Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9519
Modified Files:
emboss.info
Added Files:
emboss.patch
Log Message:
upstream patch
--- NEW FILE: emboss.patch ---
diff -Naur EMBOSS-3.0.0/ajax/ajindex.c EMBOSS-3.0.0-patched/ajax/ajindex.c
--- EMBOSS-3.0.0/ajax/ajindex.c 2005-06-20 03:41:01.000000000 -0400
+++ EMBOSS-3.0.0-patched/ajax/ajindex.c 2005-08-04 22:50:00.000000000 -0400
@@ -35,10 +35,14 @@
AjBool isread);
static AjPBtpage btreeFindINode(AjPBtcache cache, AjPBtpage page,
const char *item);
+static AjPBtpage btreeSecFindINode(AjPBtcache cache, AjPBtpage page,
+ const char *item);
static AjPBtpage btreePageFromKey(AjPBtcache cache, unsigned char *buf,
const char *item);
+static AjPBtpage btreeSecPageFromKey(AjPBtcache cache, unsigned char *buf,
+ const char *item);
static ajint btreeNumInBucket(AjPBtcache cache, ajlong pageno);
static AjPBucket btreeReadBucket(AjPBtcache cache, ajlong pageno);
static void btreeWriteBucket(AjPBtcache cache, const AjPBucket bucket,
@@ -55,6 +59,7 @@
AjPStr const *keys, const ajlong *ptrs,
ajint nkeys);
static AjBool btreeNodeIsFull(const AjPBtcache cache, AjPBtpage page);
+static AjBool btreeNodeIsFullSec(const AjPBtcache cache, AjPBtpage page);
static void btreeInsertNonFull(AjPBtcache cache, AjPBtpage page,
const AjPStr key, ajlong less,
ajlong greater);
@@ -808,7 +813,7 @@
root = btreeCacheLocate(cache,0L);
if(!root)
- ajFatal("Something has unlocked the PRI root cache page\n");
+ ajFatal("The PRI root cache page has been unlocked\n");
if(!cache->level)
return root;
@@ -863,6 +868,48 @@
+/* @funcstatic btreeSecFindINode
*************************************************
+**
+** Recursive search for insert node in a secondary tree
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] page [AjPBtpage] page
+** @param [r] item [const char*] key to search for
+**
+** @return [AjPBtpage] leaf node where item should be inserted
+** @@
+******************************************************************************/
+
+static AjPBtpage btreeSecFindINode(AjPBtcache cache, AjPBtpage page,
+ const char *item)
+{
+ AjPBtpage ret = NULL;
+ AjPBtpage pg = NULL;
+
+ unsigned char *buf = NULL;
+ ajint status = 0;
+ ajint ival = 0;
+
+ /* ajDebug("In btreeSecFindINode\n"); */
+
+ ret = page;
+ buf = page->buf;
+ GBT_NODETYPE(buf,&ival);
+ if(ival != BT_LEAF)
+ {
+ status = ret->dirty;
+ ret->dirty = BT_LOCK; /* Lock in case of lots of overflow pages */
+ pg = btreeSecPageFromKey(cache,buf,item);
+ ret->dirty = status;
+ ret = btreeSecFindINode(cache,pg,item);
+ }
+
+ return ret;
+}
+
+
+
+
/* @funcstatic btreePageFromKey *******************************************
**
** Return next lower index page given a key
@@ -928,6 +975,71 @@
+/* @funcstatic btreeSecPageFromKey *******************************************
+**
+** Return next lower index page given a key in a secondary tree
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] buf [unsigned char *] page buffer
+** @param [r] key [const char *] key to search for
+**
+** @return [AjPBtpage] pointer to a page
+** @@
+******************************************************************************/
+
+static AjPBtpage btreeSecPageFromKey(AjPBtcache cache, unsigned char *buf,
+ const char *key)
+{
+ unsigned char *rootbuf = NULL;
+ ajint nkeys = 0;
+ ajint order = 0;
+ ajint i;
+
+ ajlong blockno = 0L;
+ AjPStr *karray = NULL;
+ ajlong *parray = NULL;
+ AjPBtpage page = NULL;
+
+ /* ajDebug("In btreePageFromKey\n"); */
+
+ rootbuf = buf;
+
+
+ GBT_NKEYS(rootbuf,&nkeys);
+ order = cache->sorder;
+
+ AJCNEW0(karray,order);
+ AJCNEW0(parray,order);
+ for(i=0;i<order;++i)
+ karray[i] = ajStrNew();
+
+ btreeGetKeys(cache,rootbuf,&karray,&parray);
+ i = 0;
+ while(i!=nkeys && strcmp(key,karray[i]->Ptr)>=0)
+ ++i;
+ if(i==nkeys)
+ {
+ if(strcmp(key,karray[i-1]->Ptr)<0)
+ blockno = parray[i-1];
+ else
+ blockno = parray[i];
+ }
+ else
+ blockno = parray[i];
+
+ for(i=0;i<order;++i)
+ ajStrDel(&karray[i]);
+ AJFREE(karray);
+ AJFREE(parray);
+
+ page = ajBtreeCacheRead(cache,blockno);
+
+ return page;
+}
+
+
+
+
/* @func ajBtreeIdNew *********************************************
**
** Constructor for index bucket ID informationn
@@ -1617,6 +1729,36 @@
+/* @funcstatic btreeNodeIsFullSec *****************************************
+**
+** Tests whether a secondary node is full of keys
+**
+** @param [r] cache [const AjPBtcache] cache
+** @param [u] page [AjPBtpage] original page
+**
+** @return [AjBool] true if full
+** @@
+******************************************************************************/
+
+static AjBool btreeNodeIsFullSec(const AjPBtcache cache, AjPBtpage page)
+{
+ unsigned char *buf = NULL;
+ ajint nkeys = 0;
+
+ /* ajDebug("In btreeNodeIsFull\n"); */
+
+ buf = page->buf;
+ GBT_NKEYS(buf,&nkeys);
+
+ if(nkeys == cache->sorder - 1)
+ return ajTrue;
+
+ return ajFalse;
+}
+
+
+
+
/* @funcstatic btreeInsertNonFull *****************************************
**
** Insert a key into a non-full node
@@ -6967,7 +7109,7 @@
pripage = btreeCacheLocate(cache,0L);
pripage->dirty = BT_LOCK;
- ajDebug("Created secondary tree at block %d\n",(ajint)secrootpage);
+ /* ajDebug("Created 2ry tree at block %d\n",(ajint)secrootpage); */
}
else
{
@@ -9070,7 +9212,7 @@
if(!cache->slevel)
return root;
- ret = btreeFindINode(cache,root,key);
+ ret = btreeSecFindINode(cache,root,key);
return ret;
}
@@ -9694,7 +9836,7 @@
/* ajDebug("In btreeInsertKeySec\n"); */
- if(!btreeNodeIsFull(cache,page))
+ if(!btreeNodeIsFullSec(cache,page))
{
btreeInsertNonFullSec(cache,page,key,less,greater);
return;
@@ -10572,7 +10714,7 @@
list = ajListNew();
- order = cache->order;
+ order = cache->sorder;
AJCNEW0(karray,order);
AJCNEW0(parray,order);
diff -Naur EMBOSS-3.0.0/ajax/ajpdb.c EMBOSS-3.0.0-patched/ajax/ajpdb.c
--- EMBOSS-3.0.0/ajax/ajpdb.c 2005-07-12 12:29:41.000000000 -0400
+++ EMBOSS-3.0.0-patched/ajax/ajpdb.c 2005-08-19 16:49:00.000000000 -0400
@@ -1198,7 +1198,7 @@
osstr = ajStrNew();
xstr = ajStrNew();
- /* Start of main application loop */
+ /* Start of main loop */
while(ajFileReadLine(inf,&line))
{
if(ajStrPrefixC(line,"XX"))
@@ -1313,6 +1313,8 @@
(ret)->Nchn = ncha;
(ret)->Ngp = ngrp;
+
+ continue;
}
@@ -1382,7 +1384,11 @@
ajStrToken(&token,&handle,NULL);
ajStrToInt(token,&mod);
if((mode == 0) && (mod!=1))
- break;
+ {
+ /* break; */
+ /* Discard remaining AT lines */
+ while(ajFileReadLine(inf,&line) && ajStrPrefixC(line,"AT"));
+ }
/* Chain number */
ajStrToken(&token,&handle,NULL);
@@ -1463,7 +1469,10 @@
"[EMAIL PROTECTED]");
}
else
+ {
ajListPushApp((ret)->Chains[chn-1]->Atoms,(void *)atom);
+ }
+ continue;
}
/* Parse residue line */
@@ -1479,8 +1488,11 @@
ajStrToken(&token,&handle,NULL);
ajStrToInt(token,&mod);
if((mode == 0) && (mod!=1))
- break;
-
+ {
+ /* break;*/
+ /* Discard remaining RE lines */
+ while(ajFileReadLine(inf,&line) && ajStrPrefixC(line,"RE"));
+ }
/* Chain number */
ajStrToken(&token,&handle,NULL);
ajStrToInt(token,&chn);
@@ -1585,6 +1597,8 @@
ajStrToFloat(token,&residue->pol_rel);
ajListPushApp((ret)->Chains[chn-1]->Residues,(void *)residue);
+
+ continue;
}
}
/* End of main application loop */
diff -Naur EMBOSS-3.0.0/jemboss/org/emboss/jemboss/server/JembossServer.java
EMBOSS-3.0.0-patched/jemboss/org/emboss/jemboss/server/JembossServer.java
--- EMBOSS-3.0.0/jemboss/org/emboss/jemboss/server/JembossServer.java
2004-10-29 08:07:02.000000000 -0400
+++ EMBOSS-3.0.0-patched/jemboss/org/emboss/jemboss/server/JembossServer.java
2005-08-30 13:22:00.000000000 -0400
@@ -973,7 +973,10 @@
{
public boolean accept(File cwd, String name)
{
- return name.endsWith(".png");
+ if( name.endsWith(".png") ||
+ name.endsWith(".dat") )
+ return true;
+ return false;
};
});
Index: emboss.info
===================================================================
RCS file:
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/emboss.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- emboss.info 19 Jul 2005 00:16:05 -0000 1.7
+++ emboss.info 13 Sep 2005 01:18:52 -0000 1.8
@@ -1,6 +1,6 @@
Package: emboss
Version: 3.0.0
-Revision: 1
+Revision: 2
Depends: %N-shlibs (= %v-%r), x11, libpng3-shlibs, libjpeg-shlibs, gd2-shlibs,
system-java14
BuildDepends: libpng3, libjpeg, gd2, libiconv-dev, x11-dev, system-java14-dev
#Replaces: emboss (<< 2.7.1-2)
@@ -9,6 +9,7 @@
Primary: ftp://emboss.open-bio.org/pub/EMBOSS/
<<
Source-MD5: fa72feded9ab9272e3e731c09f545dcc
+Patch: %n.patch
ConfigureParams:
--with-java=/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home
--with-javaos=/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home/include
Installscript: <<
make install DESTDIR=%d
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