From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 22 Jun 2016 10:41:24 +0000 (+0100)
Subject: JAL-2110 remove hardwired detection of search context from the dataset ‘isNucleotide... 
X-Git-Tag: Release_2_10_0~140^2~5^2~48
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b10330c2e330e409d2fd3812f1001f9542dc1b36;p=jalview.git

JAL-2110 remove hardwired detection of search context from the dataset ‘isNucleotide()’ flag
---

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 9fd87df..d96ab58 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -54,12 +54,6 @@ public class CrossRef
   private AlignmentI dataset;
 
   /*
-   * true if we are searching for cross-references from nucleotide,
-   * i.e. for protein sequences, false if the reverse
-   */
-  private boolean fromDna;
-
-  /*
    * the sequences for which we are seeking cross-references
    */
   private SequenceI[] fromSeqs;
@@ -76,7 +70,6 @@ public class CrossRef
   public CrossRef(SequenceI[] seqs, AlignmentI ds)
   {
     fromSeqs = seqs;
-    fromDna = ds.isNucleotide();
     dataset = ds.getDataset() == null ? ds : ds.getDataset();
   }
 
@@ -88,16 +81,20 @@ public class CrossRef
    * reference from another sequence in the dataset which has a cross-reference
    * to a direct DBRefEntry on the given sequence</li>
    * </ul>
+   * 
+   * @param dna
+   *          - when true, cross-references *from* dna returned. When false,
+   *          cross-references *from* protein are returned
    * @return
    */
-  public List<String> findXrefSourcesForSequences()
+  public List<String> findXrefSourcesForSequences(boolean dna)
   {
     List<String> sources = new ArrayList<String>();
     for (SequenceI seq : fromSeqs)
     {
       if (seq != null)
       {
-        findXrefSourcesForSequence(seq, sources);
+        findXrefSourcesForSequence(seq, dna, sources);
       }
     }
     return sources;
@@ -117,7 +114,8 @@ public class CrossRef
    * @param sources
    *          a list of sources to add matches to
    */
-  void findXrefSourcesForSequence(SequenceI seq, List<String> sources)
+  void findXrefSourcesForSequence(SequenceI seq, boolean fromDna,
+          List<String> sources)
   {
     /*
      * first find seq's xrefs (dna-to-peptide or peptide-to-dna)
@@ -136,7 +134,7 @@ public class CrossRef
        * find sequences in the alignment which xref one of these DBRefs
        * i.e. is xref-ed to a common sequence identifier
        */
-      searchDatasetXrefs(seq, lrfs, rseqs, null);
+      searchDatasetXrefs(fromDna, seq, lrfs, rseqs, null);
 
       /*
        * add those sequences' (dna-to-peptide or peptide-to-dna) dbref sources
@@ -194,7 +192,7 @@ public class CrossRef
    * @param source
    * @return cross-referenced sequences (as dataset sequences)
    */
-  public Alignment findXrefSequences(String source)
+  public Alignment findXrefSequences(String source, boolean fromDna)
   {
 
     List<SequenceI> rseqs = new ArrayList<SequenceI>();
@@ -226,7 +224,7 @@ public class CrossRef
          *  which have a dbref to an accession id for this sequence,
          *  and add them to the results
          */
-        found = searchDatasetXrefs(dss, lrfs, rseqs, cf);
+        found = searchDatasetXrefs(fromDna, dss, lrfs, rseqs, cf);
       }
       if (xrfs == null && !found)
       {
@@ -297,7 +295,7 @@ public class CrossRef
                   + xref.getAccessionId());
           if (matchedSeq != null)
           {
-            if (constructMapping(seq, matchedSeq, xref, cf))
+            if (constructMapping(seq, matchedSeq, xref, cf, fromDna))
             {
               found = true;
             }
@@ -308,7 +306,7 @@ public class CrossRef
         {
           // do a bit more work - search for sequences with references matching
           // xrefs on this sequence.
-          found = searchDataset(dss, xref, rseqs, cf, false);
+          found = searchDataset(fromDna, dss, xref, rseqs, cf, false);
         }
         if (found)
         {
@@ -337,7 +335,7 @@ public class CrossRef
 
         if (retrieved != null)
         {
-          updateDbrefMappings(seq, xrfs, retrieved, cf);
+          updateDbrefMappings(seq, xrfs, retrieved, cf, fromDna);
           for (SequenceI retrievedSequence : retrieved)
           {
             SequenceI retrievedDss = retrievedSequence.getDatasetSequence() == null ? retrievedSequence
@@ -595,8 +593,8 @@ public class CrossRef
    * @param retrieved
    * @param acf
    */
-  void updateDbrefMappings(SequenceI mapFrom,
-          DBRefEntry[] xrefs, SequenceI[] retrieved, AlignedCodonFrame acf)
+  void updateDbrefMappings(SequenceI mapFrom, DBRefEntry[] xrefs,
+          SequenceI[] retrieved, AlignedCodonFrame acf, boolean fromDna)
   {
     SequenceIdMatcher matcher = new SequenceIdMatcher(retrieved);
     for (DBRefEntry xref : xrefs)
@@ -612,7 +610,7 @@ public class CrossRef
         }
         for (SequenceI seq : matches)
         {
-          constructMapping(mapFrom, seq, xref, acf);
+          constructMapping(mapFrom, seq, xref, acf, fromDna);
         }
       }
     }
@@ -639,7 +637,7 @@ public class CrossRef
    * @return
    */
   boolean constructMapping(SequenceI mapFrom, SequenceI mapTo,
-          DBRefEntry xref, AlignedCodonFrame mappings)
+          DBRefEntry xref, AlignedCodonFrame mappings, boolean fromDna)
   {
     MapList mapping = null;
 
@@ -700,12 +698,15 @@ public class CrossRef
    * dataset (that is not equal to sequenceI) Identifies matching DBRefEntry
    * based on source and accession string only - Map and Version are nulled.
    * 
+   * @param fromDna
+   *          - true if context was searching from Dna sequences, false if
+   *          context was searching from Protein sequences
    * @param sequenceI
    * @param lrfs
    * @param rseqs
    * @return true if matches were found.
    */
-  private boolean searchDatasetXrefs(SequenceI sequenceI,
+  private boolean searchDatasetXrefs(boolean fromDna, SequenceI sequenceI,
           DBRefEntry[] lrfs, List<SequenceI> rseqs, AlignedCodonFrame cf)
   {
     boolean found = false;
@@ -719,7 +720,7 @@ public class CrossRef
       // add in wildcards
       xref.setVersion(null);
       xref.setMap(null);
-      found |= searchDataset(sequenceI, xref, rseqs, cf, false);
+      found |= searchDataset(fromDna, sequenceI, xref, rseqs, cf, false);
     }
     return found;
   }
@@ -728,6 +729,9 @@ public class CrossRef
    * Searches dataset for DBRefEntrys matching the given one (xrf) and adds the
    * associated sequence to rseqs
    * 
+   * @param fromDna
+   *          true if context was searching for refs *from* dna sequence, false
+   *          if context was searching for refs *from* protein sequence
    * @param sequenceI
    *          a sequence to ignore (start point of search)
    * @param xrf
@@ -740,8 +744,9 @@ public class CrossRef
    *          - search all references or only subset
    * @return true if relationship found and sequence added.
    */
-  boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
-          List<SequenceI> rseqs, AlignedCodonFrame cf, boolean direct)
+  boolean searchDataset(boolean fromDna, SequenceI sequenceI,
+          DBRefEntry xrf, List<SequenceI> rseqs, AlignedCodonFrame cf,
+          boolean direct)
   {
     boolean found = false;
     if (dataset == null)
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 18ee912..c5fb11f 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4651,7 +4651,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       final boolean dna = viewport.getAlignment().isNucleotide();
       List<String> ptypes = (seqs == null || seqs.length == 0) ? null
               : new CrossRef(seqs, dataset)
-                      .findXrefSourcesForSequences();
+                      .findXrefSourcesForSequences(dna);
 
       for (final String source : ptypes)
       {
@@ -4691,7 +4691,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param source
    *          the database to show cross-references for
    */
-  protected void showProductsFor(final SequenceI[] sel, final boolean dna,
+  protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
           final String source)
   {
     Runnable foo = new Runnable()
@@ -4710,8 +4710,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   .getAlignment();
           AlignmentI dataset = alignment.getDataset() == null ? alignment
                   : alignment.getDataset();
-          AlignmentI xrefs = new CrossRef(sel, alignment)
-                  .findXrefSequences(source);
+          boolean dna = alignment.isNucleotide();
+          if (_odna!=dna)
+          {
+            System.err
+                    .println("Conflict: showProducts for alignment originally "
+                            + "thought to be "
+                            + (_odna ? "DNA" : "Protein")
+                            + " now searching for "
+                            + (dna ? "DNA" : "Protein") + " Context.");
+          }
+          AlignmentI xrefs = new CrossRef(sel, dataset)
+                  .findXrefSequences(source, dna);
           if (xrefs == null)
           {
             return;
@@ -4891,7 +4901,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           sprods[s].updatePDBIds();
         }
         Alignment al = new Alignment(sprods);
-        al.setDataset((Alignment) dataset);
+        al.setDataset(dataset);
         return al;
       }
 
diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index ecfedb1..eab8d5d 100644
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -103,7 +103,7 @@ public class CrossRefTest
      * first with no dbrefs to search
      */
     sources = new CrossRef(new SequenceI[] { seq }, al)
-            .findXrefSourcesForSequences();
+            .findXrefSourcesForSequences(false);
     assertTrue(sources.isEmpty());
 
     /*
@@ -120,7 +120,7 @@ public class CrossRefTest
     seq.addDBRef(new DBRefEntry("ENSEMBL", "0", "E2349"));
     seq.addDBRef(new DBRefEntry("ENSEMBLGENOMES", "0", "E2350"));
     sources = new CrossRef(new SequenceI[] { seq }, al)
-            .findXrefSourcesForSequences();
+            .findXrefSourcesForSequences(false);
     assertEquals(4, sources.size());
     assertEquals("[EMBL, EMBLCDS, GENEDB, ENSEMBL]",
             sources.toString());
@@ -140,7 +140,7 @@ public class CrossRefTest
     // TODO include ENSEMBLGENOMES in DBRefSource.DNACODINGDBS ?
     al.addSequence(seq2);
     sources = new CrossRef(new SequenceI[] { seq }, al)
-            .findXrefSourcesForSequences();
+            .findXrefSourcesForSequences(false);
     assertEquals(3, sources.size());
     assertEquals("[EMBLCDS, EMBL, GENEDB]", sources.toString());
   }
@@ -171,7 +171,7 @@ public class CrossRefTest
      */
     AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
     Alignment xrefs = new CrossRef(new SequenceI[] { emblSeq }, al)
-            .findXrefSequences("UNIPROT");
+            .findXrefSequences("UNIPROT", true);
     assertEquals(1, xrefs.getHeight());
     assertSame(uniprotSeq, xrefs.getSequenceAt(0));
   }
@@ -206,7 +206,8 @@ public class CrossRefTest
      */
     AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
     Alignment xrefs = new CrossRef(new SequenceI[] { uniprotSeq },
-            al).findXrefSequences("EMBL");
+ al)
+            .findXrefSequences("EMBL", true);
     assertEquals(1, xrefs.getHeight());
     assertSame(emblSeq, xrefs.getSequenceAt(0));
   }
@@ -233,7 +234,7 @@ public class CrossRefTest
      */
     AlignmentI al = new Alignment(new SequenceI[] { dna1, dna2 });
     Alignment xrefs = new CrossRef(new SequenceI[] { dna2 }, al)
-            .findXrefSequences("UNIPROT");
+            .findXrefSequences("UNIPROT", true);
     assertNull(xrefs);
   }
 
@@ -262,7 +263,8 @@ public class CrossRefTest
      */
     DBRefEntry dbref = new DBRefEntry("UNIPROT", "0", "P30419");
     CrossRef testee = new CrossRef(al.getSequencesArray(), al);
-    boolean found = testee.searchDataset(dna1, dbref, result, null, true);
+    boolean found = testee.searchDataset(true, dna1, dbref, result, null,
+            true);
     assertFalse(found);
     assertTrue(result.isEmpty());
 
@@ -273,7 +275,7 @@ public class CrossRefTest
      * search for a protein sequence with dbref UNIPROT:Q9ZTS2
      */
     dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
-    found = testee.searchDataset(dna1, dbref, result, null, true);
+    found = testee.searchDataset(true, dna1, dbref, result, null, true);
     assertTrue(found);
     assertEquals(1, result.size());
     assertSame(pep1, result.get(0));
@@ -283,7 +285,7 @@ public class CrossRefTest
      */
     result.clear();
     dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
-    found = testee.searchDataset(pep1, dbref, result, null, false);
+    found = testee.searchDataset(false, pep1, dbref, result, null, false);
     assertTrue(found);
     assertEquals(1, result.size());
     assertSame(dna1, result.get(0));
@@ -332,7 +334,7 @@ public class CrossRefTest
      */
     AlignmentI al = new Alignment(new SequenceI[] { dna1 });
     Alignment xrefs = new CrossRef(new SequenceI[] { dna1 }, al)
-            .findXrefSequences("UNIPROT");
+            .findXrefSequences("UNIPROT", true);
     assertEquals(2, xrefs.getHeight());
 
     /*
@@ -418,7 +420,7 @@ public class CrossRefTest
      */
     AlignmentI al = new Alignment(new SequenceI[] { dna1 });
     Alignment xrefs = new CrossRef(new SequenceI[] { dna1 }, al)
-            .findXrefSequences("UNIPROT");
+            .findXrefSequences("UNIPROT", true);
     assertEquals(2, xrefs.getHeight());
     assertSame(pep1, xrefs.getSequenceAt(0));
     assertSame(pep2, xrefs.getSequenceAt(1));
@@ -500,7 +502,8 @@ public class CrossRefTest
     SequenceI[] seqs = new SequenceI[] { gene, braf001, braf002 };
     AlignmentI al = new Alignment(seqs);
     Alignment xrefs = new CrossRef(seqs, al)
-            .findXrefSequences("UNIPROT");
+.findXrefSequences("UNIPROT",
+            true);
     assertEquals(2, xrefs.getHeight());
     assertSame(pep1, xrefs.getSequenceAt(0));
     assertSame(pep2, xrefs.getSequenceAt(1));
@@ -652,8 +655,8 @@ public class CrossRefTest
      */
     SequenceI[] seqs = new SequenceI[] { p0ce19, p0ce20 };
     AlignmentI al = new Alignment(seqs);
-    Alignment xrefs = new CrossRef(seqs, al)
-            .findXrefSequences("EMBL");
+    Alignment xrefs = new CrossRef(seqs, al).findXrefSequences("EMBL",
+            false);
 
     /*
      * verify retrieved sequences
diff --git a/test/jalview/ws/SequenceFetcherTest.java b/test/jalview/ws/SequenceFetcherTest.java
index 50fb3c0..4e08430 100644
--- a/test/jalview/ws/SequenceFetcherTest.java
+++ b/test/jalview/ws/SequenceFetcherTest.java
@@ -108,7 +108,7 @@ public class SequenceFetcherTest
             // try and find products
             CrossRef crossRef = new CrossRef(al.getSequencesArray(),
                     al);
-            List<String> types = crossRef.findXrefSourcesForSequences();
+            List<String> types = crossRef.findXrefSourcesForSequences(dna);
             if (types != null)
             {
               System.out.println("Xref Types for: "
@@ -116,7 +116,7 @@ public class SequenceFetcherTest
               for (String source : types)
               {
                 System.out.println("Type: " + source);
-                SequenceI[] prod = crossRef.findXrefSequences(source)
+                SequenceI[] prod = crossRef.findXrefSequences(source, dna)
                         .getSequencesArray();
                 System.out.println("Found "
                         + ((prod == null) ? "no" : "" + prod.length)
@@ -199,8 +199,8 @@ public class SequenceFetcherTest
           // have a bash at finding the products amongst all the retrieved
           // sequences.
           SequenceI[] seqs = al.getSequencesArray();
-          Alignment prodal = new CrossRef(seqs, ds)
-                  .findXrefSequences(null);
+          Alignment prodal = new CrossRef(seqs, ds).findXrefSequences(null,
+                  dna);
           System.out.println("Found "
                   + ((prodal == null) ? "no" : "" + prodal.getHeight())
                   + " products");
diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index 8ee4f40..b3c7e10 100644
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -179,7 +179,7 @@ public class DbRefFetcherTest
     assertEquals("Expected local reference map to be 3 nucleotides", dr[0]
             .getMap().getWidth(), 3);
     AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
-            .findXrefSequences(dr[0].getSource());
+            .findXrefSequences(dr[0].getSource(), true);
     assertNotNull(
             "Couldn't recover cross reference sequence from dataset. Was it ever added ?",
             sprods);