X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=0ee03445558468a9896249320ecda8c689e886d9;hb=375e9f7d622c89e41fc7831fd517e23d1ea52fbd;hp=1134857428850bf8e49716f31013e37c56b2c37b;hpb=49428d3a57e4f4863acbdeb3f77049ed95efd6c3;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 1134857..0ee0344 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -44,7 +44,7 @@ import java.util.Vector;
  */
 public class Alignment implements AlignmentI
 {
-  protected Alignment dataset;
+  private Alignment dataset;
 
   protected List<SequenceI> sequences;
 
@@ -109,7 +109,10 @@ public class Alignment implements AlignmentI
     /*
      * Share the same dataset sequence mappings (if any). 
      */
-    this.setCodonFrames(al.getCodonFrames());
+    if (dataset == null && al.getDataset() == null)
+    {
+      this.setCodonFrames(al.getCodonFrames());
+    }
   }
 
   /**
@@ -986,7 +989,7 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void setDataset(Alignment data)
+  public void setDataset(AlignmentI data)
   {
     if (dataset == null && data == null)
     {
@@ -994,7 +997,12 @@ public class Alignment implements AlignmentI
     }
     else if (dataset == null && data != null)
     {
-      dataset = data;
+      if (!(data instanceof Alignment))
+      {
+        throw new Error(
+                "Implementation Error: jalview.datamodel.Alignment does not yet support other implementations of AlignmentI as its dataset reference");
+      }
+      dataset = (Alignment) data;
       for (int i = 0; i < getHeight(); i++)
       {
         SequenceI currentSeq = getSequenceAt(i);
@@ -1340,6 +1348,10 @@ public class Alignment implements AlignmentI
   @Override
   public List<AlignedCodonFrame> getCodonFrames()
   {
+    // TODO: Fix this method to fix failing AlignedCodonFrame tests
+    // this behaviour is currently incorrect. method should return codon frames
+    // for just the alignment,
+    // selected from dataset
     return dataset != null ? dataset.getCodonFrames() : codonFrameList;
   }
 
@@ -1365,7 +1377,7 @@ public class Alignment implements AlignmentI
     {
       System.err.println("Self append may cause a deadlock.");
     }
-    // TODO test this method for a future 2.5 release
+    // TODO JAL-1270 needs test coverage
     // currently tested for use in jalview.gui.SequenceFetcher
     boolean samegap = toappend.getGapCharacter() == getGapCharacter();
     char oldc = toappend.getGapCharacter();
@@ -1401,6 +1413,7 @@ public class Alignment implements AlignmentI
       addAnnotation(alan[a]);
     }
 
+    // use add method
     getCodonFrames().addAll(toappend.getCodonFrames());
 
     List<SequenceGroup> sg = toappend.getGroups();
@@ -1691,9 +1704,11 @@ public class Alignment implements AlignmentI
    * Parameters control whether gaps in exon (mapped) and intron (unmapped)
    * regions are preserved. Gaps that connect introns to exons are treated
    * conservatively, i.e. only preserved if both intron and exon gaps are
-   * preserved.
+   * preserved. TODO: check caveats below where the implementation fails
    * 
    * @param al
+   *          - must have same dataset, and sequences in al must have equivalent
+   *          dataset sequence and start/end bounds under given mapping
    * @param preserveMappedGaps
    *          if true, gaps within and between mapped codons are preserved
    * @param preserveUnmappedGaps
@@ -1704,31 +1719,17 @@ public class Alignment implements AlignmentI
           boolean preserveUnmappedGaps)
   {
     // TODO should this method signature be the one in the interface?
-    int count = 0;
     boolean thisIsNucleotide = this.isNucleotide();
     boolean thatIsProtein = !al.isNucleotide();
     if (!thatIsProtein && !thisIsNucleotide)
     {
       return AlignmentUtils.alignProteinAsDna(this, al);
     }
-
-    char thisGapChar = this.getGapCharacter();
-    String gap = thisIsNucleotide && thatIsProtein ? String
-            .valueOf(new char[] { thisGapChar, thisGapChar, thisGapChar })
-            : String.valueOf(thisGapChar);
-
-    // TODO handle intron regions? Needs a 'holistic' alignment of dna,
-    // not just sequence by sequence. But how to 'gap' intron regions?
-
-    /*
-     * Get mappings from 'that' alignment's sequences to this.
-     */
-    for (SequenceI alignTo : getSequences())
+    else if (thatIsProtein && thisIsNucleotide)
     {
-      count += AlignmentUtils.alignSequenceAs(alignTo, al, gap,
-              preserveMappedGaps, preserveUnmappedGaps) ? 1 : 0;
+      return AlignmentUtils.alignCdsAsProtein(this, al);
     }
-    return count;
+    return AlignmentUtils.alignAs(this, al);
   }
 
   /**
@@ -1811,4 +1812,40 @@ public class Alignment implements AlignmentI
     }
     return null;
   }
+
+  @Override
+  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols)
+  {
+    int[] alignmentStartEnd = new int[] { 0, getWidth() - 1 };
+    int startPos = alignmentStartEnd[0];
+    int endPos = alignmentStartEnd[1];
+
+    int[] lowestRange = new int[] { -1, -1 };
+    int[] higestRange = new int[] { -1, -1 };
+
+    for (int[] hiddenCol : hiddenCols)
+    {
+      lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+      higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+    }
+
+    if (lowestRange[0] == -1 && lowestRange[1] == -1)
+    {
+      startPos = alignmentStartEnd[0];
+    }
+    else
+    {
+      startPos = lowestRange[1] + 1;
+    }
+
+    if (higestRange[0] == -1 && higestRange[1] == -1)
+    {
+      endPos = alignmentStartEnd[1];
+    }
+    else
+    {
+      endPos = higestRange[0] - 1;
+    }
+    return new int[] { startPos, endPos };
+  }
 }