[med-svn] r7905 - trunk/packages/rostlab/libzerg/trunk/debian/patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Thu Sep 22 17:27:23 UTC 2011
Author: lkajan-guest
Date: 2011-09-22 17:27:22 +0000 (Thu, 22 Sep 2011)
New Revision: 7905
Modified:
trunk/packages/rostlab/libzerg/trunk/debian/patches/blastpgp
Log:
ALN -> ALI in constant names for new alignment tokens (not released yet); some source formatting
Modified: trunk/packages/rostlab/libzerg/trunk/debian/patches/blastpgp
===================================================================
--- trunk/packages/rostlab/libzerg/trunk/debian/patches/blastpgp 2011-09-22 16:28:04 UTC (rev 7904)
+++ trunk/packages/rostlab/libzerg/trunk/debian/patches/blastpgp 2011-09-22 17:27:22 UTC (rev 7905)
@@ -1,7 +1,7 @@
Index: libzerg-1.0.7/zerglexer.lex
===================================================================
--- libzerg-1.0.7.orig/zerglexer.lex 2009-01-27 21:47:40.000000000 +0100
-+++ libzerg-1.0.7/zerglexer.lex 2011-09-21 15:53:22.000000000 +0200
++++ libzerg-1.0.7/zerglexer.lex 2011-09-22 19:14:02.017700383 +0200
@@ -35,10 +35,11 @@
static char _zerg_internal_buffer[INTERNAL_BUFFER_LENGTH];
static char* _zerg_description_score;
@@ -54,10 +54,10 @@
%x s_query_orientation_2
%x s_query_start
%x s_query_start_2
-+%x s_query_aln
-+%x s_query_aln_2
-+%x s_subject_aln
-+%x s_subject_aln_2
++%x s_query_ali
++%x s_query_ali_2
++%x s_subject_ali
++%x s_subject_ali_2
%x s_reference
%x s_score
%x s_score_2
@@ -252,9 +252,9 @@
- BEGIN(s_subject_end_2);
- }
+<s_query_start>[0-9]+ RET(s_query_start_2,yytext,QUERY_START);
-+<s_query_start_2>[ ]+ BEGIN(s_query_aln);
-+<s_query_aln>[[:alpha:]-]+ RET(s_query_aln_2,yytext,QUERY_ALN);
-+<s_query_aln_2>[ ]+ BEGIN(s_query_end);
++<s_query_start_2>[ ]+ BEGIN(s_query_ali);
++<s_query_ali>[[:alpha:]-]+ RET(s_query_ali_2,yytext,QUERY_ALI);
++<s_query_ali_2>[ ]+ BEGIN(s_query_end);
+<s_query_end>[0-9]+ RET(s_query_end_2,yytext,QUERY_END);
+
+%{
@@ -271,12 +271,12 @@
+[...]
+*/
+%}
-+<s_query_aln,s_query_end,s_query_end_2>\n.+\n"Sbjct:"" "+ BEGIN(s_subject_start);
++<s_query_ali,s_query_end,s_query_end_2>\n.+\n"Sbjct:"" "+ BEGIN(s_subject_start);
+<s_subject_start>[0-9]+ RET(s_subject_start_2,yytext,SUBJECT_START);
-+<s_subject_start_2>[ ]+ BEGIN(s_subject_aln);
-+<s_subject_aln>[[:alpha:]-]+ RET(s_subject_aln_2,yytext,SUBJECT_ALN);
-+<s_subject_aln_2>[ ]+ BEGIN(s_subject_end);
++<s_subject_start_2>[ ]+ BEGIN(s_subject_ali);
++<s_subject_ali>[[:alpha:]-]+ RET(s_subject_ali_2,yytext,SUBJECT_ALI);
++<s_subject_ali_2>[ ]+ BEGIN(s_subject_end);
+%{
+/* handle this:
+[...]
@@ -286,7 +286,7 @@
+[...]
+*/
+%}
-+<s_subject_aln,s_subject_end>[0-9]+ RET(s_subject_end_2,yytext,SUBJECT_END);
++<s_subject_ali,s_subject_end>[0-9]+ RET(s_subject_end_2,yytext,SUBJECT_END);
<s_subject_end_2>\n+ BEGIN(s_hsp);
@@ -392,34 +392,87 @@
Index: libzerg-1.0.7/zerg.h
===================================================================
--- libzerg-1.0.7.orig/zerg.h 2005-01-10 23:55:46.000000000 +0100
-+++ libzerg-1.0.7/zerg.h 2011-09-21 10:27:44.857737236 +0200
-@@ -6,6 +6,8 @@
++++ libzerg-1.0.7/zerg.h 2011-09-22 19:14:33.101700455 +0200
+@@ -6,37 +6,51 @@
#ifndef _zerg_h_
#define _zerg_h_
-+#define BUFFER_OVERFLOW -1
+-#define BLAST_VERSION 1 /* Esta tem que ser a primeira */
+-#define QUERY_NAME 2
+-#define QUERY_ANNOTATION 3
+-#define QUERY_LENGTH 4
+-#define NOHITS 5
+-#define DESCRIPTION_HITNAME 6
+-#define DESCRIPTION_ANNOTATION 7
+-#define DESCRIPTION_SCORE 8
+-#define DESCRIPTION_EVALUE 9
+-#define SUBJECT_NAME 10
+-#define SUBJECT_ANNOTATION 11
+-#define SUBJECT_LENGTH 12
+-#define SCORE_BITS 13
+-#define SCORE 14
+-#define EVALUE 15
+-#define IDENTITIES 16
+-#define ALIGNMENT_LENGTH 17
+-#define PERCENT_IDENTITIES 18
+-#define GAPS 19
+-#define QUERY_ORIENTATION 20
+-#define SUBJECT_ORIENTATION 21
+-#define QUERY_START 22
+-#define QUERY_END 23
+-#define SUBJECT_START 24
+-#define SUBJECT_END 25
+-#define END_OF_REPORT 26
+-#define POSITIVES 27
+-#define PERCENT_POSITIVES 28
+-#define QUERY_FRAME 29
+-#define SUBJECT_FRAME 30
+-#define UNMATCHED 31 /* Esta tem que ser a ultima */
++#define BUFFER_OVERFLOW -1
+
- #define BLAST_VERSION 1 /* Esta tem que ser a primeira */
- #define QUERY_NAME 2
- #define QUERY_ANNOTATION 3
-@@ -36,7 +38,19 @@
- #define PERCENT_POSITIVES 28
- #define QUERY_FRAME 29
- #define SUBJECT_FRAME 30
--#define UNMATCHED 31 /* Esta tem que ser a ultima */
-+#define UNMATCHED 31
-+#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 REFERENCE 40
-+#define TAIL_OF_REPORT 41
-+#define DATABASE 42
-+#define AFTER_LAST_TOKEN 43 // dummy token, must be last
++#define BLAST_VERSION 1 /* Esta tem que ser a primeira */
++#define QUERY_NAME 2
++#define QUERY_ANNOTATION 3
++#define QUERY_LENGTH 4
++#define NOHITS 5
++#define DESCRIPTION_HITNAME 6
++#define DESCRIPTION_ANNOTATION 7
++#define DESCRIPTION_SCORE 8
++#define DESCRIPTION_EVALUE 9
++#define SUBJECT_NAME 10
++#define SUBJECT_ANNOTATION 11
++#define SUBJECT_LENGTH 12
++#define SCORE_BITS 13
++#define SCORE 14
++#define EVALUE 15
++#define IDENTITIES 16
++#define ALIGNMENT_LENGTH 17
++#define PERCENT_IDENTITIES 18
++#define GAPS 19
++#define QUERY_ORIENTATION 20
++#define SUBJECT_ORIENTATION 21
++#define QUERY_START 22
++#define QUERY_END 23
++#define SUBJECT_START 24
++#define SUBJECT_END 25
++#define END_OF_REPORT 26
++#define POSITIVES 27
++#define PERCENT_POSITIVES 28
++#define QUERY_FRAME 29
++#define SUBJECT_FRAME 30
++#define UNMATCHED 31
++#define ROUND_NUMBER 32
++#define HSP_METHOD 33
++#define SEARCHING 34
++#define QUERY_ALI 35
++#define SUBJECT_ALI 36
++#define ROUND_SEQ_FOUND 37
++#define ROUND_SEQ_NEW 38
++#define CONVERGED 39
++#define REFERENCE 40
++#define TAIL_OF_REPORT 41
++#define DATABASE 42
++#define AFTER_LAST_TOKEN 43 // dummy token, must be last
#ifdef __cplusplus
extern "C" {
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