From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 6 Jan 2017 09:03:27 +0000 (+0000)
Subject: Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
X-Git-Tag: Release_2_10_3b1~357^2~16^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a6875ff6ca7894443c98b1d068f78ea25c5bfc87;hp=-c;p=jalview.git

Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
---

a6875ff6ca7894443c98b1d068f78ea25c5bfc87
diff --combined src/jalview/datamodel/Alignment.java
index 49f6268,90bdcae..a6f2bf4
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@@ -54,7 -54,11 +54,7 @@@ public class Alignment implements Align
  
    protected char gapCharacter = '-';
  
 -  protected int type = NUCLEOTIDE;
 -
 -  public static final int PROTEIN = 0;
 -
 -  public static final int NUCLEOTIDE = 1;
 +  private boolean nucleotide = true;
  
    public boolean hasRNAStructure = false;
  
@@@ -72,7 -76,14 +72,7 @@@
      hiddenSequences = new HiddenSequences(this);
      codonFrameList = new ArrayList<AlignedCodonFrame>();
  
 -    if (Comparison.isNucleotide(seqs))
 -    {
 -      type = NUCLEOTIDE;
 -    }
 -    else
 -    {
 -      type = PROTEIN;
 -    }
 +    nucleotide = Comparison.isNucleotide(seqs);
  
      sequences = Collections.synchronizedList(new ArrayList<SequenceI>());
  
@@@ -207,9 -218,7 +207,9 @@@
    }
  
    /**
 -   * Adds a sequence to the alignment. Recalculates maxLength and size.
 +   * Adds a sequence to the alignment. Recalculates maxLength and size. Note
 +   * this currently does not recalculate whether or not the alignment is
 +   * nucleotide, so mixed alignments may have undefined behaviour.
     * 
     * @param snew
     */
@@@ -357,17 -366,18 +357,18 @@@
     * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
     */
    @Override
-   public SequenceGroup findGroup(SequenceI s)
+   public SequenceGroup findGroup(SequenceI seq, int position)
    {
      synchronized (groups)
      {
-       for (int i = 0; i < this.groups.size(); i++)
+       for (SequenceGroup sg : groups)
        {
-         SequenceGroup sg = groups.get(i);
- 
-         if (sg.getSequences(null).contains(s))
+         if (sg.getSequences(null).contains(seq))
          {
-           return sg;
+           if (position >= sg.getStartRes() && position <= sg.getEndRes())
+           {
+             return sg;
+           }
          }
        }
      }
@@@ -968,9 -978,29 +969,9 @@@
    }
  
    @Override
 -  public void setNucleotide(boolean b)
 -  {
 -    if (b)
 -    {
 -      type = NUCLEOTIDE;
 -    }
 -    else
 -    {
 -      type = PROTEIN;
 -    }
 -  }
 -
 -  @Override
    public boolean isNucleotide()
    {
 -    if (type == NUCLEOTIDE)
 -    {
 -      return true;
 -    }
 -    else
 -    {
 -      return false;
 -    }
 +    return nucleotide;
    }
  
    @Override
@@@ -1561,6 -1591,7 +1562,6 @@@
            String calcId, boolean autoCalc, SequenceI seqRef,
            SequenceGroup groupRef)
    {
 -    assert (name != null);
      if (annotations != null)
      {
        for (AlignmentAnnotation annot : getAlignmentAnnotation())
@@@ -1592,18 -1623,14 +1593,18 @@@
    @Override
    public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
    {
 -    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
 -    for (AlignmentAnnotation a : getAlignmentAnnotation())
 +    List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
 +    AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
 +    if (alignmentAnnotation != null)
      {
 -      if (a.getCalcId() == calcId
 -              || (a.getCalcId() != null && calcId != null && a.getCalcId()
 -                      .equals(calcId)))
 +      for (AlignmentAnnotation a : alignmentAnnotation)
        {
 -        aa.add(a);
 +        if (a.getCalcId() == calcId
 +                || (a.getCalcId() != null && calcId != null && a
 +                        .getCalcId().equals(calcId)))
 +        {
 +          aa.add(a);
 +        }
        }
      }
      return aa;
diff --combined src/jalview/datamodel/AlignmentI.java
index 1b5cc0b,2df099a..a0b3ff1
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@@ -156,15 -156,16 +156,16 @@@ public interface AlignmentI extends Ann
    int findIndex(SequenceI s);
  
    /**
-    * Finds group that given sequence is part of.
+    * Returns the first group (in the order in which groups were added) that
+    * includes the given sequence and aligned position (base 0), or null if none
+    * found
     * 
-    * @param s
-    *          Sequence in alignment.
+    * @param seq
+    * @param position
     * 
-    * @return First group found for sequence. WARNING : Sequences may be members
-    *         of several groups. This method is incomplete.
+    * @return
     */
-   SequenceGroup findGroup(SequenceI s);
+   SequenceGroup findGroup(SequenceI seq, int position);
  
    /**
     * Finds all groups that a given sequence is part of.
@@@ -298,6 -299,12 +299,6 @@@
    boolean hasRNAStructure();
  
    /**
 -   * Set alignment to be a nucleotide sequence
 -   * 
 -   */
 -  void setNucleotide(boolean b);
 -
 -  /**
     * Get the associated dataset for the alignment.
     * 
     * @return Alignment containing dataset sequences or null of this is a
diff --combined test/jalview/datamodel/AlignmentTest.java
index 0d6c8ae,618bac5..7af77f5
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@@ -611,12 -611,6 +611,12 @@@ public class AlignmentTes
      AlignmentAnnotation ann = iter.next();
      assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
      assertFalse(iter.hasNext());
 +
 +    // invalid id
 +    anns = al.findAnnotation("CalcIdForD.melanogaster.?");
 +    assertFalse(iter.hasNext());
 +    anns = al.findAnnotation(null);
 +    assertFalse(iter.hasNext());
    }
  
    @Test(groups = { "Functional" })
@@@ -1137,4 -1131,63 +1137,63 @@@
      assertSame(pep.getDatasetSequence(), cds.getDBRefs()[0].map.to);
    }
  
+   @Test(groups = { "Functional" })
+   public void testFindGroup()
+   {
+     SequenceI seq1 = new Sequence("seq1", "ABCDEF---GHI");
+     SequenceI seq2 = new Sequence("seq2", "---JKLMNO---");
+     AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2 });
+ 
+     assertNull(a.findGroup(null, 0));
+     assertNull(a.findGroup(seq1, 1));
+     assertNull(a.findGroup(seq1, -1));
+ 
+     /*
+      * add a group consisting of just "DEF"
+      */
+     SequenceGroup sg1 = new SequenceGroup();
+     sg1.addSequence(seq1, false);
+     sg1.setStartRes(3);
+     sg1.setEndRes(5);
+     a.addGroup(sg1);
+ 
+     assertNull(a.findGroup(seq1, 2)); // position not in group
+     assertNull(a.findGroup(seq1, 6)); // position not in group
+     assertNull(a.findGroup(seq2, 5)); // sequence not in group
+     assertSame(a.findGroup(seq1, 3), sg1); // yes
+     assertSame(a.findGroup(seq1, 4), sg1);
+     assertSame(a.findGroup(seq1, 5), sg1);
+ 
+     /*
+      * add a group consisting of 
+      * EF--
+      * KLMN
+      */
+     SequenceGroup sg2 = new SequenceGroup();
+     sg2.addSequence(seq1, false);
+     sg2.addSequence(seq2, false);
+     sg2.setStartRes(4);
+     sg2.setEndRes(7);
+     a.addGroup(sg2);
+ 
+     assertNull(a.findGroup(seq1, 2)); // unchanged
+     assertSame(a.findGroup(seq1, 3), sg1); // unchanged
+     /*
+      * if a residue is in more than one group, method returns
+      * the first found (in order groups were added)
+      */
+     assertSame(a.findGroup(seq1, 4), sg1);
+     assertSame(a.findGroup(seq1, 5), sg1);
+ 
+     /*
+      * seq2 only belongs to the second group
+      */
+     assertSame(a.findGroup(seq2, 4), sg2);
+     assertSame(a.findGroup(seq2, 5), sg2);
+     assertSame(a.findGroup(seq2, 6), sg2);
+     assertSame(a.findGroup(seq2, 7), sg2);
+     assertNull(a.findGroup(seq2, 3));
+     assertNull(a.findGroup(seq2, 8));
+   }
+ 
  }