libzerg-perl/0000755000175000017500000000000007537136714012127 5ustar apuaapualibzerg-perl/Zerg/0000755000175000017500000000000010403336167013024 5ustar apuaapualibzerg-perl/Zerg/README0000644000175000017500000000242707541711134013711 0ustar apuaapuaIntroduction ============ This is the Perl module for the Zerg BLAST parsing library version 1.0. License terms ============= Copyright (C) 2002 Apuã Paquola - Instituto de Química - Universidade de São Paulo - Brasil This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program (see COPYING file); if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Installation ============ Make sure that libzerg is installed in yopur system. To install this module type the following: perl Makefile.PL make make test make install Documentation ============= After installation, type man Zerg (or perldoc Zerg). Dependencies ============ This module requires these other modules and libraries: libzerg libzerg-perl/Zerg/Report/0000755000175000017500000000000010403340331014263 5ustar apuaapualibzerg-perl/Zerg/Report/README0000644000175000017500000000172107541710666015171 0ustar apuaapuaZerg/Report version 0.01 ======================== The README is used to introduce the module and provide instructions on how to install the module, any machine dependencies it may have (for example C compilers and installed libraries) and any other information that should be provided before the module is installed. A README file is required for CPAN modules since CPAN extracts the README file from a module distribution so that people browsing the archive can use it get an idea of the modules uses. It is usually a good idea to provide version information here so that people can decide whether fixes for the module are worth downloading. INSTALLATION To install this module type the following: perl Makefile.PL make make test make install DEPENDENCIES This module requires these other modules and libraries: blah blah blah COPYRIGHT AND LICENCE Put the correct copyright and licence information here. Copyright (C) 2002 A. U. Thor blah blah blah libzerg-perl/Zerg/Report/Changes0000644000175000017500000000023407541710666015602 0ustar apuaapuaRevision history for Perl extension Zerg::Report. 0.01 Tue Sep 17 17:33:58 2002 - original version; created by h2xs 1.21 with options -X Zerg::Report libzerg-perl/Zerg/Report/test.pl0000644000175000017500000000075407541710666015632 0ustar apuaapua# Before `make install' is performed this script should be runnable with # `make test'. After `make install' it should work as `perl test.pl' ######################### # change 'tests => 1' to 'tests => last_test_to_print'; use Test; BEGIN { plan tests => 1 }; use Zerg::Report; ok(1); # If we made it this far, we're ok. ######################### # Insert your test code below, the Test module is use()ed here so read # its man page ( perldoc Test ) for help writing this test script. libzerg-perl/Zerg/Report/Makefile.PL0000644000175000017500000000076307746012347016266 0ustar apuaapuause ExtUtils::MakeMaker; # See lib/ExtUtils/MakeMaker.pm for details of how to influence # the contents of the Makefile that is written. WriteMakefile( 'NAME' => 'Zerg::Report', 'VERSION_FROM' => 'Report.pm', # finds $VERSION 'PREREQ_PM' => {}, # e.g., Module::Name => 1.1 ($] >= 5.005 ? ## Add these new keywords supported since 5.005 (ABSTRACT_FROM => 'Report.pm', # retrieve abstract from module AUTHOR => 'Abimael A. Machado ') : ()), ); libzerg-perl/Zerg/Report/Report.pm0000644000175000017500000001725410403340216016107 0ustar apuaapua# Copyright (C) 2002 Apuã Paquola, Abimael Machado - Instituto de Química - # Universidade de São Paulo - Brasil # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # package Zerg::Report; use strict; use Zerg; our $VERSION = '1.0.4'; sub new { my $self = { }; my $class = shift; my $file = shift; my $blast_report = (); Zerg::zerg_open_file($file); Zerg::zerg_unignore_all(); $self->{report} = $blast_report; bless $self,$class; return $self; } sub getReport { my $self=shift; my $blast_report = $self->{report}; my ($c,$v,$hit_counter,$hsp_counter); $hit_counter=-1; $hsp_counter=-1; while((($c, $v)= Zerg::zerg_get_token()) && $c) { if($c==BLAST_VERSION) { $blast_report->{blast_version}=$v; $blast_report->{byte_offset}=Zerg::zerg_get_token_offset(); $hit_counter=-1; } elsif($c==QUERY_NAME) { $blast_report->{query_name}=$v; } elsif($c==QUERY_ANNOTATION) { $blast_report->{query_annotation}=$v; } elsif($c==QUERY_LENGTH) { $blast_report->{query_length}=$v; } elsif($c==SUBJECT_NAME) { $hit_counter++; $hsp_counter=-1; $blast_report->{hits}[$hit_counter]{"subject_name"}=$v; } elsif($c==SUBJECT_ANNOTATION) { $blast_report->{hits}[$hit_counter]{"subject_annotation"}=$v; } elsif($c==SUBJECT_LENGTH) { $blast_report->{hits}[$hit_counter]{"subject_length"}=$v; } elsif($c==SCORE_BITS) { $hsp_counter++; $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"score_bits"}=$v; } elsif($c==SCORE) { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"score"}=$v; } elsif($c==EVALUE) { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"evalue"}=$v; } elsif($c==IDENTITIES) { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"identities"}=$v; } elsif($c==ALIGNMENT_LENGTH) { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"alignment_length"}=$v; } elsif($c==PERCENT_IDENTITIES) { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"percent_identities"}=$v; } elsif($c==GAPS) { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"gaps"}=$v; } elsif($c==QUERY_ORIENTATION) { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_orientation"}=$v; } elsif($c==SUBJECT_ORIENTATION) { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_orientation"}=$v; } elsif($c==QUERY_START) { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_start"}=$v; } elsif($c==QUERY_END) { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_end"}=$v; } elsif($c==SUBJECT_START) { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_start"}=$v; } elsif($c==SUBJECT_END) { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_end"}=$v; } elsif($c==POSITIVES) { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"positives"}=$v; } elsif($c==PERCENT_POSITIVES) { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"percent_positives"}=$v; } elsif($c==QUERY_FRAME) { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_frame"}=$v; } elsif($c==SUBJECT_FRAME) { $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_frame"}=$v; } elsif($c==UNMATCHED) { die "Syntax error in blast report\n"; } elsif($c==END_OF_REPORT) { my $r=$blast_report; $blast_report=(); return $r; } } return (); } sub closeFile { Zerg::zerg_close_file(); } 1; # Items to export into callers namespace by default. Note: do not export # names by default without a very good reason. Use EXPORT_OK instead. # Do not simply export all your public functions/methods/constants. # This allows declaration use Zerg::Report ':all'; # If you do not need this, moving things directly into @EXPORT or @EXPORT_OK # will save memory. # Preloaded methods go here. # Autoload methods go after =cut, and are processed by the autosplit program. __END__ # Below is stub documentation for your module. You better edit it! =head1 NAME Zerg::Report - get attributes from a BLAST file in a data structure =head1 SYNOPSIS use Zerg::Report; my $zerg_report = new Zerg::Report("output.blastn"); while($r=$zerg_report->getReport()) { foreach my $hit (@{$r->{hits}}) { foreach my $hsp (@{$hit->{hsps}}) { print "$r->{query_name} $hit->{subject_name} $hsp->{score_bits}\n"; } } } $zerg_report->closeFile(); =head1 DESCRIPTION Zerg::Report uses Zerg to parse a file containing multiple BLAST reports and, for each report, stores the obtained fields in a data structure made of arrays and hashes. Please consult the Zerg man page to see which fields are extracted. The method getReport() reads a BLAST report from the input file and returns a reference to a data structure like the one in the example below. When no report is found, it returns false. It dies from syntax errors in BLAST reports. Example of a data structure returned by getReport(): $r = { 'query_name' => 'ME1-0081T-R227-B12-U.G', 'blast_version' => 'BLASTX 1.3.6 [2002-03-05]', 'byte_offset' => 4981, 'query_length' => '444', 'query_annotation' => '' 'hits' => [ { 'subject_annotation' => '(NC_003210) similar to cation (calcium) transporting ATPase [Listeria monocytogenes EGD-e]', 'hsps' => [ { 'query_end' => '428', 'subject_end' => '151', 'identities' => '59', 'score' => '252', 'percent_positives' => '57', 'gaps' => '0', 'score_bits' => '101', 'alignment_length' => '142', 'evalue' => '2e-21', 'percent_identities' => '41', 'positives' => '83', 'query_start' => '3', 'subject_start' => '22', 'query_frame' => '+3' } ], 'subject_length' => '880', 'subject_name' => 'gi|16802882|ref|NP_464367.1|' }, ], }; =head1 AUTHORS Apuã Paquola , Abimael Machado IQ-USP Bioinformatics Lab =head1 SEE ALSO Zerg =cut libzerg-perl/Zerg/Report/MANIFEST0000644000175000017500000000006607541710666015443 0ustar apuaapuaChanges Makefile.PL MANIFEST README Report.pm test.pl libzerg-perl/Zerg/Changes0000644000175000017500000000103710403336167014320 0ustar apuaapuaRevision history for Perl extension Zerg. 0.01 Wed Aug 21 18:18:14 2002 - original version; created by h2xs 1.21 with options -n Zerg ../libzerg/zerg.h -L/usr/local/lib -lzerg 1.0.2 Thu Oct 23 15:52:17 BRST 2003 - Added byte offset support in Zerg::Report 1.0.3 Thu Oct 23 15:52:17 BRST 2003 - Added function zerg_close_file() - thanks to Marcos Renato Araújo 1.0.4 Tue Mar 7 13:55:51 BRT 2006 - Zerg::Report now outputs the blast_version field - thanks to Alexandre Gattiker libzerg-perl/Zerg/test.pl0000644000175000017500000000074407531001626014342 0ustar apuaapua# Before `make install' is performed this script should be runnable with # `make test'. After `make install' it should work as `perl test.pl' ######################### # change 'tests => 1' to 'tests => last_test_to_print'; use Test; BEGIN { plan tests => 1 }; use Zerg; ok(1); # If we made it this far, we're ok. ######################### # Insert your test code below, the Test module is use()ed here so read # its man page ( perldoc Test ) for help writing this test script. libzerg-perl/Zerg/Makefile.PL0000644000175000017500000000143107531003031014762 0ustar apuaapuause ExtUtils::MakeMaker; # See lib/ExtUtils/MakeMaker.pm for details of how to influence # the contents of the Makefile that is written. WriteMakefile( 'NAME' => 'Zerg', 'VERSION_FROM' => 'Zerg.pm', # finds $VERSION 'PREREQ_PM' => {}, # e.g., Module::Name => 1.1 ($] >= 5.005 ? ## Add these new keywords supported since 5.005 (ABSTRACT_FROM => 'Zerg.pm', # retrieve abstract from module AUTHOR => 'Apuã Paquola ') : ()), 'LIBS' => ['-L/usr/local/lib -lzerg'], # e.g., '-lm' 'DEFINE' => '', # e.g., '-DHAVE_SOMETHING' # Insert -I. if you add *.h files later: 'INC' => '', # e.g., '-I/usr/include/other' # Un-comment this if you add C files to link with later: # 'OBJECT' => '$(O_FILES)', # link all the C files too ); libzerg-perl/Zerg/Zerg.pm0000644000175000017500000002041610403336065014271 0ustar apuaapua# Copyright (C) 2002 Apuã Paquola - Instituto de Química - # Universidade de São Paulo - Brasil # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # package Zerg; use 5.006; use strict; use warnings; use Errno; use Carp; require Exporter; require DynaLoader; use AutoLoader; our @ISA = qw(Exporter DynaLoader); # Items to export into callers namespace by default. Note: do not export # names by default without a very good reason. Use EXPORT_OK instead. # Do not simply export all your public functions/methods/constants. # This allows declaration use Zerg ':all'; # If you do not need this, moving things directly into @EXPORT or @EXPORT_OK # will save memory. our %EXPORT_TAGS = ( 'all' => [ qw( ALIGNMENT_LENGTH BLAST_VERSION DESCRIPTION_ANNOTATION DESCRIPTION_EVALUE DESCRIPTION_HITNAME DESCRIPTION_SCORE END_OF_REPORT EVALUE GAPS IDENTITIES NOHITS PERCENT_IDENTITIES PERCENT_POSITIVES POSITIVES QUERY_ANNOTATION QUERY_END QUERY_FRAME QUERY_LENGTH QUERY_NAME QUERY_ORIENTATION QUERY_START SCORE SCORE_BITS SUBJECT_ANNOTATION SUBJECT_END SUBJECT_FRAME SUBJECT_LENGTH SUBJECT_NAME SUBJECT_ORIENTATION SUBJECT_START UNMATCHED ) ] ); our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } ); our @EXPORT = qw( ALIGNMENT_LENGTH BLAST_VERSION DESCRIPTION_ANNOTATION DESCRIPTION_EVALUE DESCRIPTION_HITNAME DESCRIPTION_SCORE END_OF_REPORT EVALUE GAPS IDENTITIES NOHITS PERCENT_IDENTITIES PERCENT_POSITIVES POSITIVES QUERY_ANNOTATION QUERY_END QUERY_FRAME QUERY_LENGTH QUERY_NAME QUERY_ORIENTATION QUERY_START SCORE SCORE_BITS SUBJECT_ANNOTATION SUBJECT_END SUBJECT_FRAME SUBJECT_LENGTH SUBJECT_NAME SUBJECT_ORIENTATION SUBJECT_START UNMATCHED ); our $VERSION = '1.0.4'; sub AUTOLOAD { # This AUTOLOAD is used to 'autoload' constants from the constant() # XS function. If a constant is not found then control is passed # to the AUTOLOAD in AutoLoader. my $constname; our $AUTOLOAD; ($constname = $AUTOLOAD) =~ s/.*:://; croak "& not defined" if $constname eq 'constant'; my $val = constant($constname, @_ ? $_[0] : 0); if ($! != 0) { if ($!{EINVAL}) { $AutoLoader::AUTOLOAD = $AUTOLOAD; goto &AutoLoader::AUTOLOAD; } else { croak "Your vendor has not defined Zerg macro $constname"; } } { no strict 'refs'; # Fixed between 5.005_53 and 5.005_61 *$AUTOLOAD = sub { $val }; } goto &$AUTOLOAD; } bootstrap Zerg $VERSION; # Preloaded methods go here. # Autoload methods go after =cut, and are processed by the autosplit program. 1; __END__ # Below is stub documentation for your module. You better edit it! =head1 NAME Zerg - a lexical scanner for BLAST reports. =head1 SYNOPSIS use Zerg; =head1 DESCRIPTION This manpage describes the Zerg library and its interface for use with Perl. The Zerg library contains a C/flex lexical scanner for BLAST reports and a set of supporting functions. It is centered on a "get_token" function that scans the input for specified lexical elements and, when one is found, returns its code and value to the user. It is intended to be fast: for that we used flex, which provides simple regular expression matching and input buffering in the generated C scanner. And it is intended to be simple in the sense of providing just a lexical scanner, with no features whose support could slow down its main function. =head2 FUNCTIONS zerg_get_token() is the core function of this module. Each time it is called, it scans the input BLAST report for the next "interesting" lexical element and returns its code and value. Codes are listed in the section "EXPORTED CONSTANTS (TOKEN CODES)". Code zero (not listed) means end of file. ($code, $value) = Zerg::zerg_get_token(); zerg_open_file($filename) opens $filename in read-only mode and set it as the input to the scanner. If this function is not called, the standard input is used. Zerg::zerg_open_file($filename); zerg_close_file() closes the file opened with zerg_open_file(). zerg_get_token_offset() returns the byte offset (relative to the beginning of file) of the last token read. (See section BUGS). zerg_ignore($code) instructs zerg_get_token not to return when it finds a token with code $code. zerg_ignore_all() does zerg_ignore on all token codes. zerg_unignore($code) instructs zerg_get_token to return when it finds a token with code $code. zerg_unignore_all() does zerg_unignore on all token codes. Example: Zerg::zerg_ignore_all(); Zerg::zerg_unignore(QUERY_NAME); Zerg::zerg_unignore(SUBJECT_NAME); =head2 EXPORTED CONSTANTS (TOKEN CODES) ALIGNMENT_LENGTH BLAST_VERSION DESCRIPTION_ANNOTATION DESCRIPTION_EVALUE DESCRIPTION_HITNAME DESCRIPTION_SCORE END_OF_REPORT EVALUE GAPS IDENTITIES NOHITS PERCENT_IDENTITIES PERCENT_POSITIVES POSITIVES QUERY_ANNOTATION QUERY_END QUERY_FRAME QUERY_LENGTH QUERY_NAME QUERY_ORIENTATION QUERY_START SCORE SCORE_BITS SUBJECT_ANNOTATION SUBJECT_END SUBJECT_FRAME SUBJECT_LENGTH SUBJECT_NAME SUBJECT_ORIENTATION SUBJECT_START UNMATCHED =head2 NOTES ON THE SCANNER Some BLAST parsers rely on some simple regular expression matches to conclude about token types and values. For example: an input line matching /^Query=\s(\S+)/ should make such a "loose" parser to infer that a token was found, it is a query name and its value is $1. Although improbable, it is perfectly possible for an anotation field to match /^Query=\s(\S+)/. Worse than this is the fact that those parsers are often unable to detect corrupt or truncated BLAST reports, possibly producing inaccurate information. The scanner provided by this library is much more stringent: for a token to match it must be in its place in the context of a BLAST report. For example: in a single BLAST report, a QUERY_NAME cannot follow another QUERY_NAME. The scanner can be thought as, and in fact it is, a big regular expression that matches an entire BLAST report. A special token code (UNMATCHED) is provided for cases in which the input text does not match any other lexical rule of the scanner. When an umnacthed character is found, either the report is corrupt or the scanner has a bug. If you are interested in only a few token codes, try to zerg_ignore() as much codes you can. This will avoid unnecessary function calls that eat a lot of CPU. =head1 EXAMPLES This program prints the code and the value of each token it finds. #!/usr/bin/perl -w use strict; use Zerg; my ($code, $value); while((($code, $value)= Zerg::zerg_get_token()) && $code) { print "$code\t$value\n"; } The program below is a "syntax checker". The presence of UNMATCHEDs is a strong indicator of problems in the BLAST report. (See section NOTES ON THE SCANNER) #!/usr/bin/perl -w use strict; use Zerg; my ($code, $value); Zerg::zerg_ignore_all(); Zerg::zerg_unignore(UNMATCHED); while((($code, $value)= Zerg::zerg_get_token()) && $code) { print "UNMATCHED CHAR:\t$value\n"; } =head1 BUGS The tokens DESCRIPTION_ANNOTATION, DESCRIPTION_SCORE and DESCRIPTION_EVALUE are scanned all at once and released one by one on user request. So, if the user wants to get any of these fields, they must be unignored BEFORE scanning DESCRIPTION_ANNOTATION. zerg_get_token_offset() may return incorrect values for these tokens and those that are modified by the parser, namely: QUERY_LENGTH, SUBJECT_LENGTH, EVALUE, GAPS. =head1 TO DO Add more tokens to the scanner as the need for that appears. =head1 AUTHOR Apuã Paquola, IQ-USP Bioinformatics Lab, apua@iq.usp.br =head1 SEE ALSO perl(1), flex(1), http://www.bioperl.org, http://www.ncbi.nlm.nih.gov/BLAST =cut libzerg-perl/Zerg/Zerg.xs0000644000175000017500000002132710170604137014310 0ustar apuaapua/* Copyright (C) 2002 Apuã Paquola - Instituto de Química - Universidade de São Paulo - Brasil This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */ #include "EXTERN.h" #include "perl.h" #include "XSUB.h" #include static int not_here(char *s) { croak("%s not implemented on this architecture", s); return -1; } static double constant_PE(char *name, int len, int arg) { if (2 + 6 >= len ) { errno = EINVAL; return 0; } switch (name[2 + 6]) { case 'I': if (strEQ(name + 2, "RCENT_IDENTITIES")) { /* PE removed */ #ifdef PERCENT_IDENTITIES return PERCENT_IDENTITIES; #else goto not_there; #endif } case 'P': if (strEQ(name + 2, "RCENT_POSITIVES")) { /* PE removed */ #ifdef PERCENT_POSITIVES return PERCENT_POSITIVES; #else goto not_there; #endif } } errno = EINVAL; return 0; not_there: errno = ENOENT; return 0; } static double constant_P(char *name, int len, int arg) { switch (name[1 + 0]) { case 'E': return constant_PE(name, len, arg); case 'O': if (strEQ(name + 1, "OSITIVES")) { /* P removed */ #ifdef POSITIVES return POSITIVES; #else goto not_there; #endif } } errno = EINVAL; return 0; not_there: errno = ENOENT; return 0; } static double constant_Q(char *name, int len, int arg) { if (1 + 5 >= len ) { errno = EINVAL; return 0; } switch (name[1 + 5]) { case 'A': if (strEQ(name + 1, "UERY_ANNOTATION")) { /* Q removed */ #ifdef QUERY_ANNOTATION return QUERY_ANNOTATION; #else goto not_there; #endif } case 'E': if (strEQ(name + 1, "UERY_END")) { /* Q removed */ #ifdef QUERY_END return QUERY_END; #else goto not_there; #endif } case 'F': if (strEQ(name + 1, "UERY_FRAME")) { /* Q removed */ #ifdef QUERY_FRAME return QUERY_FRAME; #else goto not_there; #endif } case 'L': if (strEQ(name + 1, "UERY_LENGTH")) { /* Q removed */ #ifdef QUERY_LENGTH return QUERY_LENGTH; #else goto not_there; #endif } case 'N': if (strEQ(name + 1, "UERY_NAME")) { /* Q removed */ #ifdef QUERY_NAME return QUERY_NAME; #else goto not_there; #endif } case 'O': if (strEQ(name + 1, "UERY_ORIENTATION")) { /* Q removed */ #ifdef QUERY_ORIENTATION return QUERY_ORIENTATION; #else goto not_there; #endif } case 'S': if (strEQ(name + 1, "UERY_START")) { /* Q removed */ #ifdef QUERY_START return QUERY_START; #else goto not_there; #endif } } errno = EINVAL; return 0; not_there: errno = ENOENT; return 0; } static double constant_SC(char *name, int len, int arg) { if (2 + 3 > len ) { errno = EINVAL; return 0; } switch (name[2 + 3]) { case '\0': if (strEQ(name + 2, "ORE")) { /* SC removed */ #ifdef SCORE return SCORE; #else goto not_there; #endif } case '_': if (strEQ(name + 2, "ORE_BITS")) { /* SC removed */ #ifdef SCORE_BITS return SCORE_BITS; #else goto not_there; #endif } } errno = EINVAL; return 0; not_there: errno = ENOENT; return 0; } static double constant_SU(char *name, int len, int arg) { if (2 + 6 >= len ) { errno = EINVAL; return 0; } switch (name[2 + 6]) { case 'A': if (strEQ(name + 2, "BJECT_ANNOTATION")) { /* SU removed */ #ifdef SUBJECT_ANNOTATION return SUBJECT_ANNOTATION; #else goto not_there; #endif } case 'E': if (strEQ(name + 2, "BJECT_END")) { /* SU removed */ #ifdef SUBJECT_END return SUBJECT_END; #else goto not_there; #endif } case 'F': if (strEQ(name + 2, "BJECT_FRAME")) { /* SU removed */ #ifdef SUBJECT_FRAME return SUBJECT_FRAME; #else goto not_there; #endif } case 'L': if (strEQ(name + 2, "BJECT_LENGTH")) { /* SU removed */ #ifdef SUBJECT_LENGTH return SUBJECT_LENGTH; #else goto not_there; #endif } case 'N': if (strEQ(name + 2, "BJECT_NAME")) { /* SU removed */ #ifdef SUBJECT_NAME return SUBJECT_NAME; #else goto not_there; #endif } case 'O': if (strEQ(name + 2, "BJECT_ORIENTATION")) { /* SU removed */ #ifdef SUBJECT_ORIENTATION return SUBJECT_ORIENTATION; #else goto not_there; #endif } case 'S': if (strEQ(name + 2, "BJECT_START")) { /* SU removed */ #ifdef SUBJECT_START return SUBJECT_START; #else goto not_there; #endif } } errno = EINVAL; return 0; not_there: errno = ENOENT; return 0; } static double constant_S(char *name, int len, int arg) { switch (name[1 + 0]) { case 'C': return constant_SC(name, len, arg); case 'U': return constant_SU(name, len, arg); } errno = EINVAL; return 0; not_there: errno = ENOENT; return 0; } static double constant_D(char *name, int len, int arg) { if (1 + 11 >= len ) { errno = EINVAL; return 0; } switch (name[1 + 11]) { case 'A': if (strEQ(name + 1, "ESCRIPTION_ANNOTATION")) { /* D removed */ #ifdef DESCRIPTION_ANNOTATION return DESCRIPTION_ANNOTATION; #else goto not_there; #endif } case 'E': if (strEQ(name + 1, "ESCRIPTION_EVALUE")) { /* D removed */ #ifdef DESCRIPTION_EVALUE return DESCRIPTION_EVALUE; #else goto not_there; #endif } case 'H': if (strEQ(name + 1, "ESCRIPTION_HITNAME")) { /* D removed */ #ifdef DESCRIPTION_HITNAME return DESCRIPTION_HITNAME; #else goto not_there; #endif } case 'S': if (strEQ(name + 1, "ESCRIPTION_SCORE")) { /* D removed */ #ifdef DESCRIPTION_SCORE return DESCRIPTION_SCORE; #else goto not_there; #endif } } errno = EINVAL; return 0; not_there: errno = ENOENT; return 0; } static double constant_E(char *name, int len, int arg) { switch (name[1 + 0]) { case 'N': if (strEQ(name + 1, "ND_OF_REPORT")) { /* E removed */ #ifdef END_OF_REPORT return END_OF_REPORT; #else goto not_there; #endif } case 'V': if (strEQ(name + 1, "VALUE")) { /* E removed */ #ifdef EVALUE return EVALUE; #else goto not_there; #endif } } errno = EINVAL; return 0; not_there: errno = ENOENT; return 0; } static double constant(char *name, int len, int arg) { errno = 0; switch (name[0 + 0]) { case 'A': if (strEQ(name + 0, "ALIGNMENT_LENGTH")) { /* removed */ #ifdef ALIGNMENT_LENGTH return ALIGNMENT_LENGTH; #else goto not_there; #endif } case 'B': if (strEQ(name + 0, "BLAST_VERSION")) { /* removed */ #ifdef BLAST_VERSION return BLAST_VERSION; #else goto not_there; #endif } case 'D': return constant_D(name, len, arg); case 'E': return constant_E(name, len, arg); case 'G': if (strEQ(name + 0, "GAPS")) { /* removed */ #ifdef GAPS return GAPS; #else goto not_there; #endif } case 'I': if (strEQ(name + 0, "IDENTITIES")) { /* removed */ #ifdef IDENTITIES return IDENTITIES; #else goto not_there; #endif } case 'N': if (strEQ(name + 0, "NOHITS")) { /* removed */ #ifdef NOHITS return NOHITS; #else goto not_there; #endif } case 'P': return constant_P(name, len, arg); case 'Q': return constant_Q(name, len, arg); case 'S': return constant_S(name, len, arg); case 'U': if (strEQ(name + 0, "UNMATCHED")) { /* removed */ #ifdef UNMATCHED return UNMATCHED; #else goto not_there; #endif } } errno = EINVAL; return 0; not_there: errno = ENOENT; return 0; } MODULE = Zerg PACKAGE = Zerg double constant(sv,arg) PROTOTYPE: DISABLE PREINIT: STRLEN len; INPUT: SV * sv char * s = SvPV(sv, len); int arg CODE: RETVAL = constant(s,len,arg); OUTPUT: RETVAL void zerg_open_file(filename) char* filename CODE: zerg_open_file(filename); void zerg_close_file() CODE: zerg_close_file(); void zerg_ignore(code) int code CODE: zerg_ignore(code); void zerg_ignore_all() CODE: zerg_ignore_all(); void zerg_unignore(code) int code CODE: zerg_unignore(code); void zerg_unignore_all() CODE: zerg_unignore_all(); void zerg_get_token() PPCODE: int c; char *v; zerg_get_token(&c, &v); XPUSHs(sv_2mortal(newSViv(c))); XPUSHs(sv_2mortal(newSVpv(v,0))); int zerg_get_token_offset() CODE: RETVAL=zerg_get_token_offset(); OUTPUT: RETVAL libzerg-perl/Zerg/COPYING0000644000175000017500000004311007537141153014061 0ustar apuaapua GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. 8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Library General Public License instead of this License. libzerg-perl/Zerg/MANIFEST0000644000175000017500000000007407531001626014153 0ustar apuaapuaChanges Makefile.PL MANIFEST README test.pl Zerg.pm Zerg.xs