[med-svn] r21126 - trunk/packages/rostlab/libzerg-perl/trunk/debian/patches
Andreas Tille
tille at moszumanska.debian.org
Mon Jan 11 15:42:08 UTC 2016
Author: tille
Date: 2016-01-11 15:42:07 +0000 (Mon, 11 Jan 2016)
New Revision: 21126
Modified:
trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/new_tokens
trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/series
Log:
Refresh patches
Modified: trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/new_tokens
===================================================================
--- trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/new_tokens 2016-01-11 15:30:01 UTC (rev 21125)
+++ trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/new_tokens 2016-01-11 15:42:07 UTC (rev 21126)
@@ -2,10 +2,8 @@
Description: added new tags to handle iterated blast
Forwarded: no
-Index: libzerg-perl-1.0.4/Zerg/Zerg.pm
-===================================================================
---- libzerg-perl-1.0.4.orig/Zerg/Zerg.pm 2006-03-07 18:00:37.000000000 +0100
-+++ libzerg-perl-1.0.4/Zerg/Zerg.pm 2011-09-22 21:44:27.000000000 +0200
+--- a/Zerg/Zerg.pm
++++ b/Zerg/Zerg.pm
@@ -1,5 +1,5 @@
-# Copyright (C) 2002 Apuã Paquola - Instituto de Química -
-# Universidade de São Paulo - Brasil
@@ -14,7 +12,7 @@
#
# 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
-@@ -37,73 +37,95 @@
+@@ -37,73 +37,95 @@ our @ISA = qw(Exporter DynaLoader);
# If you do not need this, moving things directly into @EXPORT or @EXPORT_OK
# will save memory.
our %EXPORT_TAGS = ( 'all' => [ qw(
@@ -172,7 +170,7 @@
);
our $VERSION = '1.0.4';
-@@ -209,37 +231,48 @@
+@@ -209,37 +231,48 @@ zerg_unignore_all() does zerg_unignore o
=head2 EXPORTED CONSTANTS (TOKEN CODES)
@@ -252,7 +250,7 @@
=head2 NOTES ON THE SCANNER
-@@ -312,13 +345,15 @@
+@@ -312,13 +345,15 @@ zerg_get_token_offset() may return incor
and those that are modified by the parser, namely: QUERY_LENGTH,
SUBJECT_LENGTH, EVALUE, GAPS.
@@ -270,10 +268,8 @@
=head1 SEE ALSO
-Index: libzerg-perl-1.0.4/Zerg/Zerg.xs
-===================================================================
---- libzerg-perl-1.0.4.orig/Zerg/Zerg.xs 2005-01-10 23:57:35.000000000 +0100
-+++ libzerg-perl-1.0.4/Zerg/Zerg.xs 2011-09-22 21:44:27.000000000 +0200
+--- a/Zerg/Zerg.xs
++++ b/Zerg/Zerg.xs
@@ -1,6 +1,6 @@
/*
- Copyright (C) 2002 Apuã Paquola - Instituto de Química -
@@ -283,7 +279,7 @@
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
-@@ -94,7 +94,14 @@
+@@ -94,7 +94,14 @@ constant_Q(char *name, int len, int arg)
}
switch (name[1 + 5]) {
case 'A':
@@ -299,7 +295,7 @@
#ifdef QUERY_ANNOTATION
return QUERY_ANNOTATION;
#else
-@@ -159,6 +166,45 @@
+@@ -159,6 +166,45 @@ not_there:
}
static double
@@ -345,7 +341,7 @@
constant_SC(char *name, int len, int arg)
{
if (2 + 3 > len ) {
-@@ -200,7 +246,14 @@
+@@ -200,7 +246,14 @@ constant_SU(char *name, int len, int arg
}
switch (name[2 + 6]) {
case 'A':
@@ -361,7 +357,7 @@
#ifdef SUBJECT_ANNOTATION
return SUBJECT_ANNOTATION;
#else
-@@ -270,6 +323,14 @@
+@@ -270,6 +323,14 @@ constant_S(char *name, int len, int arg)
switch (name[1 + 0]) {
case 'C':
return constant_SC(name, len, arg);
@@ -376,7 +372,7 @@
case 'U':
return constant_SU(name, len, arg);
}
-@@ -284,6 +345,13 @@
+@@ -284,6 +345,13 @@ not_there:
static double
constant_D(char *name, int len, int arg)
{
@@ -390,7 +386,7 @@
if (1 + 11 >= len ) {
errno = EINVAL;
return 0;
-@@ -380,6 +448,14 @@
+@@ -380,6 +448,14 @@ constant(char *name, int len, int arg)
goto not_there;
#endif
}
@@ -405,7 +401,7 @@
case 'D':
return constant_D(name, len, arg);
case 'E':
-@@ -392,6 +468,14 @@
+@@ -392,6 +468,14 @@ constant(char *name, int len, int arg)
goto not_there;
#endif
}
@@ -420,7 +416,7 @@
case 'I':
if (strEQ(name + 0, "IDENTITIES")) { /* removed */
#ifdef IDENTITIES
-@@ -412,8 +496,18 @@
+@@ -412,8 +496,18 @@ constant(char *name, int len, int arg)
return constant_P(name, len, arg);
case 'Q':
return constant_Q(name, len, arg);
@@ -439,10 +435,8 @@
case 'U':
if (strEQ(name + 0, "UNMATCHED")) { /* removed */
#ifdef UNMATCHED
-Index: libzerg-perl-1.0.4/Zerg/Report/Report.pm
-===================================================================
---- libzerg-perl-1.0.4.orig/Zerg/Report/Report.pm 2006-03-07 18:19:10.000000000 +0100
-+++ libzerg-perl-1.0.4/Zerg/Report/Report.pm 2011-09-23 21:25:38.141700224 +0200
+--- a/Zerg/Report/Report.pm
++++ b/Zerg/Report/Report.pm
@@ -17,6 +17,7 @@
#
package Zerg::Report;
@@ -451,7 +445,7 @@
use Zerg;
our $VERSION = '1.0.4';
-@@ -30,14 +31,10 @@
+@@ -30,14 +31,10 @@ sub new
my $file = shift;
@@ -467,7 +461,7 @@
bless $self,$class;
return $self;
-@@ -49,7 +46,7 @@
+@@ -49,7 +46,7 @@ sub getReport
my $self=shift;
@@ -476,7 +470,7 @@
my ($c,$v,$hit_counter,$hsp_counter);
-@@ -59,6 +56,8 @@
+@@ -59,6 +56,8 @@ sub getReport
while((($c, $v)= Zerg::zerg_get_token()) && $c)
{
@@ -485,7 +479,7 @@
if($c==BLAST_VERSION)
{
$blast_report->{blast_version}=$v;
-@@ -86,96 +85,104 @@
+@@ -86,96 +85,104 @@ sub getReport
$blast_report->{hits}[$hit_counter]{"subject_name"}=$v;
}
elsif($c==SUBJECT_ANNOTATION)
@@ -666,7 +660,7 @@
}
sub closeFile
-@@ -218,8 +225,9 @@
+@@ -218,8 +225,9 @@ Zerg::Report - get attributes from a BLA
foreach my $hit (@{$r->{hits}})
{
foreach my $hsp (@{$hit->{hsps}})
@@ -678,7 +672,7 @@
}
}
-@@ -227,15 +235,15 @@
+@@ -227,15 +235,15 @@ Zerg::Report - get attributes from a BLA
=head1 DESCRIPTION
@@ -700,7 +694,7 @@
Example of a data structure returned by getReport():
-@@ -245,26 +253,27 @@
+@@ -245,26 +253,27 @@ Zerg::Report - get attributes from a BLA
'byte_offset' => 4981,
'query_length' => '444',
'query_annotation' => ''
@@ -743,7 +737,7 @@
}
],
'subject_length' => '880',
-@@ -275,11 +284,13 @@
+@@ -275,11 +284,13 @@ Zerg::Report - get attributes from a BLA
=head1 AUTHORS
Modified: trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/series
===================================================================
--- trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/series 2016-01-11 15:30:01 UTC (rev 21125)
+++ trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/series 2016-01-11 15:42:07 UTC (rev 21126)
@@ -1,2 +1 @@
new_tokens
-debian-changes-1.0.4-1
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