[med-svn] r2242 - trunk/packages/emboss/trunk/debian/patches
plessy at alioth.debian.org
plessy at alioth.debian.org
Wed Jul 16 06:54:47 UTC 2008
Author: plessy
Date: 2008-07-16 06:54:46 +0000 (Wed, 16 Jul 2008)
New Revision: 2242
Removed:
trunk/packages/emboss/trunk/debian/patches/clustalw2-fix.patch
trunk/packages/emboss/trunk/debian/patches/patch-1-9
Modified:
trunk/packages/emboss/trunk/debian/patches/series
trunk/packages/emboss/trunk/debian/patches/using-pager-in-tfm.patch
Log:
Deleted patches integrated in the 6.0.0 release and documented the tfm patch.
Deleted: trunk/packages/emboss/trunk/debian/patches/clustalw2-fix.patch
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/clustalw2-fix.patch 2008-07-16 06:48:32 UTC (rev 2241)
+++ trunk/packages/emboss/trunk/debian/patches/clustalw2-fix.patch 2008-07-16 06:54:46 UTC (rev 2242)
@@ -1,25 +0,0 @@
-This patch allows to use versions of clustalw >= 2.0.
-(See http://lists.open-bio.org/pipermail/emboss/2008-April/003275.html )
-Index: EMBOSS-5.0.0/emboss/emma.c
-===================================================================
---- EMBOSS-5.0.0.orig/emboss/emma.c
-+++ EMBOSS-5.0.0/emboss/emma.c
-@@ -176,12 +176,12 @@
- dna_matrix = ajAcdGetListSingle( "dnamatrix");
- m2c = ajStrGetCharFirst(dna_matrix);
-
-- if(m2c=='b')
-- ajStrAssignC(&m2str,"iub");
-- else if(m2c=='p')
-- ajStrAssignC(&m2str,"clustalw");
-- else if(m2c=='g')
-- ajStrAssignC(&m2str,"own");
-+ if(m2c=='i')
-+ ajStrAssignC(&m2str,"iub");
-+ else if(m2c=='c')
-+ ajStrAssignC(&m2str,"clustalw");
-+ else if(m2c=='o')
-+ ajStrAssignC(&m2str,"own");
-
-
- ma_matrix = ajAcdGetInfile("mamatrixfile");
Deleted: trunk/packages/emboss/trunk/debian/patches/patch-1-9
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/patch-1-9 2008-07-16 06:48:32 UTC (rev 2241)
+++ trunk/packages/emboss/trunk/debian/patches/patch-1-9 2008-07-16 06:54:46 UTC (rev 2242)
@@ -1,2367 +0,0 @@
-This patch was downloaded from:
-ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-3.gz
-
-Explanations for the changes are pasted from:
-ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README.fixes
-
-Fix 1. EMBOSS-5.0.0/emboss/psiphi.c
-
-27 Jul 2007: Fixes a problem with reading more recent CCF files.
- Error traps cases where chains have no atom information.
-
-Fix 2. EMBOSS-5.0.0/ajax/ajindex.c
-
-9 Jan 2008: Fixes rare secondary index problem with input files over 2Gb.
-
-Fix 3. EMBOSS-5.0.0/nucleus/embindex.c
-
-18 Jan 2008: Order and fill fixes to sort out potential problems
- with kw/de/tx indexes.
-
-Fix 4. EMBOSS-5.0.0/ajax/ajseqdb.c
-
-19 Feb 2008: Fixes changed ID format in GCG databases.
- Fixes reading from PIR databases
-
-Fix 5. EMBOSS-5.0.0/ajax/ajseqtype.c
-
-19 Feb 2008: Fixes a problem with O in protein sequences for pyrrolysine.
- Lower case o worked, but upper case O was excluded as a
- gap character in early versions of PHYLIP. 'O' is no
- longer a gap character in EMBOSS.
-
-Fix 6. EMBOSS-5.0.0/ajax/ajseqwrite.c
-
-19 Feb 2008: Fixes a problem in GENBANK output format for mulitple
- lines of ACCESSION or KEYWORD records in an entry.
-
-Fix 7. EMBOSS-5.0.0/ajax/ajseqread.c
-
-19 Feb 2008: Fixes a problem in reading protein sequences from the
- Staden "spin" interface. The partial EMBL/SwissProt
- format was set to "nucleotide". All incomplete
- EMBL/SwissProt entries are now tested for amino acid
- characters and set to protein if any non-nucleotide
- characters are found.
-
-
-Fix 8. EMBOSS-5.0.0/emboss/dbxfasta.c
-
-19 Feb 2008: Fixes tokens that are longer than the maximum length in
- the resource definition.
- For IDs issues a warning when any ID is truncated.
-
-
-Fix 9. EMBOSS-5.0.0/nucleus/embindex.c
- EMBOSS-5.0.0/ajax/ajindex.c
- EMBOSS-5.0.0/ajax/ajindex.h
-
-6 Mar 2008: Fixes failure on some databases if the PAGESIZE was set large
- and the CACHESIZE was set small. Platform-independence
- modifications added.
-
-
-diff -c -N --recursive EMBOSS-5.0.0old/ajax/ajindex.c EMBOSS-5.0.0/ajax/ajindex.c
-*** EMBOSS-5.0.0old/ajax/ajindex.c 2007-07-06 13:18:48.000000000 +0100
---- EMBOSS-5.0.0/ajax/ajindex.c 2008-03-06 10:15:13.000000000 +0000
-***************
-*** 1364,1370 ****
- {
- id = bucket->Ids[i];
- len = BT_BUCKIDLEN(id->id);
-! if((lptr-buf+1)+len > cache->pagesize) /* overflow */
- {
- ajDebug("WriteBucket: Overflow\n");
- if(!overflow) /* No overflow buckets yet */
---- 1364,1370 ----
- {
- id = bucket->Ids[i];
- len = BT_BUCKIDLEN(id->id);
-! if((lptr-buf+1) + (len+1+BT_DDOFFROFF) > cache->pagesize) /* overflow */
- {
- ajDebug("WriteBucket: Overflow\n");
- if(!overflow) /* No overflow buckets yet */
-***************
-*** 1986,1991 ****
---- 1986,1994 ----
- ajlong blockno = 0L;
- ajlong rblockno = 0L;
- ajlong lblockno = 0L;
-+ ajlong ibn = 0L;
-+
-+
- AjPStr mediankey = NULL;
- ajlong medianless = 0L;
- ajlong mediangtr = 0L;
-***************
-*** 2139,2148 ****
- }
-
-
-! ipage = rpage;
- if(strcmp(key->Ptr,mediankey->Ptr)<0)
-! ipage = lpage;
-
- btreeInsertNonFull(cache,ipage,key,less,greater);
-
-
---- 2142,2153 ----
- }
-
-
-! ibn = rblockno;
- if(strcmp(key->Ptr,mediankey->Ptr)<0)
-! ibn = lblockno;
-
-+ ipage = ajBtreeCacheRead(cache,ibn);
-+
- btreeInsertNonFull(cache,ipage,key,less,greater);
-
-
-***************
-*** 2516,2522 ****
-
- static ajint btreeNumIdCompare(const void *a, const void *b)
- {
-! return (*(AjPBtNumId const *)a)->offset - (*(AjPBtNumId const *)b)->offset;
- }
-
-
---- 2521,2534 ----
-
- static ajint btreeNumIdCompare(const void *a, const void *b)
- {
-! ajlong val;
-!
-! val = (*(AjPBtNumId const *)a)->offset - (*(AjPBtNumId const *)b)->offset;
-!
-! if(!val)
-! return 0;
-!
-! return (val < 0L) ? -1 : 1;
- }
-
-
-***************
-*** 9895,9901 ****
-
- /* @funcstatic btreeInsertKeySec *****************************************
- **
-! ** Insert a secpndary key into a potentially full node
- **
- ** @param [u] cache [AjPBtcache] cache
- ** @param [u] page [AjPBtpage] original page
---- 9907,9913 ----
-
- /* @funcstatic btreeInsertKeySec *****************************************
- **
-! ** Insert a secondary key into a potentially full node
- **
- ** @param [u] cache [AjPBtcache] cache
- ** @param [u] page [AjPBtpage] original page
-***************
-*** 9936,9942 ****
- ajlong blockno = 0L;
- ajlong rblockno = 0L;
- ajlong lblockno = 0L;
-!
- AjPStr mediankey = NULL;
- ajlong medianless = 0L;
- ajlong mediangtr = 0L;
---- 9948,9955 ----
- ajlong blockno = 0L;
- ajlong rblockno = 0L;
- ajlong lblockno = 0L;
-! ajlong ibn = 0L;
-!
- AjPStr mediankey = NULL;
- ajlong medianless = 0L;
- ajlong mediangtr = 0L;
-***************
-*** 10090,10099 ****
- }
-
-
-! ipage = rpage;
- if(strcmp(key->Ptr,mediankey->Ptr)<0)
-! ipage = lpage;
-
- btreeInsertNonFullSec(cache,ipage,key,less,greater);
-
-
---- 10103,10114 ----
- }
-
-
-! ibn = rblockno;
- if(strcmp(key->Ptr,mediankey->Ptr)<0)
-! ibn = lblockno;
-
-+ ipage = ajBtreeCacheRead(cache,ibn);
-+
- btreeInsertNonFullSec(cache,ipage,key,less,greater);
-
-
-***************
-*** 10258,10264 ****
- btreeWriteNode(cache,spage,kSarray,pSarray,skeys);
- btreeWriteNode(cache,tpage,kTarray,pTarray,tkeys);
- btreeWriteNode(cache,ppage,kParray,pParray,pkeys);
-! if(!ppage->pageno)
- ppage->dirty = BT_LOCK;
-
- i = 0;
---- 10273,10279 ----
- btreeWriteNode(cache,spage,kSarray,pSarray,skeys);
- btreeWriteNode(cache,tpage,kTarray,pTarray,tkeys);
- btreeWriteNode(cache,ppage,kParray,pParray,pkeys);
-! if(ppage->pageno == cache->secrootblock)
- ppage->dirty = BT_LOCK;
-
- i = 0;
-***************
-*** 10355,10361 ****
- btreeWriteNode(cache,spage,kSarray,pSarray,skeys);
- btreeWriteNode(cache,tpage,kTarray,pTarray,tkeys);
- btreeWriteNode(cache,ppage,kParray,pParray,pkeys);
-! if(!ppage->pageno)
- ppage->dirty = BT_LOCK;
-
- i = 0;
---- 10370,10376 ----
- btreeWriteNode(cache,spage,kSarray,pSarray,skeys);
- btreeWriteNode(cache,tpage,kTarray,pTarray,tkeys);
- btreeWriteNode(cache,ppage,kParray,pParray,pkeys);
-! if(ppage->pageno == cache->secrootblock)
- ppage->dirty = BT_LOCK;
-
- i = 0;
-***************
-*** 10668,10674 ****
- btreeWriteNode(cache,spage,kSarray,pSarray,skeys);
- btreeWriteNode(cache,tpage,kTarray,pTarray,tkeys);
- btreeWriteNode(cache,ppage,kParray,pParray,pkeys);
-! if(!ppage->pageno)
- ppage->dirty = BT_LOCK;
-
- page = ajBtreeCacheRead(cache,pSarray[skeys]);
---- 10683,10689 ----
- btreeWriteNode(cache,spage,kSarray,pSarray,skeys);
- btreeWriteNode(cache,tpage,kTarray,pTarray,tkeys);
- btreeWriteNode(cache,ppage,kParray,pParray,pkeys);
-! if(ppage->pageno == cache->secrootblock)
- ppage->dirty = BT_LOCK;
-
- page = ajBtreeCacheRead(cache,pSarray[skeys]);
-***************
-*** 10726,10732 ****
- btreeWriteNode(cache,spage,kSarray,pSarray,skeys);
- btreeWriteNode(cache,tpage,kTarray,pTarray,tkeys);
- btreeWriteNode(cache,ppage,kParray,pParray,pkeys);
-! if(!ppage->pageno)
- ppage->dirty = BT_LOCK;
-
- page = ajBtreeCacheRead(cache,pSarray[0]);
---- 10741,10747 ----
- btreeWriteNode(cache,spage,kSarray,pSarray,skeys);
- btreeWriteNode(cache,tpage,kTarray,pTarray,tkeys);
- btreeWriteNode(cache,ppage,kParray,pParray,pkeys);
-! if(ppage->pageno == cache->secrootblock)
- ppage->dirty = BT_LOCK;
-
- page = ajBtreeCacheRead(cache,pSarray[0]);
-***************
-*** 11956,11963 ****
-
- static ajint btreeOffsetCompare(const void *a, const void *b)
- {
-! return (*(AjPBtId const *)a)->offset -
-! (*(AjPBtId const *)b)->offset;
- }
-
-
---- 11971,11984 ----
-
- static ajint btreeOffsetCompare(const void *a, const void *b)
- {
-! ajlong val;
-!
-! val = (*(AjPBtId const *)a)->offset - (*(AjPBtId const *)b)->offset;
-!
-! if(!val)
-! return 0;
-!
-! return (val < 0L) ? -1 : 1;
- }
-
-
-***************
-*** 13386,13391 ****
---- 13407,13414 ----
- ajlong blockno = 0L;
- ajlong rblockno = 0L;
- ajlong lblockno = 0L;
-+ ajlong ibn = 0L;
-+
- AjPStr mediankey = NULL;
- ajlong medianless = 0L;
- ajlong mediangtr = 0L;
-***************
-*** 13534,13546 ****
- }
-
-
-! ipage = rpage;
- if(strcmp(key->Ptr,mediankey->Ptr)<0)
-! ipage = lpage;
-
- lpage->dirty = BT_DIRTY;
- rpage->dirty = BT_DIRTY;
-
- btreeInsertNonFull(cache,ipage,key,less,greater);
-
-
---- 13557,13571 ----
- }
-
-
-! ibn = rblockno;
- if(strcmp(key->Ptr,mediankey->Ptr)<0)
-! ibn = lblockno;
-
- lpage->dirty = BT_DIRTY;
- rpage->dirty = BT_DIRTY;
-
-+ ipage = ajBtreeCacheRead(cache,ibn);
-+
- btreeInsertNonFull(cache,ipage,key,less,greater);
-
-
-***************
-*** 15020,15025 ****
---- 15045,15052 ----
- ajlong blockno = 0L;
- ajlong rblockno = 0L;
- ajlong lblockno = 0L;
-+ ajlong ibn = 0L;
-+
- ajlong mediankey = 0L;
- ajlong medianless = 0L;
- ajlong mediangtr = 0L;
-***************
-*** 15162,15173 ****
- }
-
-
-! ipage = rpage;
- if(key < mediankey)
-! ipage = lpage;
-
- lpage->dirty = BT_DIRTY;
- rpage->dirty = BT_DIRTY;
-
- btreeNumInsertNonFull(cache,ipage,key,less,greater);
-
---- 15189,15202 ----
- }
-
-
-! ibn = rblockno;
- if(key < mediankey)
-! ibn = lblockno;
-
- lpage->dirty = BT_DIRTY;
- rpage->dirty = BT_DIRTY;
-+
-+ ipage = ajBtreeCacheRead(cache,ibn);
-
- btreeNumInsertNonFull(cache,ipage,key,less,greater);
-
-***************
-*** 15502,15508 ****
- btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
- btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
- btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
-! if(!ppage->pageno)
- ppage->dirty = BT_LOCK;
-
- page = ajBtreeCacheRead(cache,pSarray[skeys]);
---- 15531,15537 ----
- btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
- btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
- btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
-! if(ppage->pageno == cache->secrootblock)
- ppage->dirty = BT_LOCK;
-
- page = ajBtreeCacheRead(cache,pSarray[skeys]);
-***************
-*** 15551,15557 ****
- btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
- btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
- btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
-! if(!ppage->pageno)
- ppage->dirty = BT_LOCK;
-
- page = ajBtreeCacheRead(cache,pSarray[0]);
---- 15580,15586 ----
- btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
- btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
- btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
-! if(ppage->pageno == cache->secrootblock)
- ppage->dirty = BT_LOCK;
-
- page = ajBtreeCacheRead(cache,pSarray[0]);
-***************
-*** 15727,15733 ****
- btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
- btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
- btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
-! if(!ppage->pageno)
- ppage->dirty = BT_LOCK;
-
- i = 0;
---- 15756,15762 ----
- btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
- btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
- btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
-! if(ppage->pageno == cache->secrootblock)
- ppage->dirty = BT_LOCK;
-
- i = 0;
-***************
-*** 15817,15823 ****
- btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
- btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
- btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
-! if(!ppage->pageno)
- ppage->dirty = BT_LOCK;
-
- i = 0;
---- 15846,15852 ----
- btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
- btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
- btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
-! if(ppage->pageno == cache->secrootblock)
- ppage->dirty = BT_LOCK;
-
- i = 0;
-diff -c -N --recursive EMBOSS-5.0.0old/ajax/ajindex.h EMBOSS-5.0.0/ajax/ajindex.h
-*** EMBOSS-5.0.0old/ajax/ajindex.h 2007-07-11 17:07:25.000000000 +0100
---- EMBOSS-5.0.0/ajax/ajindex.h 2008-03-06 10:15:22.000000000 +0000
-***************
-*** 38,43 ****
---- 38,103 ----
- #define TX_EXTENSION "xtx"
-
-
-+ /* Useful page filling values */
-+
-+ /*
-+ * Length of integers after the ID string in a primary bucket
-+ * i.e. dbno + dups + offset + refoffset
-+ */
-+ #define BT_DDOFFROFF (sizeof(ajint) + sizeof(ajint) + sizeof(ajlong) + \
-+ sizeof(ajlong))
-+
-+ /*
-+ * Preamble before key lengths in an internal node
-+ * i.e. nodetype+blocknumber+nkeys+totlen+left+right+overflow+prev
-+ */
-+ #define BT_NODEPREAMBLE (sizeof(ajint) + sizeof(ajlong) + sizeof(ajint) + \
-+ sizeof(ajint) + sizeof(ajlong) + sizeof(ajlong) + sizeof(ajlong) + \
-+ sizeof(ajlong))
-+
-+ /*
-+ * This is the length of extra pointer required in primary index
-+ * page space calculations i.e. the total space taken by
-+ * key/pointer pairs in an internal page is:
-+ * BT_PTRLEN + ((keylenmax + sizeof(long))*nkeys)
-+ * This is because there is one more pointer than the
-+ * value of 'order' in a B+ tree.
-+ */
-+ #define BT_PTRLEN sizeof(ajlong)
-+
-+
-+ /*
-+ * Length of extra space, on top of a key string, taken up by a
-+ * key in an internal node. This is an ajint holding the length
-+ * of a string plus the length of a block pointer (ajlong)
-+ */
-+ #define BT_IDKEYEXTRA (sizeof(ajint) + sizeof(ajlong))
-+
-+
-+ /*
-+ * Preamble before key lengths in an id bucket
-+ * i.e. nodetype+nentries+overflow
-+ */
-+ #define BT_BUCKPREAMBLE (sizeof(ajint) + sizeof(ajint) + sizeof(ajlong))
-+
-+
-+ /*
-+ * Size of a key in a key length table block in an internal node or bucket
-+ */
-+ #define BT_KEYLENENTRY sizeof(ajint)
-+
-+ /*
-+ * Size of an offset key
-+ */
-+ #define BT_OFFKEYLEN sizeof(ajlong)
-+
-+ /*
-+ * Length of integers per entry in a num bucket
-+ * i.e. dbno + offset + refoffset
-+ */
-+ #define BT_DOFFROFF (sizeof(ajint) + sizeof(ajlong) + sizeof(ajlong))
-+
-+
-
-
- /* @data AjPBtNode ***********************************************************
-diff -c -N --recursive EMBOSS-5.0.0old/ajax/ajseqdb.c EMBOSS-5.0.0/ajax/ajseqdb.c
-*** EMBOSS-5.0.0old/ajax/ajseqdb.c 2007-07-06 13:22:40.000000000 +0100
---- EMBOSS-5.0.0/ajax/ajseqdb.c 2008-03-06 10:14:40.000000000 +0000
-***************
-*** 4314,4320 ****
-
- if(!seqRegGcgId)
- {
-! seqRegGcgId =ajRegCompC("^>...([^ ]+) +([^ ]+) +([^ ]+) +([^ ]+) +([0-9]+)");
- seqRegGcgId2=ajRegCompC("^>[PF]1;([^ ]+)");
- }
-
---- 4314,4320 ----
-
- if(!seqRegGcgId)
- {
-! seqRegGcgId =ajRegCompC("^>...([^ ]+) +(Dummy Header|[^ ]+) +([^ ]+) +([^ ]+) +([0-9]+)");
- seqRegGcgId2=ajRegCompC("^>[PF]1;([^ ]+)");
- }
-
-***************
-*** 4352,4358 ****
- else if(ajRegExec(seqRegGcgId2, line))
- {
- ajStrAssignC(&gcgtype, "ASCII");
-! ajRegSubI(seqRegGcgId, 1, &tmpstr);
- ispir = ajTrue;
- }
- else
---- 4352,4358 ----
- else if(ajRegExec(seqRegGcgId2, line))
- {
- ajStrAssignC(&gcgtype, "ASCII");
-! ajRegSubI(seqRegGcgId2, 1, &tmpstr);
- ispir = ajTrue;
- }
- else
-***************
-*** 5546,5552 ****
-
- if(!seqRegGcgId)
- {
-! seqRegGcgId =ajRegCompC("^>...([^ ]+) +([^ ]+) +([^ ]+) +([^ ]+) +([0-9]+)");
- seqRegGcgId2=ajRegCompC("^>[PF]1;([^ ]+)");
- }
-
---- 5546,5552 ----
-
- if(!seqRegGcgId)
- {
-! seqRegGcgId =ajRegCompC("^>...([^ ]+) +(Dummy Header|[^ ]+) +([^ ]+) +([^ ]+) +([0-9]+)");
- seqRegGcgId2=ajRegCompC("^>[PF]1;([^ ]+)");
- }
-
-***************
-*** 5584,5590 ****
- else if(ajRegExec(seqRegGcgId2, line))
- {
- ajStrAssignC(&gcgtype, "ASCII");
-! ajRegSubI(seqRegGcgId, 1, &tmpstr);
- ispir = ajTrue;
- }
- else
---- 5584,5590 ----
- else if(ajRegExec(seqRegGcgId2, line))
- {
- ajStrAssignC(&gcgtype, "ASCII");
-! ajRegSubI(seqRegGcgId2, 1, &tmpstr);
- ispir = ajTrue;
- }
- else
-diff -c -N --recursive EMBOSS-5.0.0old/ajax/ajseqread.c EMBOSS-5.0.0/ajax/ajseqread.c
-*** EMBOSS-5.0.0old/ajax/ajseqread.c 2007-07-11 13:09:51.000000000 +0100
---- EMBOSS-5.0.0/ajax/ajseqread.c 2008-03-06 10:14:41.000000000 +0000
-***************
-*** 604,610 ****
- /* Feature Gap, ReadFunction, Multiset, Padding */
- {"unknown", "Unknown format",
- AJFALSE, AJFALSE, AJTRUE, AJTRUE,
-! AJTRUE, AJTRUE, seqReadText, AJTRUE, 0}, /* alias for text */
- {"gcg", "GCG sequence format",
- AJFALSE, AJTRUE, AJTRUE, AJTRUE,
- AJFALSE, AJTRUE, seqReadGcg, AJFALSE, 0}, /* do first, headers mislead */
---- 604,610 ----
- /* Feature Gap, ReadFunction, Multiset, Padding */
- {"unknown", "Unknown format",
- AJFALSE, AJFALSE, AJTRUE, AJTRUE,
-! AJTRUE, AJTRUE, seqReadText, AJFALSE, 0}, /* alias for text */
- {"gcg", "GCG sequence format",
- AJFALSE, AJTRUE, AJTRUE, AJTRUE,
- AJFALSE, AJTRUE, seqReadGcg, AJFALSE, 0}, /* do first, headers mislead */
-***************
-*** 6637,6642 ****
---- 6637,6643 ----
- else /* test for a SwissProt/SpTrEMBL entry */
- {
- if(ajStrFindC(seqReadLine, " PRT; ")>= 0 ||
-+ ajStrFindC(seqReadLine, " Unreviewed; ") >= 0 ||
- ajStrFindC(seqReadLine, " Reviewed; ") >= 0 ||
- ajStrFindC(seqReadLine, " Preliminary; ") >= 0
- )
-***************
-*** 6650,6656 ****
-
- ok = ajFileBuffGetStore(buff, &seqReadLine, seqin->Text, &thys->TextPtr);
-
-! while(ok && !ajStrPrefixC(seqReadLine, "SQ "))
- {
- bufflines++;
-
---- 6651,6657 ----
-
- ok = ajFileBuffGetStore(buff, &seqReadLine, seqin->Text, &thys->TextPtr);
-
-! while(ok && !ajStrPrefixC(seqReadLine, "SQ"))
- {
- bufflines++;
-
-***************
-*** 7028,7033 ****
---- 7029,7045 ----
- }
- }
-
-+ if(!ajSeqIsNuc(thys))
-+ {
-+ ajFileBuffReset(buff);
-+ ajStrDel(&tmpstr);
-+ ajStrDel(&token);
-+ ajStrDel(&datestr);
-+ ajStrDel(&relstr);
-+ ajStrTokenDel(&handle);
-+ return ajFalse;
-+ }
-+
- ajSeqSetNuc(thys);
-
- ajFileBuffClear(buff, 0);
-***************
-*** 7830,7837 ****
-
- if(ajStrMatchC(typstr, "Protein"))
- ajSeqSetProt(thys);
-! else
- ajSeqSetNuc(thys);
-
- ajFileBuffClear(buff, 0);
-
---- 7842,7851 ----
-
- if(ajStrMatchC(typstr, "Protein"))
- ajSeqSetProt(thys);
-! else if(ajSeqIsNuc(thys))
- ajSeqSetNuc(thys);
-+ else
-+ ajSeqSetProt(thys);
-
- ajFileBuffClear(buff, 0);
-
-diff -c -N --recursive EMBOSS-5.0.0old/ajax/ajseqtype.c EMBOSS-5.0.0/ajax/ajseqtype.c
-*** EMBOSS-5.0.0old/ajax/ajseqtype.c 2007-02-09 18:30:59.000000000 +0000
---- EMBOSS-5.0.0/ajax/ajseqtype.c 2008-03-06 10:14:41.000000000 +0000
-***************
-*** 160,166 ****
- ** - Phylip and some alignment output
- ** ~ GCG for gaps at ends
- ** * Staden for DNA but stop for protein (fix on input?)
-! ** O Phylip (fix on input?)
- */
-
-
---- 160,166 ----
- ** - Phylip and some alignment output
- ** ~ GCG for gaps at ends
- ** * Staden for DNA but stop for protein (fix on input?)
-! ** O Phylip (fix on input?) - no longer possible: O is pyrrolysine in proteins
- */
-
-
-***************
-*** 174,187 ****
- char seqCharNuc[] = "ACGTUBDHKMNRSVWXY?";
- char seqCharNucPure[] = "ACGTU";
- char seqCharNucAmbig[] = "BDHKMNRSVWXY?";
-! char seqCharGap[] = ".~O-"; /* phylip uses O */
- char seqCharNucDna[] = "ACGTBDHKMNRSVWXY?";
- char seqCharNucRna[] = "ACGUBDHKMNRSVWXY?";
-! char seqCharGapany[] = ".~O-"; /* phylip uses O */
- char seqCharGapdash[] = "-";
- char seqCharGapdot[] = ".";
- char seqGap = '-'; /* the (only) EMBOSS gap character */
-! char seqCharGapTest[] = " .~O-"; /* phylip uses O - don't forget space */
- char seqCharPhylo[] = "?"; /* phylip uses ? for unknown or gap */
-
-
---- 174,187 ----
- char seqCharNuc[] = "ACGTUBDHKMNRSVWXY?";
- char seqCharNucPure[] = "ACGTU";
- char seqCharNucAmbig[] = "BDHKMNRSVWXY?";
-! char seqCharGap[] = ".~-"; /* phylip uses O */
- char seqCharNucDna[] = "ACGTBDHKMNRSVWXY?";
- char seqCharNucRna[] = "ACGUBDHKMNRSVWXY?";
-! char seqCharGapany[] = ".~-"; /* phylip uses O */
- char seqCharGapdash[] = "-";
- char seqCharGapdot[] = ".";
- char seqGap = '-'; /* the (only) EMBOSS gap character */
-! char seqCharGapTest[] = " .~-"; /* phylip uses O - don't forget space */
- char seqCharPhylo[] = "?"; /* phylip uses ? for unknown or gap */
-
-
-diff -c -N --recursive EMBOSS-5.0.0old/ajax/ajseqwrite.c EMBOSS-5.0.0/ajax/ajseqwrite.c
-*** EMBOSS-5.0.0old/ajax/ajseqwrite.c 2007-07-06 13:10:46.000000000 +0100
---- EMBOSS-5.0.0/ajax/ajseqwrite.c 2008-03-06 10:14:42.000000000 +0000
-***************
-*** 2788,2805 ****
- {
- if(ilen + ajStrGetLen(cur) > 79)
- {
-! ajFmtPrintF(outseq->File, ";\n", cur);
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "AC ", cur);
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ", cur);
- ilen += 2;
- }
-
---- 2788,2805 ----
- {
- if(ilen + ajStrGetLen(cur) > 79)
- {
-! ajFmtPrintF(outseq->File, ";\n");
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "AC ");
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ");
- ilen += 2;
- }
-
-***************
-*** 2808,2814 ****
-
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ";\n", cur);
- }
-
- if(ajStrGetLen(outseq->Sv))
---- 2808,2814 ----
-
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ";\n");
- }
-
- if(ajStrGetLen(outseq->Sv))
-***************
-*** 2827,2851 ****
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n", cur);
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "KW ", cur);
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ", cur);
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
- ilen += ajStrGetLen(cur);
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n", cur);
- }
-
- if(ajStrGetLen(outseq->Tax))
---- 2827,2851 ----
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n");
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "KW ");
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ");
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
- ilen += ajStrGetLen(cur);
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n");
- }
-
- if(ajStrGetLen(outseq->Tax))
-***************
-*** 2859,2883 ****
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n", cur);
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "OC ", cur);
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ", cur);
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
- ilen += ajStrGetLen(cur);
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n", cur);
- }
-
- if(seqoutUfoLocal(outseq))
---- 2859,2883 ----
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n");
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "OC ");
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ");
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
- ilen += ajStrGetLen(cur);
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n");
- }
-
- if(seqoutUfoLocal(outseq))
-***************
-*** 2973,2990 ****
- {
- if(ilen + ajStrGetLen(cur) > 79)
- {
-! ajFmtPrintF(outseq->File, ";\n", cur);
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "AC ", cur);
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ", cur);
- ilen += 2;
- }
-
---- 2973,2990 ----
- {
- if(ilen + ajStrGetLen(cur) > 79)
- {
-! ajFmtPrintF(outseq->File, ";\n");
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "AC ");
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ");
- ilen += 2;
- }
-
-***************
-*** 2993,2999 ****
-
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ";\n", cur);
- }
-
- if(ajStrGetLen(outseq->Sv))
---- 2993,2999 ----
-
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ";\n");
- }
-
- if(ajStrGetLen(outseq->Sv))
-***************
-*** 3021,3045 ****
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n", cur);
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "KW ", cur);
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ", cur);
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
- ilen += ajStrGetLen(cur);
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n", cur);
- }
-
- if(ajStrGetLen(outseq->Tax))
---- 3021,3045 ----
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n");
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "KW ");
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ");
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
- ilen += ajStrGetLen(cur);
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n");
- }
-
- if(ajStrGetLen(outseq->Tax))
-***************
-*** 3053,3077 ****
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n", cur);
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "OC ", cur);
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ", cur);
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
- ilen += ajStrGetLen(cur);
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n", cur);
- }
-
- if(seqoutUfoLocal(outseq))
---- 3053,3077 ----
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n");
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "OC ");
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ");
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
- ilen += ajStrGetLen(cur);
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n");
- }
-
- if(seqoutUfoLocal(outseq))
-***************
-*** 3209,3215 ****
-
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ";\nXX\n", cur);
- }
-
- /* no SV line in the new format - see the ID line */
---- 3209,3215 ----
-
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ";\nXX\n");
- }
-
- /* no SV line in the new format - see the ID line */
-***************
-*** 3237,3243 ****
- "DT %D (Rel. %S, Last updated, Version %S)\n",
- outseq->Date->ModDate, outseq->Date->ModRel,
- outseq->Date->ModVer);
-! ajFmtPrintF(outseq->File, "XX\n", cur);
- }
-
- if(ajStrGetLen(outseq->Desc))
---- 3237,3243 ----
- "DT %D (Rel. %S, Last updated, Version %S)\n",
- outseq->Date->ModDate, outseq->Date->ModRel,
- outseq->Date->ModVer);
-! ajFmtPrintF(outseq->File, "XX\n");
- }
-
- if(ajStrGetLen(outseq->Desc))
-***************
-*** 3250,3256 ****
- ajFmtPrintF(outseq->File, "DE %S\n", tmpline);
- tmpline = ajStrParseC(NULL, "\n");
- }
-! ajFmtPrintF(outseq->File, "XX\n", cur);
- }
-
- if(ajListGetLength(outseq->Keylist))
---- 3250,3256 ----
- ajFmtPrintF(outseq->File, "DE %S\n", tmpline);
- tmpline = ajStrParseC(NULL, "\n");
- }
-! ajFmtPrintF(outseq->File, "XX\n");
- }
-
- if(ajListGetLength(outseq->Keylist))
-***************
-*** 3261,3285 ****
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n", cur);
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "KW ", cur);
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ", cur);
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
- ilen += ajStrGetLen(cur);
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\nXX\n", cur);
- }
-
- if(ajStrGetLen(outseq->Tax))
---- 3261,3285 ----
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n");
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "KW ");
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ");
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
- ilen += ajStrGetLen(cur);
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\nXX\n");
- }
-
- if(ajStrGetLen(outseq->Tax))
-***************
-*** 3293,3317 ****
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n", cur);
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "OC ", cur);
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ", cur);
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
- ilen += ajStrGetLen(cur);
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n", cur);
- }
- if(ajStrGetLen(outseq->Organelle))
- ajFmtPrintF(outseq->File, "OG %S\n", outseq->Organelle);
---- 3293,3317 ----
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n");
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "OC ");
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ");
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
- ilen += ajStrGetLen(cur);
- }
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n");
- }
- if(ajStrGetLen(outseq->Organelle))
- ajFmtPrintF(outseq->File, "OG %S\n", outseq->Organelle);
-***************
-*** 3319,3325 ****
- if(ajStrGetLen(outseq->Tax) ||
- ajStrGetLen(outseq->Organelle) ||
- ajListGetLength(outseq->Taxlist) > 1)
-! ajFmtPrintF(outseq->File, "XX\n", cur);
-
- if(ajListGetLength(outseq->Reflist))
- {
---- 3319,3325 ----
- if(ajStrGetLen(outseq->Tax) ||
- ajStrGetLen(outseq->Organelle) ||
- ajListGetLength(outseq->Taxlist) > 1)
-! ajFmtPrintF(outseq->File, "XX\n");
-
- if(ajListGetLength(outseq->Reflist))
- {
-***************
-*** 3438,3444 ****
- }
- }
- ajListIterDel(&it);
-! ajFmtPrintF(outseq->File, "XX\n", cur);
- }
-
- if(ajListGetLength(outseq->Cmtlist))
---- 3438,3444 ----
- }
- }
- ajListIterDel(&it);
-! ajFmtPrintF(outseq->File, "XX\n");
- }
-
- if(ajListGetLength(outseq->Cmtlist))
-***************
-*** 3457,3463 ****
- ajFmtPrintF(outseq->File, "CC %S\n", tmpline);
- tmpline = ajStrParseC(NULL, "\n");
- }
-! ajFmtPrintF(outseq->File, "XX\n", cur);
- }
- ajListIterDel(&it);
- }
---- 3457,3463 ----
- ajFmtPrintF(outseq->File, "CC %S\n", tmpline);
- tmpline = ajStrParseC(NULL, "\n");
- }
-! ajFmtPrintF(outseq->File, "XX\n");
- }
- ajListIterDel(&it);
- }
-***************
-*** 3471,3477 ****
- if(!ajFeatWrite(outseq->Ftquery, outseq->Fttable))
- ajWarn("seqWriteEmbl features output failed UFO: '%S'",
- outseq->Ufo);
-! ajFmtPrintF(outseq->File, "XX\n", cur);
- }
-
- ajSeqoutGetBasecount(outseq, b);
---- 3471,3477 ----
- if(!ajFeatWrite(outseq->Ftquery, outseq->Fttable))
- ajWarn("seqWriteEmbl features output failed UFO: '%S'",
- outseq->Ufo);
-! ajFmtPrintF(outseq->File, "XX\n");
- }
-
- ajSeqoutGetBasecount(outseq, b);
-***************
-*** 3541,3558 ****
- {
- if(ilen + ajStrGetLen(cur) > 79)
- {
-! ajFmtPrintF(outseq->File, ";\n", cur);
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "AC ", cur);
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ", cur);
- ilen += 2;
- }
-
---- 3541,3558 ----
- {
- if(ilen + ajStrGetLen(cur) > 79)
- {
-! ajFmtPrintF(outseq->File, ";\n");
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "AC ");
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ");
- ilen += 2;
- }
-
-***************
-*** 3562,3568 ****
- }
-
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ";\n", cur);
- }
-
- if(ajStrGetLen(outseq->Desc))
---- 3562,3568 ----
- }
-
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ";\n");
- }
-
- if(ajStrGetLen(outseq->Desc))
-***************
-*** 3579,3596 ****
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n", cur);
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "OC ", cur);
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ", cur);
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
---- 3579,3596 ----
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n");
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "OC ");
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ");
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
-***************
-*** 3598,3604 ****
- }
-
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n", cur);
- }
-
- if(ajListGetLength(outseq->Keylist))
---- 3598,3604 ----
- }
-
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n");
- }
-
- if(ajListGetLength(outseq->Keylist))
-***************
-*** 3609,3626 ****
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n", cur);
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "KW ", cur);
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ", cur);
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
---- 3609,3626 ----
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n");
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "KW ");
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ");
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
-***************
-*** 3628,3634 ****
- }
-
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n", cur);
- }
-
- if(seqoutUfoLocal(outseq))
---- 3628,3634 ----
- }
-
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n");
- }
-
- if(seqoutUfoLocal(outseq))
-***************
-*** 3708,3725 ****
- {
- if(ilen + ajStrGetLen(cur) > 79)
- {
-! ajFmtPrintF(outseq->File, ";\n", cur);
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "AC ", cur);
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ", cur);
- ilen += 2;
- }
-
---- 3708,3725 ----
- {
- if(ilen + ajStrGetLen(cur) > 79)
- {
-! ajFmtPrintF(outseq->File, ";\n");
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "AC ");
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ");
- ilen += 2;
- }
-
-***************
-*** 3729,3735 ****
- }
-
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ";\n", cur);
- }
-
- if(ajStrGetLen(outseq->Desc))
---- 3729,3735 ----
- }
-
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ";\n");
- }
-
- if(ajStrGetLen(outseq->Desc))
-***************
-*** 3746,3763 ****
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n", cur);
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "OC ", cur);
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ", cur);
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
---- 3746,3763 ----
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n");
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "OC ");
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ");
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
-***************
-*** 3765,3771 ****
- }
-
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n", cur);
- }
-
- if(ajListGetLength(outseq->Keylist))
---- 3765,3771 ----
- }
-
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n");
- }
-
- if(ajListGetLength(outseq->Keylist))
-***************
-*** 3776,3793 ****
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n", cur);
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "KW ", cur);
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ", cur);
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
---- 3776,3793 ----
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n");
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "KW ");
- ilen = 6;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ");
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
-***************
-*** 3795,3801 ****
- }
-
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n", cur);
- }
-
- if(seqoutUfoLocal(outseq))
---- 3795,3801 ----
- }
-
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n");
- }
-
- if(seqoutUfoLocal(outseq))
-***************
-*** 3918,3940 ****
- it = ajListIterNewread(outseq->Acclist);
- while((cur = (AjPStr) ajListIterGet(it)))
- {
-- if(ilen + ajStrGetLen(cur) > 79)
-- {
-- ajFmtPrintF(outseq->File, "\n", cur);
-- ilen = 0;
-- }
--
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "ACCESSION ", cur);
-! ilen = 12;
- }
-! else
- {
-! ajFmtPrintF(outseq->File, " ", cur);
-! ilen += 1;
- }
-
- ajFmtPrintF(outseq->File, "%S", cur);
- ilen += ajStrGetLen(cur);
-
---- 3918,3937 ----
- it = ajListIterNewread(outseq->Acclist);
- while((cur = (AjPStr) ajListIterGet(it)))
- {
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "ACCESSION ");
-! ilen = 11;
- }
-! if(ilen + ajStrGetLen(cur) > 79)
- {
-! ajFmtPrintF(outseq->File, "\n ");
-! ilen = 11;
- }
-
-+ ajFmtPrintF(outseq->File, " ");
-+ ilen += 1;
-+
- ajFmtPrintF(outseq->File, "%S", cur);
- ilen += ajStrGetLen(cur);
-
-***************
-*** 3942,3948 ****
-
- ajListIterDel(&it) ;
- if(ilen > 0)
-! ajFmtPrintF(outseq->File, "\n", cur);
- }
-
- if(ajStrGetLen(outseq->Sv))
---- 3939,3945 ----
-
- ajListIterDel(&it) ;
- if(ilen > 0)
-! ajFmtPrintF(outseq->File, "\n");
- }
-
- if(ajStrGetLen(outseq->Sv))
-***************
-*** 3960,3987 ****
- it = ajListIterNewread(outseq->Keylist);
- while((cur = (AjPStr) ajListIterGet(it)))
- {
-- if(ilen+ajStrGetLen(cur) >= 79)
-- {
-- ajFmtPrintF(outseq->File, ";\n", cur);
-- ilen = 0;
-- }
--
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "KEYWORDS ", cur);
-! ilen = 12;
- }
-! else
- {
-! ajFmtPrintF(outseq->File, "; ", cur);
-! ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
- ilen += ajStrGetLen(cur);
- }
-
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n", cur);
- }
-
- if(ajStrGetLen(outseq->Tax))
---- 3957,3982 ----
- it = ajListIterNewread(outseq->Keylist);
- while((cur = (AjPStr) ajListIterGet(it)))
- {
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, "KEYWORDS ");
-! ilen = 11;
- }
-! if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n ");
-! ilen = 11;
- }
-+
-+ ajFmtPrintF(outseq->File, "; ");
-+ ilen += 2;
-+
- ajFmtPrintF(outseq->File, "%S", cur);
- ilen += ajStrGetLen(cur);
- }
-
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n");
- }
-
- if(ajStrGetLen(outseq->Tax))
-***************
-*** 3997,4014 ****
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n", cur);
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, " ", cur);
- ilen = 12;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ", cur);
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
---- 3992,4009 ----
- {
- if(ilen+ajStrGetLen(cur) >= 79)
- {
-! ajFmtPrintF(outseq->File, ";\n");
- ilen = 0;
- }
-
- if(ilen == 0)
- {
-! ajFmtPrintF(outseq->File, " ");
- ilen = 12;
- }
- else
- {
-! ajFmtPrintF(outseq->File, "; ");
- ilen += 2;
- }
- ajFmtPrintF(outseq->File, "%S", cur);
-***************
-*** 4016,4022 ****
- }
-
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n", cur);
- }
- }
-
---- 4011,4017 ----
- }
-
- ajListIterDel(&it) ;
-! ajFmtPrintF(outseq->File, ".\n");
- }
- }
-
-diff -c -N --recursive EMBOSS-5.0.0old/emboss/dbxfasta.c EMBOSS-5.0.0/emboss/dbxfasta.c
-*** EMBOSS-5.0.0old/emboss/dbxfasta.c 2007-07-06 13:15:29.000000000 +0100
---- EMBOSS-5.0.0/emboss/dbxfasta.c 2008-03-06 10:14:54.000000000 +0000
-***************
-*** 34,39 ****
---- 34,41 ----
-
- static AjPRegexp dbxfasta_wrdexp = NULL;
-
-+ static ajuint maxidlen = 0;
-+ static ajuint idtrunc = 0;
-
- static AjBool dbxfasta_NextEntry(EmbPBtreeEntry entry, AjPFile inf,
- AjPRegexp typeexp, ajint idtype);
-***************
-*** 187,193 ****
- embBtreeDumpParameters(entry);
- embBtreeCloseCaches(entry);
-
-!
- embBtreeEntryDel(&entry);
- ajStrDel(&tmpstr);
- ajStrDel(&filename);
---- 189,197 ----
- embBtreeDumpParameters(entry);
- embBtreeCloseCaches(entry);
-
-! if(maxidlen)
-! ajUser("Resource idlen truncated %u IDs. Maximum ID length was %u.",
-! idtrunc, maxidlen);
- embBtreeEntryDel(&entry);
- ajStrDel(&tmpstr);
- ajStrDel(&filename);
-***************
-*** 431,442 ****
- return ajFalse;
- }
-
- ajStrFmtLower(&entry->id);
-
- if(entry->do_accession && ajStrGetLen(ac))
- {
- str = ajStrNew();
-! ajStrAssignS(&str,ac);
- ajListPush(entry->ac,(void *)str);
- }
-
---- 435,461 ----
- return ajFalse;
- }
-
-+ if(ajStrGetLen(entry->id) > entry->idlen)
-+ {
-+ if(ajStrGetLen(entry->id) > maxidlen)
-+ {
-+ ajWarn("id '%S' too long, truncating to idlen %d",
-+ entry->id, entry->idlen);
-+ maxidlen = ajStrGetLen(entry->id);
-+ }
-+ idtrunc++;
-+ ajStrKeepRange(&entry->id,0,entry->idlen-1);
-+ }
-+
- ajStrFmtLower(&entry->id);
-
- if(entry->do_accession && ajStrGetLen(ac))
- {
- str = ajStrNew();
-! if(ajStrGetLen(ac) > entry->aclen)
-! ajStrAssignSubS(&str,ac,0,entry->aclen-1);
-! else
-! ajStrAssignS(&str,ac);
- ajListPush(entry->ac,(void *)str);
- }
-
-***************
-*** 444,456 ****
- ajStrAssignS(&sv,gi);
-
- if(entry->do_sv && ajStrGetLen(sv))
- {
- str = ajStrNew();
- ajStrAssignS(&str,sv);
- ajListPush(entry->ac,(void *)str);
- }
-!
- if(entry->do_description && ajStrGetLen(de))
- while(ajRegExec(dbxfasta_wrdexp,de))
- {
- ajRegSubI(dbxfasta_wrdexp, 1, &tmpfd);
---- 463,479 ----
- ajStrAssignS(&sv,gi);
-
- if(entry->do_sv && ajStrGetLen(sv))
-+ embBtreeFastaDE(sv, entry->sv, entry->svlen);
-+ /*
- {
- str = ajStrNew();
- ajStrAssignS(&str,sv);
- ajListPush(entry->ac,(void *)str);
- }
-! */
- if(entry->do_description && ajStrGetLen(de))
-+ embBtreeFastaDE(de, entry->de, entry->delen);
-+ /*
- while(ajRegExec(dbxfasta_wrdexp,de))
- {
- ajRegSubI(dbxfasta_wrdexp, 1, &tmpfd);
-***************
-*** 459,465 ****
- ajListPush(entry->de,(void *)str);
- ajRegPost(dbxfasta_wrdexp, &de);
- }
-!
-
- ajStrDel(&de);
- ajStrDel(&ac);
---- 482,488 ----
- ajListPush(entry->de,(void *)str);
- ajRegPost(dbxfasta_wrdexp, &de);
- }
-! */
-
- ajStrDel(&de);
- ajStrDel(&ac);
-diff -c -N --recursive EMBOSS-5.0.0old/emboss/psiphi.c EMBOSS-5.0.0/emboss/psiphi.c
-*** EMBOSS-5.0.0old/emboss/psiphi.c 2007-07-06 13:15:29.000000000 +0100
---- EMBOSS-5.0.0/emboss/psiphi.c 2008-03-06 10:14:15.000000000 +0000
-***************
-*** 160,166 ****
- finishres = ajAcdGetInt("finishresiduenumber");
-
- /* reserve memory for and read in structure */
-! /* JISON */ pdb = ajPdbReadoldNew(pdbfile);
-
- /* check and set number of chain to be analysed */
- highest = pdb->Nchn;
---- 160,166 ----
- finishres = ajAcdGetInt("finishresiduenumber");
-
- /* reserve memory for and read in structure */
-! /* JISON */ pdb = ajPdbReadNew(pdbfile,0);
-
- /* check and set number of chain to be analysed */
- highest = pdb->Nchn;
-***************
-*** 440,445 ****
---- 440,448 ----
- ajint lowestres = 0;
-
- AjPAtom inlist = NULL;
-+
-+ if(!ajListGetLength(pdb->Chains[myindex]->Atoms))
-+ ajFatal("Chain %d has no atoms",myindex+1);
-
- /* read first atom in list into memory, but keep it on list */
- ajListPeek(pdb->Chains[myindex]->Atoms,
-diff -c -N --recursive EMBOSS-5.0.0old/nucleus/embindex.c EMBOSS-5.0.0/nucleus/embindex.c
-*** EMBOSS-5.0.0old/nucleus/embindex.c 2007-07-06 13:15:00.000000000 +0100
---- EMBOSS-5.0.0/nucleus/embindex.c 2008-03-06 10:19:18.000000000 +0000
-***************
-*** 1071,1222 ****
-
- resource = ajStrGetPtr(entry->dbrs);
- if(!ajNamRsAttrValueC(resource,"type",&value))
-! ajFatal("Missing resource entry (%S) for indexing",entry->dbrs);
- if(!ajStrMatchCaseC(value,"Index"))
-! ajFatal("Incorrect 'type' field for resource (%S)",entry->dbrs);
-
-
-
- if(!ajNamRsAttrValueC(resource,"idlen",&value))
-! entry->idlen = BTREE_DEF_IDLEN;
- else
- {
-! if(ajStrToUint(value,&n))
-! entry->idlen = n;
-! else
-! {
-! ajErr("Bad value for index resource 'idlen'");
-! entry->idlen = BTREE_DEF_IDLEN;
-! }
- }
-
- if(!ajNamRsAttrValueC(resource,"acclen",&value))
-! entry->aclen = BTREE_DEF_ACLEN;
- else
- {
-! if(ajStrToUint(value,&n))
-! entry->aclen = n;
-! else
-! {
-! ajErr("Bad value for index resource 'acclen'");
-! entry->aclen = BTREE_DEF_ACLEN;
-! }
- }
-
- if(!ajNamRsAttrValueC(resource,"svlen",&value))
-! entry->svlen = BTREE_DEF_SVLEN;
- else
- {
-! if(ajStrToUint(value,&n))
-! entry->svlen = n;
-! else
-! {
-! ajErr("Bad value for index resource 'svlen'");
-! entry->svlen = BTREE_DEF_SVLEN;
-! }
- }
-
- if(!ajNamRsAttrValueC(resource,"keylen",&value))
-! entry->kwlen = BTREE_DEF_KWLEN;
- else
- {
-! if(ajStrToUint(value,&n))
-! entry->kwlen = n;
-! else
-! {
-! ajErr("Bad value for index resource 'keylen'");
-! entry->kwlen = BTREE_DEF_KWLEN;
-! }
- }
-
- if(!ajNamRsAttrValueC(resource,"deslen",&value))
-! entry->delen = BTREE_DEF_DELEN;
- else
- {
-! if(ajStrToUint(value,&n))
-! entry->delen = n;
-! else
-! {
-! ajErr("Bad value for index resource 'deslen'");
-! entry->delen = BTREE_DEF_DELEN;
-! }
- }
-
- if(!ajNamRsAttrValueC(resource,"orglen",&value))
-! entry->txlen = BTREE_DEF_TXLEN;
- else
- {
-! if(ajStrToUint(value,&n))
-! entry->txlen = n;
-! else
-! {
-! ajErr("Bad value for index resource 'orglen'");
-! entry->txlen = BTREE_DEF_TXLEN;
-! }
- }
-
- if(!ajNamGetValueC("CACHESIZE",&value))
-! entry->cachesize = BTREE_DEF_CACHESIZE;
- else
- {
-! if(ajStrToUint(value,&n))
-! entry->cachesize = n;
-! else
-! {
-! ajErr("Bad value for environment variable 'CACHESIZE'");
-! entry->cachesize = BTREE_DEF_CACHESIZE;
-! }
- }
-
- if(!ajNamGetValueC("PAGESIZE",&value))
-! entry->pagesize = BTREE_DEF_PAGESIZE;
- else
- {
-! if(ajStrToUint(value,&n))
-! entry->pagesize = n;
-! else
-! {
-! ajErr("Bad value for environment variable 'PAGESIZE'");
-! entry->pagesize = BTREE_DEF_PAGESIZE;
-! }
- }
-
-
-! entry->idorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
-! entry->idfill = (entry->pagesize - 16) / (entry->idlen + 28);
-! entry->acorder = (entry->pagesize - 60) / ((entry->aclen + 1) + 12);
-! entry->acfill = (entry->pagesize - 16) / (entry->aclen + 28);
-! entry->svorder = (entry->pagesize - 60) / ((entry->svlen + 1) + 12);
-! entry->svfill = (entry->pagesize - 16) / (entry->svlen + 28);
-!
-! entry->kworder = (entry->pagesize - 60) / ((entry->kwlen + 1) + 12);
-! entry->kwfill = (entry->pagesize - 16) / (entry->kwlen + 28);
-! entry->deorder = (entry->pagesize - 60) / ((entry->delen + 1) + 12);
-! entry->defill = (entry->pagesize - 16) / (entry->delen + 28);
-! entry->txorder = (entry->pagesize - 60) / ((entry->txlen + 1) + 12);
-! entry->txfill = (entry->pagesize - 16) / (entry->txlen + 28);
-!
-! entry->kwsecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
-! entry->desecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
-! entry->txsecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
-!
-! entry->kwsecfill = (entry->pagesize - 16) / (entry->idlen + 4);
-! entry->desecfill = (entry->pagesize - 16) / (entry->idlen + 4);
-! entry->txsecfill = (entry->pagesize - 16) / (entry->idlen + 4);
-
-! entry->idsecorder = (entry->pagesize - 60) / 24;
-! entry->idsecfill = (entry->pagesize - 60) / 20;
-
-! entry->acsecorder = (entry->pagesize - 60) / 24;
-! entry->acsecfill = (entry->pagesize - 60) / 20;
-
-- entry->svsecorder = (entry->pagesize - 60) / 24;
-- entry->svsecfill = (entry->pagesize - 60) / 20;
--
- ajStrDel(&value);
-
- return;
-! }
-
-
-
---- 1071,1278 ----
-
- resource = ajStrGetPtr(entry->dbrs);
- if(!ajNamRsAttrValueC(resource,"type",&value))
-! ajFatal("Missing resource entry (%S) for indexing",entry->dbrs);
- if(!ajStrMatchCaseC(value,"Index"))
-! ajFatal("Incorrect 'type' field for resource (%S)",entry->dbrs);
-
-
-
- if(!ajNamRsAttrValueC(resource,"idlen",&value))
-! entry->idlen = BTREE_DEF_IDLEN;
- else
- {
-! if(ajStrToUint(value,&n))
-! entry->idlen = n;
-! else
-! {
-! ajErr("Bad value for index resource 'idlen'");
-! entry->idlen = BTREE_DEF_IDLEN;
-! }
- }
-
- if(!ajNamRsAttrValueC(resource,"acclen",&value))
-! entry->aclen = BTREE_DEF_ACLEN;
- else
- {
-! if(ajStrToUint(value,&n))
-! entry->aclen = n;
-! else
-! {
-! ajErr("Bad value for index resource 'acclen'");
-! entry->aclen = BTREE_DEF_ACLEN;
-! }
- }
-
- if(!ajNamRsAttrValueC(resource,"svlen",&value))
-! entry->svlen = BTREE_DEF_SVLEN;
- else
- {
-! if(ajStrToUint(value,&n))
-! entry->svlen = n;
-! else
-! {
-! ajErr("Bad value for index resource 'svlen'");
-! entry->svlen = BTREE_DEF_SVLEN;
-! }
- }
-
- if(!ajNamRsAttrValueC(resource,"keylen",&value))
-! entry->kwlen = BTREE_DEF_KWLEN;
- else
- {
-! if(ajStrToUint(value,&n))
-! entry->kwlen = n;
-! else
-! {
-! ajErr("Bad value for index resource 'keylen'");
-! entry->kwlen = BTREE_DEF_KWLEN;
-! }
- }
-
- if(!ajNamRsAttrValueC(resource,"deslen",&value))
-! entry->delen = BTREE_DEF_DELEN;
- else
- {
-! if(ajStrToUint(value,&n))
-! entry->delen = n;
-! else
-! {
-! ajErr("Bad value for index resource 'deslen'");
-! entry->delen = BTREE_DEF_DELEN;
-! }
- }
-
- if(!ajNamRsAttrValueC(resource,"orglen",&value))
-! entry->txlen = BTREE_DEF_TXLEN;
- else
- {
-! if(ajStrToUint(value,&n))
-! entry->txlen = n;
-! else
-! {
-! ajErr("Bad value for index resource 'orglen'");
-! entry->txlen = BTREE_DEF_TXLEN;
-! }
- }
-
- if(!ajNamGetValueC("CACHESIZE",&value))
-! {
-! entry->cachesize = BTREE_DEF_CACHESIZE;
-! ajUser("CACHESIZE defaults to %d", entry->cachesize);
-! }
- else
- {
-! if(ajStrToUint(value,&n))
-! {
-! entry->cachesize = n;
-! }
-! else
-! {
-! ajErr("Bad value for environment variable 'CACHESIZE'");
-! entry->cachesize = BTREE_DEF_CACHESIZE;
-! }
- }
-
- if(!ajNamGetValueC("PAGESIZE",&value))
-! {
-! entry->pagesize = BTREE_DEF_PAGESIZE;
-! ajUser("PAGESIZE defaults to %d", entry->pagesize);
-! }
- else
- {
-! if(ajStrToUint(value,&n))
-! {
-! entry->pagesize = n;
-! }
-! else
-! {
-! ajErr("Bad value for environment variable 'PAGESIZE'");
-! entry->pagesize = BTREE_DEF_PAGESIZE;
-! }
- }
-
-
-! entry->idorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
-! ((entry->idlen + 1) + BT_IDKEYEXTRA);
-
-! entry->idfill = (entry->pagesize - BT_BUCKPREAMBLE) /
-! ((entry->idlen + 1) + BT_KEYLENENTRY + BT_DDOFFROFF);
-
-! entry->acorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
-! ((entry->aclen + 1) + BT_IDKEYEXTRA);
-!
-! entry->acfill = (entry->pagesize - BT_BUCKPREAMBLE) /
-! ((entry->aclen + 1) + BT_KEYLENENTRY + BT_DDOFFROFF);
-!
-! entry->svorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
-! ((entry->svlen + 1) + BT_IDKEYEXTRA);
-!
-! entry->svfill = (entry->pagesize - BT_BUCKPREAMBLE) /
-! ((entry->svlen + 1) + BT_KEYLENENTRY + BT_DDOFFROFF);
-!
-! entry->kworder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
-! ((entry->kwlen + 1) + BT_IDKEYEXTRA);
-!
-! entry->kwfill = (entry->pagesize - BT_BUCKPREAMBLE) /
-! ((entry->kwlen + 1) + BT_KEYLENENTRY + BT_DDOFFROFF);
-!
-! entry->deorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
-! ((entry->delen + 1) + BT_IDKEYEXTRA);
-!
-! entry->defill = (entry->pagesize - BT_BUCKPREAMBLE) /
-! ((entry->delen + 1) + BT_KEYLENENTRY + BT_DDOFFROFF);
-!
-! entry->txorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
-! ((entry->txlen + 1) + BT_IDKEYEXTRA);
-!
-! entry->txfill = (entry->pagesize - BT_BUCKPREAMBLE) /
-! ((entry->txlen + 1) + BT_KEYLENENTRY + BT_DDOFFROFF);
-!
-!
-! entry->idsecorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
-! (BT_OFFKEYLEN + BT_IDKEYEXTRA);
-!
-! entry->acsecorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
-! (BT_OFFKEYLEN + BT_IDKEYEXTRA);
-!
-! entry->svsecorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
-! (BT_OFFKEYLEN + BT_IDKEYEXTRA);
-!
-!
-! entry->idsecfill = (entry->pagesize - BT_BUCKPREAMBLE) /
-! BT_DOFFROFF;
-!
-! entry->acsecfill = (entry->pagesize - BT_BUCKPREAMBLE) /
-! BT_DOFFROFF;
-!
-! entry->svsecfill = (entry->pagesize - BT_BUCKPREAMBLE) /
-! BT_DOFFROFF;
-!
-!
-! /*
-! * The secondary tree keys are the IDs of the entries containing
-! * the keywords
-! */
-!
-! entry->kwsecorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
-! ((entry->idlen + 1) + BT_IDKEYEXTRA);
-! entry->desecorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
-! ((entry->idlen + 1) + BT_IDKEYEXTRA);
-! entry->txsecorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
-! ((entry->idlen + 1) + BT_IDKEYEXTRA);
-!
-!
-! entry->kwsecfill = (entry->pagesize - BT_BUCKPREAMBLE) /
-! ((entry->idlen + 1) + BT_KEYLENENTRY);
-! entry->desecfill = (entry->pagesize - BT_BUCKPREAMBLE) /
-! ((entry->idlen + 1) + BT_KEYLENENTRY);
-! entry->txsecfill = (entry->pagesize - BT_BUCKPREAMBLE) /
-! ((entry->idlen + 1) + BT_KEYLENENTRY);
-
- ajStrDel(&value);
-
- return;
-! }
-
-
-
-***************
-*** 1251,1257 ****
- entry->cachesize,
- entry->idsecorder, slevel,
- entry->idsecfill, count,
-! entry->kwlen);
- if(!entry->idcache)
- ajFatal("Cannot open ID index");
-
---- 1307,1313 ----
- entry->cachesize,
- entry->idsecorder, slevel,
- entry->idsecfill, count,
-! entry->idlen);
- if(!entry->idcache)
- ajFatal("Cannot open ID index");
-
-***************
-*** 1267,1273 ****
- entry->cachesize,
- entry->acsecorder, slevel,
- entry->acsecfill, count,
-! entry->kwlen);
- if(!entry->accache)
- ajFatal("Cannot open ACC index");
-
---- 1323,1329 ----
- entry->cachesize,
- entry->acsecorder, slevel,
- entry->acsecfill, count,
-! entry->aclen);
- if(!entry->accache)
- ajFatal("Cannot open ACC index");
-
-***************
-*** 1282,1288 ****
- entry->cachesize,
- entry->svsecorder, slevel,
- entry->svsecfill, count,
-! entry->kwlen);
- if(!entry->svcache)
- ajFatal("Cannot open SV index");
-
---- 1338,1344 ----
- entry->cachesize,
- entry->svsecorder, slevel,
- entry->svsecfill, count,
-! entry->svlen);
- if(!entry->svcache)
- ajFatal("Cannot open SV index");
-
Modified: trunk/packages/emboss/trunk/debian/patches/series
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/series 2008-07-16 06:48:32 UTC (rev 2241)
+++ trunk/packages/emboss/trunk/debian/patches/series 2008-07-16 06:54:46 UTC (rev 2242)
@@ -1,3 +1 @@
-clustalw2-fix.patch
using-pager-in-tfm.patch
-patch-1-9
Modified: trunk/packages/emboss/trunk/debian/patches/using-pager-in-tfm.patch
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/using-pager-in-tfm.patch 2008-07-16 06:48:32 UTC (rev 2241)
+++ trunk/packages/emboss/trunk/debian/patches/using-pager-in-tfm.patch 2008-07-16 06:54:46 UTC (rev 2242)
@@ -1,5 +1,11 @@
-By default, use /usr/bin/pager, which always exist in Debian and is managed
-through the alternatives system.
+Author: Charles Plessy
+Forwarded: no
+ This patch uses a specificity of Debian.
+Description: Browse the documentation with default pager.
+ `/usr/bin/pager', always exists in Debian and is managed through the
+ alternatives system. With this patch, `tfm' will use `/usr/bin/pager' by
+ default, which points on the user's favorite pager.
+License: as if it were public domain.
--- a/emboss/tfm.c
+++ b/emboss/tfm.c
@@ -87,7 +87,7 @@
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