[med-svn] r7890 - trunk/packages/rostlab/libzerg/trunk/debian/patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Tue Sep 20 12:15:07 UTC 2011
Author: lkajan-guest
Date: 2011-09-20 12:15:07 +0000 (Tue, 20 Sep 2011)
New Revision: 7890
Modified:
trunk/packages/rostlab/libzerg/trunk/debian/patches/blastpgp
Log:
moved UNMATCHED macro to the end of list where it belongs; fixed concatenated blast outputs issue; ready to release
Modified: trunk/packages/rostlab/libzerg/trunk/debian/patches/blastpgp
===================================================================
--- trunk/packages/rostlab/libzerg/trunk/debian/patches/blastpgp 2011-09-20 11:45:41 UTC (rev 7889)
+++ trunk/packages/rostlab/libzerg/trunk/debian/patches/blastpgp 2011-09-20 12:15:07 UTC (rev 7890)
@@ -1,7 +1,7 @@
Index: libzerg-1.0.7/zerglexer.lex
===================================================================
---- libzerg-1.0.7.orig/zerglexer.lex 2011-09-20 11:41:20.787172941 +0200
-+++ libzerg-1.0.7/zerglexer.lex 2011-09-20 11:43:57.515178898 +0200
+--- libzerg-1.0.7.orig/zerglexer.lex 2009-01-27 21:47:40.000000000 +0100
++++ libzerg-1.0.7/zerglexer.lex 2011-09-20 13:17:02.013703173 +0200
@@ -36,9 +36,9 @@
static char* _zerg_description_score;
static char* _zerg_description_evalue;
@@ -43,16 +43,42 @@
%x s_reference
%x s_score
%x s_score_2
-@@ -186,7 +194,7 @@
+@@ -155,7 +163,7 @@
+ %x s_subject_orientation_2
+ %x s_subject_start
+ %x s_subject_start_2
+-%x s_end_of_report
++%x s_tail_of_report
+ %x s_positives
+ %x s_positives_2
+ %x s_positives_3
+@@ -167,13 +175,12 @@
+ %x s_gaps_3
+ %x s_pre_subject_name
+ %x s_pre_score
+-%x s_pre_end_of_report_1
+ %x s_pre_end_of_report_2
+ %x s_pre_end_of_report_3
+ %%
- <s_blast_version>\n+ BEGIN(s_reference);
+-<INITIAL,s_end_of_report>T?BLAST.+ {
++<INITIAL>T?BLAST.+ {
+
+ if(!strncmp(yytext,"BLASTN",6)) _zerg_blast_type=0;
+ else if(!strncmp(yytext,"BLASTP",6)) _zerg_blast_type=1;
+@@ -185,8 +192,8 @@
+ }
+
+
+-<s_blast_version>\n+ BEGIN(s_reference);
-<s_reference>"Reference:"(.+\n)+\n BEGIN(s_query_1);
-+<s_reference>(Reference(.+\n)+\n+)+ BEGIN(s_query_1);
++<s_blast_version>\n+ BEGIN(s_reference);
++<s_reference,s_query_1>Reference(.+\n)+\n+ RET(s_query_1,yytext,REFERENCE);
<s_query_1>"Query= " BEGIN(s_query_2);
<s_query_2>[^ \t\n]+ RET(s_query_3,yytext,QUERY_NAME);
-@@ -210,11 +218,13 @@
+@@ -210,11 +217,13 @@
<s_query_6>.+\n\n BEGIN(s_database);
<s_database>Database:(.+\n)+\n BEGIN(s_searching);
@@ -71,7 +97,7 @@
<s_description_annotation>.+\n {
-@@ -288,21 +298,14 @@
+@@ -288,21 +297,14 @@
<s_description_score>"~" RET(s_description_evalue,_zerg_description_score,DESCRIPTION_SCORE);
<s_description_evalue>"~" RET(s_descriptions,_zerg_description_evalue,DESCRIPTION_EVALUE);
@@ -99,7 +125,7 @@
<s_pre_subject_name>"~" RET(s_subject_name,_zerg_internal_buffer+32,SUBJECT_END);
-@@ -325,18 +328,7 @@
+@@ -325,18 +327,7 @@
<s_subject_length_2>\n+ BEGIN(s_hsp);
@@ -119,7 +145,7 @@
<s_pre_score>"~" RET(s_score,_zerg_internal_buffer+32,SUBJECT_END);
-@@ -344,13 +336,15 @@
+@@ -344,13 +335,15 @@
<s_score>[^ \t\n]+ RET(s_score_2,yytext,SCORE_BITS);
<s_score_2>" bits (" BEGIN(s_score_parentheses);
<s_score_parentheses>[0-9]+ RET(s_score_parentheses_2,yytext,SCORE);
@@ -137,7 +163,7 @@
<s_identities>[0-9]+ RET(s_identities_2,yytext,IDENTITIES);
<s_identities_2>"/" BEGIN(s_alignment_length);
<s_alignment_length>[0-9]+ RET(s_alignment_length_2,yytext,ALIGNMENT_LENGTH);
-@@ -398,62 +392,54 @@
+@@ -398,101 +391,79 @@
<s_gaps_3,s_subject_orientation_2,s_frame_5>\n+ BEGIN(s_hsp);
<s_hsp>(" "*\n)?"Query:"" "+ BEGIN(s_query_start);
@@ -151,7 +177,7 @@
- RET(s_query_start_2,yytext,QUERY_START);
- }
- }
-
+-
-<s_query_start_2>" "+[^ \t]+" "+ BEGIN(s_query_end);
-<s_query_end>[0-9]+ {
- if(!_zerg_ignore[QUERY_END])
@@ -165,7 +191,7 @@
- }
- BEGIN(s_query_end_2);
- }
--
+
-<s_query_end_2>\n.+\n"Sbjct:"" "+ BEGIN(s_subject_start);
-<s_subject_start>[0-9]+ {
- if(_zerg_have_hsp)
@@ -242,19 +268,32 @@
+<s_pre_hits,s_pre_end>[ \t\n]
- <s_pre_hits,s_pre_end>Database: RET(s_end_of_report,"",END_OF_REPORT);
-@@ -463,7 +449,7 @@
- }
-
-
+-<s_pre_hits,s_pre_end>Database: RET(s_end_of_report,"",END_OF_REPORT);
+-<s_pre_hits,s_pre_end>T?BLAST. {
+- yyless(0);
+- RET(s_end_of_report,"",END_OF_REPORT);
+- }
+-
+-
-<s_hsp>Database: { unput('~'); BEGIN(s_pre_end_of_report_1); }
-+<s_hsp>[ \t\n]+Database:(.|\n)* RET(s_end_of_report,yytext,END_OF_REPORT);
-
-
- <s_hsp>T?BLAST. {
-@@ -473,24 +459,12 @@
+-
+-
+-<s_hsp>T?BLAST. {
++<s_pre_hits,s_pre_end>Database: {
++ yyless(0);
++ BEGIN(s_tail_of_report);
++ }
++<s_pre_hits,s_pre_end,s_hsp,s_tail_of_report>T?BLAST. {
+ yyless(0);
+- unput('~');
+- BEGIN(s_pre_end_of_report_1);
++ RET(INITIAL,"",END_OF_REPORT);
}
++<s_hsp>" Database:" {
++ yyless(0);
++ BEGIN(s_tail_of_report);
++ }
-<s_pre_end_of_report_1>"~" {
- if(_zerg_have_hsp)
@@ -268,20 +307,55 @@
- {
- RET(s_end_of_report,"",END_OF_REPORT);
- }
-- }
-+<s_pre_end_of_report_1>"~" RET(s_end_of_report,"",END_OF_REPORT);
++<s_tail_of_report>.|\n {
++ RET(s_tail_of_report,yytext,TAIL_OF_REPORT)
+ }
<s_pre_end_of_report_2>"~" RET(s_pre_end_of_report_3,_zerg_internal_buffer+32,SUBJECT_END);
- <s_pre_end_of_report_3>"~" RET(s_end_of_report,"",END_OF_REPORT);
+-<s_pre_end_of_report_3>"~" RET(s_end_of_report,"",END_OF_REPORT);
++<s_pre_end_of_report_3>"~" RET(s_tail_of_report,"",END_OF_REPORT);
-<s_end_of_report>.|\n
-+<s_end_of_report>(.|\n)*
<*>.|\n RET(INITIAL,yytext,UNMATCHED);
- <INITIAL,s_end_of_report><<EOF>> _zerg_value=""; return 0;
+-<INITIAL,s_end_of_report><<EOF>> _zerg_value=""; return 0;
++<INITIAL,s_tail_of_report><<EOF>> _zerg_value=""; return 0;
-@@ -548,3 +522,5 @@
+ %%
+
+@@ -548,3 +519,5 @@
else
return pos - YY_CURRENT_BUFFER->yy_n_chars + yytext -YY_CURRENT_BUFFER->yy_ch_buf - _zerg_desconto;
}
+
+// vim:et:ts=2:
+Index: libzerg-1.0.7/zerg.h
+===================================================================
+--- libzerg-1.0.7.orig/zerg.h 2011-09-20 14:09:08.933712381 +0200
++++ libzerg-1.0.7/zerg.h 2011-09-20 14:01:35.000000000 +0200
+@@ -36,15 +36,17 @@
+ #define PERCENT_POSITIVES 28
+ #define QUERY_FRAME 29
+ #define SUBJECT_FRAME 30
+-#define UNMATCHED 31 // UNMATCHED TOKEN
+-#define ROUND_NUMBER 32
+-#define HSP_METHOD 33
+-#define SEARCHING 34
+-#define QUERY_ALN 35
+-#define SUBJECT_ALN 36
+-#define ROUND_SEQ_FOUND 37
+-#define ROUND_SEQ_NEW 38
+-#define CONVERGED 39
++#define ROUND_NUMBER 31
++#define HSP_METHOD 32
++#define SEARCHING 33
++#define QUERY_ALN 34
++#define SUBJECT_ALN 35
++#define ROUND_SEQ_FOUND 36
++#define ROUND_SEQ_NEW 37
++#define CONVERGED 38
++#define REFERENCE 39
++#define TAIL_OF_REPORT 40
++#define UNMATCHED 41 // UNMATCHED TOKEN, must be last
+
+ #ifdef __cplusplus
+ extern "C" {
More information about the debian-med-commit
mailing list