X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=1c14240e49f3b49414cec522c5f2d41ee372d53e;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=7002f07bf305f2a77a91974956ccbf71a9397d32;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 7002f07..1c14240 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 <http://www.gnu.org/licenses/>.
  */
 package jalview.analysis;
 
@@ -79,7 +78,7 @@ public class CrossRef
 
   /**
    * @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<prod.length;
-   *         p++) { System.out.println("Prod "+p+":
+   *         prod.length) + " products"); if (prod!=null) { for (int p=0;
+   *         p<prod.length; p++) { System.out.println("Prod "+p+":
    *         "+prod[p].getDisplayId(true)); } } } } else {
    *         System.out.println("Trying getProducts for
    *         "+al.getSequenceAt(0).getDisplayId(true));
-   *         System.out.println("Search DS Xref for: "+(dna ? "dna" : "prot")); //
-   *         have a bash at finding the products amongst all the retrieved
+   *         System.out.println("Search DS Xref for: "+(dna ? "dna" : "prot"));
+   *         // have a bash at finding the products amongst all the retrieved
    *         sequences. SequenceI[] prod =
    *         jalview.analysis.CrossRef.findXrefSequences(al
    *         .getSequencesArray(), dna, null, ds); System.out.println("Found " +
    *         ((prod == null) ? "no" : "" + prod.length) + " products"); if
    *         (prod!=null) { // select non-equivalent sequences from dataset list
-   *         for (int p=0; p<prod.length; p++) { System.out.println("Prod
-   *         "+p+": "+prod[p].getDisplayId(true)); } } } }
+   *         for (int p=0; p<prod.length; p++) { System.out.println("Prod "+p+":
+   *         "+prod[p].getDisplayId(true)); } } } }
    */
 }