X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=629850511fefc57400d34c9e07753c938e442c3e;hb=0233d3cada9302f2e78d4444de98886431bf4357;hp=8bc844bc3bc3e46d906fd80f26f0620c96d540ee;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 8bc844b..6298505 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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
*/
@@ -104,36 +103,41 @@ public class CrossRef
Vector refs = new Vector();
for (int s = 0; s < seqs.length; s++)
{
- SequenceI dss = seqs[s];
- while (dss.getDatasetSequence() != null)
- {
- dss = dss.getDatasetSequence();
- }
- DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRef());
- for (int r = 0; rfs != null && r < rfs.length; r++)
+ if (seqs[s] != null)
{
- if (!refs.contains(rfs[r].getSource()))
+
+ SequenceI dss = seqs[s];
+ while (dss.getDatasetSequence() != null)
{
- refs.addElement(rfs[r].getSource());
+ dss = dss.getDatasetSequence();
}
- }
- if (dataset != null)
- {
- // search for references to this sequence's direct references.
- DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef());
- Vector rseqs = new Vector();
- CrossRef.searchDatasetXrefs(seqs[s], !dna, lrfs, dataset, rseqs,
- null); // don't need to specify codon frame for mapping here
- Enumeration lr = rseqs.elements();
- while (lr.hasMoreElements())
+ DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRef());
+ for (int r = 0; rfs != null && r < rfs.length; r++)
{
- SequenceI rs = (SequenceI) lr.nextElement();
- DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRef());
- for (int r = 0; rfs != null && r < rfs.length; r++)
+ if (!refs.contains(rfs[r].getSource()))
{
- if (!refs.contains(rfs[r].getSource()))
+ refs.addElement(rfs[r].getSource());
+ }
+ }
+ if (dataset != null)
+ {
+ // search for references to this sequence's direct references.
+ DBRefEntry[] lrfs = CrossRef
+ .findXDbRefs(!dna, seqs[s].getDBRef());
+ Vector rseqs = new Vector();
+ CrossRef.searchDatasetXrefs(seqs[s], !dna, lrfs, dataset, rseqs,
+ null); // don't need to specify codon frame for mapping here
+ Enumeration lr = rseqs.elements();
+ while (lr.hasMoreElements())
+ {
+ SequenceI rs = (SequenceI) lr.nextElement();
+ DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRef());
+ for (int r = 0; rfs != null && r < rfs.length; r++)
{
- refs.addElement(rfs[r].getSource());
+ if (!refs.contains(rfs[r].getSource()))
+ {
+ refs.addElement(rfs[r].getSource());
+ }
}
}
}
@@ -214,7 +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,
@@ -281,7 +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.
}
@@ -326,9 +330,9 @@ public class CrossRef
try
{
retrieved = sftch.getSequences(xrfs); // problem here is we don't
- // know which of xrfs
- // resulted in which
- // retrieved element
+ // know which of xrfs
+ // resulted in which
+ // retrieved element
} catch (Exception e)
{
System.err
@@ -444,7 +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
*/
@@ -463,10 +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,
@@ -507,16 +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)
{
@@ -567,8 +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,
@@ -577,19 +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