X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=8bc844bc3bc3e46d906fd80f26f0620c96d540ee;hb=5c212e384ee48b37d899cc88fc3d12c5028cc3b4;hp=f355d1f09c6d139e8c82344e91e46c97de635cd7;hpb=6b406c397d41a0f2d84b75f13e7ab478932bf57d;p=jalview.git

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index f355d1f..8bc844b 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, 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 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.
+ * 
+ * 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
+ */
 package jalview.analysis;
 
 import java.util.Enumeration;
@@ -158,7 +176,9 @@ public class CrossRef
       {
         if (cdna[c].getSource().equals(DBRefSource.EMBLCDS))
         {
-          // retrieve CDS dataset sequences
+          System.err
+                  .println("TODO: unimplemented sequence retrieval for coding region sequence.");
+          // TODO: retrieve CDS dataset sequences
           // need global dataset sequence retriever/resolver to reuse refs
           // and construct Mapping entry.
           // insert gaps in CDS according to peptide gaps.
@@ -305,7 +325,10 @@ public class CrossRef
             xrfs = t;
             try
             {
-              retrieved = sftch.getSequences(xrfs); // problem here is we don't know which of xrfs resulted in which retrieved element
+              retrieved = sftch.getSequences(xrfs); // problem here is we don't
+                                                    // know which of xrfs
+                                                    // resulted in which
+                                                    // retrieved element
             } catch (Exception e)
             {
               System.err
@@ -318,32 +341,39 @@ public class CrossRef
               for (int rs = 0; rs < retrieved.length; rs++)
               {
                 // TODO: examine each sequence for 'redundancy'
-                jalview.datamodel.DBRefEntry[] dbr = retrieved[rs].getDBRef();
+                jalview.datamodel.DBRefEntry[] dbr = retrieved[rs]
+                        .getDBRef();
                 if (dbr != null && dbr.length > 0)
                 {
                   for (int di = 0; di < dbr.length; di++)
                   {
-                    // find any entry where we should put in the sequence being cross-referenced into the map
+                    // find any entry where we should put in the sequence being
+                    // cross-referenced into the map
                     jalview.datamodel.Mapping map = dbr[di].getMap();
                     if (map != null)
                     {
                       if (map.getTo() != null && map.getMap() != null)
                       {
-                        // should search the local dataset to find any existing candidates for To !
+                        // should search the local dataset to find any existing
+                        // candidates for To !
                         try
                         {
-                          // compare ms with dss and replace with dss in mapping if map is congruent
+                          // compare ms with dss and replace with dss in mapping
+                          // if map is congruent
                           SequenceI ms = map.getTo();
                           int sf = map.getMap().getToLowest();
                           int st = map.getMap().getToHighest();
                           SequenceI mappedrg = ms.getSubSequence(sf, st);
                           SequenceI loc = dss.getSubSequence(sf, st);
-                          if (mappedrg.getLength()>0 && mappedrg.getSequenceAsString().equals(
-                                  loc.getSequenceAsString()))
+                          if (mappedrg.getLength() > 0
+                                  && mappedrg.getSequenceAsString().equals(
+                                          loc.getSequenceAsString()))
                           {
                             System.err
                                     .println("Mapping updated for retrieved crossreference");
-                            // method to update all refs of existing To on retrieved sequence with dss and merge any props on To onto dss.
+                            // method to update all refs of existing To on
+                            // retrieved sequence with dss and merge any props
+                            // on To onto dss.
                             map.setTo(dss);
                           }
                         } catch (Exception e)
@@ -444,6 +474,7 @@ public class CrossRef
           boolean direct, boolean dna)
   {
     boolean found = false;
+    SequenceI[] typer = new SequenceI[1];
     if (dataset == null)
       return false;
     if (dataset.getSequences() == null)
@@ -464,6 +495,17 @@ public class CrossRef
         }
         if (nxt != sequenceI && nxt != sequenceI.getDatasetSequence())
         {
+          // check if this is the correct sequence type
+          {
+            typer[0] = nxt;
+            boolean isDna = jalview.util.Comparison.isNucleotide(typer);
+            if ((direct && isDna == dna) || (!direct && isDna != dna))
+            {
+              // skip this sequence because it is same molecule type
+              continue;
+            }
+          }
+
           // look for direct or indirect references in common
           DBRefEntry[] poss = null, cands = null;
           if (direct)
@@ -537,16 +579,17 @@ public class CrossRef
    *         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[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 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)); } }
-   *  } }
+   *         "+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
+   *         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)); } } } }
    */
-}
\ No newline at end of file
+}