VERSION) + +BLIMPSDIR := blimps +DOCSDIR := docs +INCLUDEDIR := include +PROTOMATDIR := protomat + +MAN1POD := fastaseqs.pod +MAN1GZ := $(MAN1POD:%.pod=%.1.gz) + +libdir ?= $(prefix)/lib + +# export LD_LIBRARY_PATH=/mnt/home/lkajan/project/rostlab/blimps/blimps-3.9/blimps + +all: blimps protomat man + +blimps: + $(MAKE) -C $(BLIMPSDIR) -f Makefile.Linux VERSION=$(VERSION) + +protomat: + $(MAKE) -C $(PROTOMATDIR) -f Makefile.Linux VERSION=$(VERSION) + +man: $(MAN1GZ) + +$(MAN1GZ) : %.1.gz : %.pod + pod2man -c 'User Commands' -r "$(VERSION)" $< | gzip -c > $@ + +# The sift package does not provide fastaseqs but expects it to exist. Fortunately this package provides it. +install: install-utils install-lib-dev install-lib install-data install-doc + +install-data: + mkdir -p $(DESTDIR)$(prefix)/share/$(PACKAGE) && \ + cp -a $(DOCSDIR) \ + $(DESTDIR)$(prefix)/share/$(PACKAGE)/ + +install-utils: + mkdir -p $(DESTDIR)$(prefix)/bin && \ + cp -a $(BLIMPSDIR)/fastaseqs \ + $(DESTDIR)$(prefix)/bin/ + mkdir -p $(DESTDIR)$(prefix)/share/man/man1 && cp $(MAN1GZ) $(DESTDIR)$(prefix)/share/man/man1/ + +install-lib-dev: + mkdir -p $(DESTDIR)$(prefix)/include/$(PACKAGE) && \ + cp $(INCLUDEDIR)/*.h $(DESTDIR)$(prefix)/include/$(PACKAGE)/ + mkdir -p $(DESTDIR)$(libdir) && \ + cp -a $(BLIMPSDIR)/*.a $(BLIMPSDIR)/*.so \ + $(DESTDIR)$(libdir)/ + +install-lib: + mkdir -p $(DESTDIR)$(prefix)/lib && \ + cp -a $(BLIMPSDIR)/*.so.* \ + $(DESTDIR)$(libdir)/ + +.PHONY: install-doc +install-doc: + mkdir -p $(DESTDIR)$(prefix)/share/doc/$(PACKAGE) && \ + cp -a LICENSE README UPDATES \ + $(DESTDIR)$(prefix)/share/doc/$(PACKAGE)/ + +clean: clean-blimps clean-protomat + rm -f *.[12345678].gz + +clean-blimps: + -if [ -d $(BLIMPSDIR) ]; then $(MAKE) -C $(BLIMPSDIR) -f Makefile.Linux clean; fi + +clean-protomat: + -if [ -d $(PROTOMATDIR) ]; then $(MAKE) -C $(PROTOMATDIR) -f Makefile.Linux clean; fi + +distclean: clean + -if [ -d "$(DISTDIR)" ]; then rm -rf $(DISTDIR); fi + rm -rf \ + $(DISTDIR) \ + $(DISTDIR).tar.gz + +dist: distdir + tar chof - "$(DISTDIR)" | gzip -c >$(DISTDIR).tar.gz + rm -rf $(DISTDIR) + +distdir: + rm -rf $(DISTDIR) && mkdir -p $(DISTDIR) && \ + rsync -avCR \ + --exclude /*-stamp \ + --exclude .*.swp \ + --exclude debian \ + ChangeLog \ + Makefile \ + $(PACKAGE).spec \ + $(MAN1POD) \ + $(DISTDIR)/; + +help: + @echo "Rules:" + @echo "all*" + @echo "*blimps" + @echo "install+" + @echo "+install-data" + @echo "+install-lib" + @echo "+install-lib-dev" + @echo "+install-utils" + @echo "clean" + @echo "distclean" + @echo "dist" + @echo "help" + @echo "*man" + @echo "*protomat" + @echo + @echo "Variables:" + @echo "DESTDIR - install to DESTDIR" + @echo "prefix - common installation prefix for all files" + @echo "libdir - install libraries here, default: /$$(prefix)/lib" + @echo " use prefix=$$HOME to build for personal use" + +.PHONY: all bin clean-blimps clean diff dist distclean distdir help install install-data install-lib install-lib-dev install-utils man untar blimps protomat clean-protomat + +# vim:ai: Index: blimps-3.9/fastaseqs.pod =================================================================== --- /dev/null 1970-01-01 00:00:00.000000000 +0000 +++ blimps-3.9/fastaseqs.pod 2012-02-03 22:01:34.372247697 +0100 @@ -0,0 +1,25 @@ +=head1 NAME + +fastaseqs - converts a file of sequences to FASTA format + +=head1 SYNOPSIS + +fastaseqs + +=head1 DESCRIPTION + +fastaseqs converts a file of sequences to FASTA format. + +=head1 AUTHOR + +J. Henikoff + +=head1 COPYRIGHT AND LICENSE + +Copyright 1998, Fred Hutchinson Cancer Research Center + +Please refer to /usr/share/doc/*blimps*/copyright for the license. + +=head1 SEE ALSO + +L debian/patches/series0000644000000000000000000000001111714027425012025 0ustar patch001 debian/libblimps3-dev.install0000644000000000000000000000005511712214531013367 0ustar usr/include/* usr/lib/lib*.a usr/lib/lib*.so debian/blimps-utils.doc-base0000644000000000000000000000066111725364114013220 0ustar Document: blimps-utils Title: blocks database improved searcher Author: J. Henikoff (Fred Hutchinson Cancer Research Center) Abstract: blocks database improved searcher BLIMPS (BLocks IMProved Searcher) is a searching tool that scores a protein sequence against blocks or a block against sequences. Section: Science/Biology Format: html Files: /usr/share/doc/blimps-utils/html/* Index: /usr/share/doc/blimps-utils/html/index.html debian/rules0000755000000000000000000000056111725370715010260 0ustar #!/usr/bin/make -f # In order to make dh verbose set this to 1: # export DH_VERBOSE=1 %: dh $@ --parallel .PHONY: override_dh_auto_install override_dh_auto_install: dh_auto_install -- prefix=/usr .PHONY: override_dh_clean override_dh_clean: dh_clean blimps/deps.mk get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs debian/control0000644000000000000000000000377611725345030010606 0ustar Source: blimps Priority: extra Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Laszlo Kajan , Andreas Tille Build-Depends: debhelper (>= 8) Standards-Version: 3.9.3 Section: non-free/libs XS-Autobuild: yes Homepage: http://blocks.fhcrc.org/blocks/uploads/blimps Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/blimps/trunk Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/blimps/trunk/ Package: blimps-utils Section: non-free/science Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libblimps3 Description: blocks database improved searcher BLIMPS (BLocks IMProved Searcher) is a searching tool that scores a protein sequence against blocks or a block against sequences. . This package contains the binaries. Package: blimps-examples Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Recommends: tcsh | csh Enhances: libblimps3-dev, blimps-utils Description: blocks database improved searcher (example data) BLIMPS (BLocks IMProved Searcher) is a searching tool that scores a protein sequence against blocks or a block against sequences. . This package contains example data. Package: libblimps3-dev Section: non-free/libdevel Architecture: any Depends: ${misc:Depends}, libblimps3 (= ${binary:Version}) Suggests: blimps-utils Provides: libblimps-dev Description: blocks database improved searcher library (development) BLIMPS (BLocks IMProved Searcher) is a searching tool that scores a protein sequence against blocks or a block against sequences. . This package provides the library development headers and the static library. Package: libblimps3 Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: blimps-utils Description: blocks database improved searcher library BLIMPS (BLocks IMProved Searcher) is a searching tool that scores a protein sequence against blocks or a block against sequences. . This package provides the shared library. debian/blimps-utils.install0000644000000000000000000000013111725370652013205 0ustar blimps/fastaseqs usr/bin www/* usr/share/doc/blimps-utils/html docs usr/share/blimps debian/upstream0000644000000000000000000000060311721214374010752 0ustar Name: blimps Contact: Jorja Henikoff Homepage: http://blocks.fhcrc.org/ Reference: Author: Henikoff JG, Pietrokovski S, McCallum CM, Henikoff S. Title: 'Blocks-based methods for detecting protein homology.' Journal: Electrophoresis Volume: 21 Number: 9 Pages: 1700-6 year: 2000 URL: http://www.ncbi.nlm.nih.gov/pubmed/10870957 PMID: 10870957