1 files changed, 115 insertions, 0 deletions
diff --git a/biology/emboss/files/patch-embindex.c b/biology/emboss/files/patch-embindex.c
new file mode 100644
index 000000000000..25569485eca7
--- /dev/null
+++ b/biology/emboss/files/patch-embindex.c
@@ -0,0 +1,115 @@
+--- nucleus/embindex.c.orig	Mon Jan 23 12:24:54 2006
++++ nucleus/embindex.c	Thu Dec 22 13:12:38 2005
+@@ -973,15 +973,14 @@
+ 	if(!do_ref)
+ 	{
+ 	    ajListPop(entry->files,(void **)&tmpstr);
+-	    ajFmtPrintF(entfile,"%S%S\n",entry->directory,tmpstr);
++	    ajFmtPrintF(entfile,"%S\n",tmpstr);
+ 	    ajListPushApp(entry->files,(void *)tmpstr);
+ 	}
+ 	else
+ 	{
+ 	    ajListPop(entry->files,(void **)&tmpstr);
+ 	    ajListPop(entry->reffiles,(void **)&refstr);
+-	    ajFmtPrintF(entfile,"%S%S %S%S\n",entry->directory,tmpstr,
+-			entry->directory,refstr);
++	    ajFmtPrintF(entfile,"%S %S\n",tmpstr, refstr);
+ 	    ajListPushApp(entry->files,(void *)tmpstr);
+ 	    ajListPushApp(entry->reffiles,(void *)refstr);
+ 	}
+@@ -1150,7 +1149,15 @@
+     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;
+@@ -1183,28 +1190,38 @@
+ 
+     if(entry->do_id)
+     {
+-	entry->idcache = ajBtreeCacheNewC(basenam,ID_EXTENSION,idir,"w+",
+-					  entry->pagesize, entry->idorder,
+-					  entry->idfill, level,
+-					  entry->cachesize);
++	entry->idcache = ajBtreeSecCacheNewC(basenam,ID_EXTENSION,idir,"w+",
++					     entry->pagesize, entry->idorder,
++					     entry->idfill, level,
++					     entry->cachesize,
++					     entry->idsecorder, slevel,
++					     entry->idsecfill, count,
++					     entry->kwlen);
+ 	ajBtreeCreateRootNode(entry->idcache,0L);
+     }
+ 
+     if(entry->do_accession)
+     {
+-	entry->accache = ajBtreeCacheNewC(basenam,AC_EXTENSION,idir,"w+",
+-					  entry->pagesize, entry->acorder,
+-					  entry->acfill, level,
+-					  entry->cachesize);
++	entry->accache = ajBtreeSecCacheNewC(basenam,AC_EXTENSION,idir,"w+",
++					     entry->pagesize,
++					     entry->acorder, entry->acfill,
++					     level,
++					     entry->cachesize,
++					     entry->acsecorder, slevel,
++					     entry->acsecfill, count,
++					     entry->kwlen);
+ 	ajBtreeCreateRootNode(entry->accache,0L);
+     }
+ 
+     if(entry->do_sv)
+     {
+-	entry->svcache = ajBtreeCacheNewC(basenam,SV_EXTENSION,idir,"w+",
+-					  entry->pagesize, entry->svorder,
+-					  entry->svfill, level,
+-					  entry->cachesize);
++	entry->svcache = ajBtreeSecCacheNewC(basenam,SV_EXTENSION,idir,"w+",
++					     entry->pagesize, entry->svorder,
++					     entry->svfill, level,
++					     entry->cachesize,
++					     entry->svsecorder, slevel,
++					     entry->svsecfill, count,
++					     entry->kwlen);
+ 	ajBtreeCreateRootNode(entry->svcache,0L);
+     }
+ 
+@@ -1270,18 +1287,27 @@
+ 
+     if(entry->do_id)
+     {
++	ajBtreeFreePriArray(entry->idcache);
++	ajBtreeFreeSecArray(entry->idcache);
++
+ 	ajBtreeCacheSync(entry->idcache,0L);
+ 	ajBtreeCacheDel(&entry->idcache);
+     }
+ 
+     if(entry->do_accession)
+     {
++	ajBtreeFreePriArray(entry->accache);
++	ajBtreeFreeSecArray(entry->accache);
++
+ 	ajBtreeCacheSync(entry->accache,0L);
+ 	ajBtreeCacheDel(&entry->accache);
+     }
+ 
+     if(entry->do_sv)
+     {
++	ajBtreeFreePriArray(entry->svcache);
++	ajBtreeFreeSecArray(entry->svcache);
++
+ 	ajBtreeCacheSync(entry->svcache,0L);
+ 	ajBtreeCacheDel(&entry->svcache);
+     }