X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=8682e8abe7bc34c8a92e00c5b46f139134a469d9;hb=9c04f4ce6bb3a8851b1abf3bb9999ca097d37685;hp=7002f07bf305f2a77a91974956ccbf71a9397d32;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 7002f07..8682e8a 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.analysis;
@@ -67,19 +66,19 @@ public class CrossRef
public static Hashtable classifyDbRefs(DBRefEntry[] rfs)
{
Hashtable classes = new Hashtable();
- classes.put(DBRefSource.PROTEINDBS, jalview.util.DBRefUtils.selectRefs(
- rfs, DBRefSource.PROTEINDBS));
+ classes.put(DBRefSource.PROTEINDBS,
+ jalview.util.DBRefUtils.selectRefs(rfs, DBRefSource.PROTEINDBS));
classes.put(DBRefSource.DNACODINGDBS, jalview.util.DBRefUtils
.selectRefs(rfs, DBRefSource.DNACODINGDBS));
- classes.put(DBRefSource.DOMAINDBS, jalview.util.DBRefUtils.selectRefs(
- rfs, DBRefSource.DOMAINDBS));
+ classes.put(DBRefSource.DOMAINDBS,
+ jalview.util.DBRefUtils.selectRefs(rfs, DBRefSource.DOMAINDBS));
// classes.put(OTHER, )
return classes;
}
/**
* @param dna
- * true if seqs are DNA seqs
+ * true if seqs are DNA seqs
* @param seqs
* @return a list of sequence database cross reference source types
*/
@@ -93,7 +92,7 @@ public class CrossRef
* any of the direct DBRefEntrys on the given sequences.
*
* @param dna
- * true if seqs are DNA seqs
+ * true if seqs are DNA seqs
* @param seqs
* @return a list of sequence database cross reference source types
*/
@@ -219,7 +218,7 @@ public class CrossRef
* @param dna
* @param source
* @param dataset
- * alignment to search for product sequences.
+ * alignment to search for product sequences.
* @return products (as dataset sequences)
*/
public static Alignment findXrefSequences(SequenceI[] seqs, boolean dna,
@@ -286,7 +285,7 @@ public class CrossRef
// xrefs on this sequence.
if (dataset != null)
{
- found |= searchDataset(dss, xrfs[r], dataset, rseqs, cf);
+ found |= searchDataset(dss, xrfs[r], dataset, rseqs, cf); // ,false,!dna);
if (found)
xrfs[r] = null; // we've recovered seqs for this one.
}
@@ -449,7 +448,7 @@ public class CrossRef
* @param xrf
* @param dataset
* @param rseqs
- * set of unique sequences
+ * set of unique sequences
* @param cf
* @return true if one or more unique sequences were found and added
*/
@@ -468,10 +467,10 @@ public class CrossRef
* @param xrf
* @param dataset
* @param rseqs
- * @param direct -
- * search all references or only subset
+ * @param direct
+ * - search all references or only subset
* @param dna
- * search dna or protein xrefs (if direct=false)
+ * search dna or protein xrefs (if direct=false)
* @return true if relationship found and sequence added.
*/
public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
@@ -512,16 +511,15 @@ public class CrossRef
}
// look for direct or indirect references in common
- DBRefEntry[] poss = null, cands = null;
+ DBRefEntry[] poss = nxt.getDBRef(), cands = null;
if (direct)
{
- cands = jalview.util.DBRefUtils.searchRefs(poss = nxt
- .getDBRef(), xrf);
+ cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
}
else
{
- cands = jalview.util.DBRefUtils.searchRefs(poss = CrossRef
- .findXDbRefs(dna, nxt.getDBRef()), xrf);
+ poss = CrossRef.findXDbRefs(dna, poss); //
+ cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
}
if (cands != null)
{
@@ -572,8 +570,8 @@ public class CrossRef
* @param dna
* @param seqs
* @param dataset
- * @param fake -
- * don't actually build lists - just get types
+ * @param fake
+ * - don't actually build lists - just get types
* @return public static Object[] buildXProductsList(boolean dna, SequenceI[]
* seqs, AlignmentI dataset, boolean fake) { String types[] =
* jalview.analysis.CrossRef.findSequenceXrefTypes( dna, seqs,
@@ -582,19 +580,19 @@ public class CrossRef
* System.out.println("Type: " + types[t]); SequenceI[] prod =
* jalview.analysis.CrossRef.findXrefSequences(seqs, dna, types[t]);
* System.out.println("Found " + ((prod == null) ? "no" : "" +
- * prod.length) + " products"); if (prod!=null) { for (int p=0; p