Update of /cvsroot/fink/dists/10.3/unstable/main/finkinfo/sci In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9952
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/10.3/unstable/main/finkinfo/sci/emboss.info,v retrieving revision 1.17 retrieving revision 1.18 diff -u -d -r1.17 -r1.18 --- emboss.info 19 Jul 2005 00:16:48 -0000 1.17 +++ emboss.info 13 Sep 2005 01:20:16 -0000 1.18 @@ -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 ------------------------------------------------------- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf _______________________________________________ Fink-commits mailing list Fink-commits@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-commits