1 files changed, 0 insertions, 115 deletions
diff --git a/biology/emboss/files/patch-embindex.c b/biology/emboss/files/patch-embindex.c
deleted file mode 100644
index 25569485eca7..000000000000
--- a/biology/emboss/files/patch-embindex.c
+++ /dev/null
@@ -1,115 +0,0 @@
---- 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);
-     }