JAL-653 realise virtual mappings and align when adding sequences

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 3f9f03f..1134857 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -22,13 +22,14 @@ package jalview.datamodel;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.io.FastaFile;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashSet;
 import java.util.Hashtable;
-import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -47,8 +48,7 @@ public class Alignment implements AlignmentI
 
   protected List<SequenceI> sequences;
 
-  protected List<SequenceGroup> groups = java.util.Collections
-          .synchronizedList(new ArrayList<SequenceGroup>());
+  protected List<SequenceGroup> groups;
 
   protected char gapCharacter = '-';
 
@@ -60,20 +60,21 @@ public class Alignment implements AlignmentI
 
   public boolean hasRNAStructure = false;
 
-  /** DOCUMENT ME!! */
   public AlignmentAnnotation[] annotations;
 
-  HiddenSequences hiddenSequences = new HiddenSequences(this);
+  HiddenSequences hiddenSequences;
 
   public Hashtable alignmentProperties;
 
-  private Set<AlignedCodonFrame> codonFrameList = new LinkedHashSet<AlignedCodonFrame>();
+  private List<AlignedCodonFrame> codonFrameList;
 
   private void initAlignment(SequenceI[] seqs)
   {
-    int i = 0;
+    groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
+    hiddenSequences = new HiddenSequences(this);
+    codonFrameList = new ArrayList<AlignedCodonFrame>();
 
-    if (jalview.util.Comparison.isNucleotide(seqs))
+    if (Comparison.isNucleotide(seqs))
     {
       type = NUCLEOTIDE;
     }
@@ -82,10 +83,9 @@ public class Alignment implements AlignmentI
       type = PROTEIN;
     }
 
-    sequences = java.util.Collections
-            .synchronizedList(new ArrayList<SequenceI>());
+    sequences = Collections.synchronizedList(new ArrayList<SequenceI>());
 
-    for (i = 0; i < seqs.length; i++)
+    for (int i = 0; i < seqs.length; i++)
     {
       sequences.add(seqs[i]);
     }
@@ -104,13 +104,12 @@ public class Alignment implements AlignmentI
       seqs[i] = new Sequence(seqs[i]);
     }
 
+    initAlignment(seqs);
+
     /*
-     * Share the same dataset sequence mappings (if any). TODO: find a better
-     * place for these to live (alignment dataset?).
+     * Share the same dataset sequence mappings (if any). 
      */
     this.setCodonFrames(al.getCodonFrames());
-
-    initAlignment(seqs);
   }
 
   /**
@@ -1281,8 +1280,8 @@ public class Alignment implements AlignmentI
   @Override
   public void addCodonFrame(AlignedCodonFrame codons)
   {
-    Set<AlignedCodonFrame> acfs = getCodonFrames();
-    if (codons != null && acfs != null)
+    List<AlignedCodonFrame> acfs = getCodonFrames();
+    if (codons != null && acfs != null && !acfs.contains(codons))
     {
       acfs.add(codons);
     }
@@ -1319,7 +1318,7 @@ public class Alignment implements AlignmentI
    * @see jalview.datamodel.AlignmentI#setCodonFrames()
    */
   @Override
-  public void setCodonFrames(Set<AlignedCodonFrame> acfs)
+  public void setCodonFrames(List<AlignedCodonFrame> acfs)
   {
     if (dataset != null)
     {
@@ -1339,7 +1338,7 @@ public class Alignment implements AlignmentI
    * @see jalview.datamodel.AlignmentI#getCodonFrames()
    */
   @Override
-  public Set<AlignedCodonFrame> getCodonFrames()
+  public List<AlignedCodonFrame> getCodonFrames()
   {
     return dataset != null ? dataset.getCodonFrames() : codonFrameList;
   }
@@ -1351,7 +1350,7 @@ public class Alignment implements AlignmentI
   @Override
   public boolean removeCodonFrame(AlignedCodonFrame codons)
   {
-    Set<AlignedCodonFrame> acfs = getCodonFrames();
+    List<AlignedCodonFrame> acfs = getCodonFrames();
     if (codons == null || acfs == null)
     {
       return false;
@@ -1770,4 +1769,46 @@ public class Alignment implements AlignmentI
     }
     return hasValidSeq;
   }
+
+  /**
+   * Update any mappings to 'virtual' sequences to compatible real ones, if
+   * present in the added sequences. Returns a count of mappings updated.
+   * 
+   * @param seqs
+   * @return
+   */
+  @Override
+  public int realiseMappings(List<SequenceI> seqs)
+  {
+    int count = 0;
+    for (SequenceI seq : seqs)
+    {
+      for (AlignedCodonFrame mapping : getCodonFrames())
+      {
+        count += mapping.realiseWith(seq);
+      }
+    }
+    return count;
+  }
+
+  /**
+   * Returns the first AlignedCodonFrame that has a mapping between the given
+   * dataset sequences
+   * 
+   * @param mapFrom
+   * @param mapTo
+   * @return
+   */
+  @Override
+  public AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo)
+  {
+    for (AlignedCodonFrame acf : getCodonFrames())
+    {
+      if (acf.getAaForDnaSeq(mapFrom) == mapTo)
+      {
+        return acf;
+      }
+    }
+    return null;
+  }
 }

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index de79488..396ef2d 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -375,12 +375,12 @@ public interface AlignmentI extends AnnotatedCollectionI
    * 
    * @return
    */
-  Set<AlignedCodonFrame> getCodonFrames();
+  List<AlignedCodonFrame> getCodonFrames();
 
   /**
-   * Set the codon frame mappings (replacing any existing set).
+   * Set the codon frame mappings (replacing any existing list).
    */
-  void setCodonFrames(Set<AlignedCodonFrame> acfs);
+  void setCodonFrames(List<AlignedCodonFrame> acfs);
 
   /**
    * get codon frames involving sequenceI
@@ -524,4 +524,23 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @return
    */
   public boolean hasValidSequence();
+
+  /**
+   * Update any mappings to 'virtual' sequences to compatible real ones, if
+   * present in the added sequences. Returns a count of mappings updated.
+   * 
+   * @param seqs
+   * @return
+   */
+  int realiseMappings(List<SequenceI> seqs);
+
+  /**
+   * Returns the first AlignedCodonFrame that has a mapping between the given
+   * dataset sequences
+   * 
+   * @param mapFrom
+   * @param mapTo
+   * @return
+   */
+  AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 }

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 9ee88db..06dc4c4 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -72,7 +72,6 @@ import java.awt.Rectangle;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
-import java.util.Set;
 import java.util.Vector;
 
 import javax.swing.JInternalFrame;
@@ -461,7 +460,7 @@ public class AlignViewport extends AlignmentViewport implements
     AlignmentI al = getAlignment();
     if (al != null)
     {
-      Set<AlignedCodonFrame> mappings = al.getCodonFrames();
+      List<AlignedCodonFrame> mappings = al.getCodonFrames();
       if (mappings != null)
       {
         StructureSelectionManager ssm = StructureSelectionManager
@@ -855,7 +854,7 @@ public class AlignViewport extends AlignmentViewport implements
      * Check if any added sequence could be the object of a mapping or
      * cross-reference; if so, make the mapping explicit 
      */
-    realiseMappings(getAlignment(), toAdd);
+    getAlignment().realiseMappings(toAdd.getSequences());
 
     /*
      * If any cDNA/protein mappings exist or can be made between the alignments, 
@@ -878,60 +877,26 @@ public class AlignViewport extends AlignmentViewport implements
     // TODO: JAL-407 regardless of above - identical sequences (based on ID and
     // provenance) should share the same dataset sequence
 
+    AlignmentI al = getAlignment();
+    String gap = String.valueOf(al.getGapCharacter());
     for (int i = 0; i < toAdd.getHeight(); i++)
     {
-      getAlignment().addSequence(toAdd.getSequenceAt(i));
-    }
-
-    setEndSeq(getAlignment().getHeight());
-    firePropertyChange("alignment", null, getAlignment().getSequences());
-  }
-
-  /**
-   * Check if any added sequence could be the object of a mapping or
-   * cross-reference; if so, make the mapping explicit. Returns the count of
-   * mappings updated.
-   * 
-   * @param al
-   * @param toAdd
-   */
-  protected int realiseMappings(AlignmentI al, AlignmentI toAdd)
-  {
-    // TODO this is proof of concept
-    // we might want to give the user some choice here
-    int count = 0;
-    for (SequenceI seq : toAdd.getSequences())
-    {
-      count += realiseMappingsTo(al, seq);
-    }
-    return count;
-  }
-
-  /**
-   * If the alignment holds any mappings to a virtual (placeholder) sequence
-   * that matches all or part of the given sequence, then update the mapping to
-   * point to the sequence. Returns the number of mappings updated.
-   * 
-   * @param al
-   * @param seq
-   * @return
-   */
-  protected int realiseMappingsTo(AlignmentI al, SequenceI seq)
-  {
-    int count = 0;
-    Set<AlignedCodonFrame> mappings = al.getCodonFrames();
-    for (AlignedCodonFrame mapping : mappings)
-    {
+      SequenceI seq = toAdd.getSequenceAt(i);
       /*
-       * TODO could just go straight to realiseWith() here unless we want
-       * to give the user some choice before going ahead
+       * experimental!
+       * - 'align' any mapped sequences as per existing 
+       *    e.g. cdna to genome, domain hit to protein sequence
+       * very experimental! (need a separate menu option for this)
+       * - only add mapped sequences ('select targets from a dataset')
        */
-      if (mapping.isRealisableWith(seq))
+      if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/)
       {
-        count += mapping.realiseWith(seq);
+        al.addSequence(seq);
       }
     }
-    return count;
+
+    setEndSeq(getAlignment().getHeight());
+    firePropertyChange("alignment", null, getAlignment().getSequences());
   }
 
   /**

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 3f1946e..3d807e2 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -65,7 +65,6 @@ import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 
 /**
  * base class holding visualization and analysis attributes and common logic for
@@ -95,6 +94,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param name
    * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
    */
+  @Override
   public void setFontName(String name)
   {
     viewStyle.setFontName(name);
@@ -104,6 +104,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param style
    * @see jalview.api.ViewStyleI#setFontStyle(int)
    */
+  @Override
   public void setFontStyle(int style)
   {
     viewStyle.setFontStyle(style);
@@ -113,6 +114,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param size
    * @see jalview.api.ViewStyleI#setFontSize(int)
    */
+  @Override
   public void setFontSize(int size)
   {
     viewStyle.setFontSize(size);
@@ -122,6 +124,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getFontStyle()
    */
+  @Override
   public int getFontStyle()
   {
     return viewStyle.getFontStyle();
@@ -131,6 +134,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getFontName()
    */
+  @Override
   public String getFontName()
   {
     return viewStyle.getFontName();
@@ -140,6 +144,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getFontSize()
    */
+  @Override
   public int getFontSize()
   {
     return viewStyle.getFontSize();
@@ -149,6 +154,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param upperCasebold
    * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
    */
+  @Override
   public void setUpperCasebold(boolean upperCasebold)
   {
     viewStyle.setUpperCasebold(upperCasebold);
@@ -158,6 +164,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isUpperCasebold()
    */
+  @Override
   public boolean isUpperCasebold()
   {
     return viewStyle.isUpperCasebold();
@@ -167,6 +174,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isSeqNameItalics()
    */
+  @Override
   public boolean isSeqNameItalics()
   {
     return viewStyle.isSeqNameItalics();
@@ -176,6 +184,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param colourByReferenceSeq
    * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
    */
+  @Override
   public void setColourByReferenceSeq(boolean colourByReferenceSeq)
   {
     viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
@@ -185,6 +194,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
    */
+  @Override
   public void setColourAppliesToAllGroups(boolean b)
   {
     viewStyle.setColourAppliesToAllGroups(b);
@@ -194,6 +204,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
    */
+  @Override
   public boolean getColourAppliesToAllGroups()
   {
     return viewStyle.getColourAppliesToAllGroups();
@@ -203,6 +214,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
    */
+  @Override
   public boolean getAbovePIDThreshold()
   {
     return viewStyle.getAbovePIDThreshold();
@@ -212,6 +224,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param inc
    * @see jalview.api.ViewStyleI#setIncrement(int)
    */
+  @Override
   public void setIncrement(int inc)
   {
     viewStyle.setIncrement(inc);
@@ -221,6 +234,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getIncrement()
    */
+  @Override
   public int getIncrement()
   {
     return viewStyle.getIncrement();
@@ -230,6 +244,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setConservationSelected(boolean)
    */
+  @Override
   public void setConservationSelected(boolean b)
   {
     viewStyle.setConservationSelected(b);
@@ -239,6 +254,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param show
    * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
    */
+  @Override
   public void setShowHiddenMarkers(boolean show)
   {
     viewStyle.setShowHiddenMarkers(show);
@@ -248,6 +264,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
    */
+  @Override
   public boolean getShowHiddenMarkers()
   {
     return viewStyle.getShowHiddenMarkers();
@@ -257,6 +274,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
    */
+  @Override
   public void setScaleRightWrapped(boolean b)
   {
     viewStyle.setScaleRightWrapped(b);
@@ -266,6 +284,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
    */
+  @Override
   public void setScaleLeftWrapped(boolean b)
   {
     viewStyle.setScaleLeftWrapped(b);
@@ -275,6 +294,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
    */
+  @Override
   public void setScaleAboveWrapped(boolean b)
   {
     viewStyle.setScaleAboveWrapped(b);
@@ -284,6 +304,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
    */
+  @Override
   public boolean getScaleLeftWrapped()
   {
     return viewStyle.getScaleLeftWrapped();
@@ -293,6 +314,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
    */
+  @Override
   public boolean getScaleAboveWrapped()
   {
     return viewStyle.getScaleAboveWrapped();
@@ -302,6 +324,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getScaleRightWrapped()
    */
+  @Override
   public boolean getScaleRightWrapped()
   {
     return viewStyle.getScaleRightWrapped();
@@ -311,6 +334,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
    */
+  @Override
   public void setAbovePIDThreshold(boolean b)
   {
     viewStyle.setAbovePIDThreshold(b);
@@ -320,6 +344,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param thresh
    * @see jalview.api.ViewStyleI#setThreshold(int)
    */
+  @Override
   public void setThreshold(int thresh)
   {
     viewStyle.setThreshold(thresh);
@@ -329,6 +354,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getThreshold()
    */
+  @Override
   public int getThreshold()
   {
     return viewStyle.getThreshold();
@@ -338,6 +364,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowJVSuffix()
    */
+  @Override
   public boolean getShowJVSuffix()
   {
     return viewStyle.getShowJVSuffix();
@@ -347,6 +374,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
    */
+  @Override
   public void setShowJVSuffix(boolean b)
   {
     viewStyle.setShowJVSuffix(b);
@@ -356,6 +384,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param state
    * @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
    */
+  @Override
   public void setWrapAlignment(boolean state)
   {
     viewStyle.setWrapAlignment(state);
@@ -365,6 +394,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param state
    * @see jalview.api.ViewStyleI#setShowText(boolean)
    */
+  @Override
   public void setShowText(boolean state)
   {
     viewStyle.setShowText(state);
@@ -374,6 +404,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param state
    * @see jalview.api.ViewStyleI#setRenderGaps(boolean)
    */
+  @Override
   public void setRenderGaps(boolean state)
   {
     viewStyle.setRenderGaps(state);
@@ -383,6 +414,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getColourText()
    */
+  @Override
   public boolean getColourText()
   {
     return viewStyle.getColourText();
@@ -392,6 +424,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param state
    * @see jalview.api.ViewStyleI#setColourText(boolean)
    */
+  @Override
   public void setColourText(boolean state)
   {
     viewStyle.setColourText(state);
@@ -401,6 +434,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getWrapAlignment()
    */
+  @Override
   public boolean getWrapAlignment()
   {
     return viewStyle.getWrapAlignment();
@@ -410,6 +444,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowText()
    */
+  @Override
   public boolean getShowText()
   {
     return viewStyle.getShowText();
@@ -419,6 +454,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getWrappedWidth()
    */
+  @Override
   public int getWrappedWidth()
   {
     return viewStyle.getWrappedWidth();
@@ -428,6 +464,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param w
    * @see jalview.api.ViewStyleI#setWrappedWidth(int)
    */
+  @Override
   public void setWrappedWidth(int w)
   {
     viewStyle.setWrappedWidth(w);
@@ -437,6 +474,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getCharHeight()
    */
+  @Override
   public int getCharHeight()
   {
     return viewStyle.getCharHeight();
@@ -446,6 +484,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param h
    * @see jalview.api.ViewStyleI#setCharHeight(int)
    */
+  @Override
   public void setCharHeight(int h)
   {
     viewStyle.setCharHeight(h);
@@ -455,6 +494,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getCharWidth()
    */
+  @Override
   public int getCharWidth()
   {
     return viewStyle.getCharWidth();
@@ -464,6 +504,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param w
    * @see jalview.api.ViewStyleI#setCharWidth(int)
    */
+  @Override
   public void setCharWidth(int w)
   {
     viewStyle.setCharWidth(w);
@@ -473,6 +514,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowBoxes()
    */
+  @Override
   public boolean getShowBoxes()
   {
     return viewStyle.getShowBoxes();
@@ -482,6 +524,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowUnconserved()
    */
+  @Override
   public boolean getShowUnconserved()
   {
     return viewStyle.getShowUnconserved();
@@ -491,6 +534,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param showunconserved
    * @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
    */
+  @Override
   public void setShowUnconserved(boolean showunconserved)
   {
     viewStyle.setShowUnconserved(showunconserved);
@@ -500,6 +544,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param default1
    * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
    */
+  @Override
   public void setSeqNameItalics(boolean default1)
   {
     viewStyle.setSeqNameItalics(default1);
@@ -791,15 +836,26 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     /*
      * A separate thread to compute cDNA consensus for a protein alignment
+     * which has mapping to cDNA
      */
     final AlignmentI al = this.getAlignment();
     if (!al.isNucleotide() && al.getCodonFrames() != null
             && !al.getCodonFrames().isEmpty())
     {
-      if (calculator
-              .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+      /*
+       * fudge - check first mapping is protein-to-nucleotide
+       * (we don't want to do this for protein-to-protein)
+       */
+      AlignedCodonFrame mapping = al.getCodonFrames().iterator().next();
+      // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
+      if (mapping.getdnaToProt()[0].getFromRatio() == 3)
       {
-        calculator.registerWorker(new ComplementConsensusThread(this, ap));
+        if (calculator
+                .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+        {
+          calculator
+                  .registerWorker(new ComplementConsensusThread(this, ap));
+        }
       }
     }
   }
@@ -1378,7 +1434,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     if (hiddenRepSequences == null)
     {
-      hiddenRepSequences = new Hashtable();
+      hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
     }
 
     hiddenRepSequences.put(repSequence, sg);
@@ -1723,14 +1779,20 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     if (!alignment.isNucleotide())
     {
-      final Set<AlignedCodonFrame> codonMappings = alignment
+      final List<AlignedCodonFrame> codonMappings = alignment
               .getCodonFrames();
       if (codonMappings != null && !codonMappings.isEmpty())
       {
-        complementConsensus = new AlignmentAnnotation("cDNA Consensus",
-                "PID for cDNA", new Annotation[1], 0f, 100f,
-                AlignmentAnnotation.BAR_GRAPH);
-        initConsensus(complementConsensus);
+        // fudge: check mappings are not protein-to-protein
+        // TODO: nicer
+        AlignedCodonFrame mapping = codonMappings.iterator().next();
+        if (mapping.getdnaToProt()[0].getFromRatio() == 3)
+        {
+          complementConsensus = new AlignmentAnnotation("cDNA Consensus",
+                  "PID for cDNA", new Annotation[1], 0f, 100f,
+                  AlignmentAnnotation.BAR_GRAPH);
+          initConsensus(complementConsensus);
+        }
       }
     }
   }
@@ -2115,6 +2177,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getTextColour()
    */
+  @Override
   public Color getTextColour()
   {
     return viewStyle.getTextColour();
@@ -2124,6 +2187,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getTextColour2()
    */
+  @Override
   public Color getTextColour2()
   {
     return viewStyle.getTextColour2();
@@ -2133,6 +2197,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getThresholdTextColour()
    */
+  @Override
   public int getThresholdTextColour()
   {
     return viewStyle.getThresholdTextColour();
@@ -2142,6 +2207,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isConservationColourSelected()
    */
+  @Override
   public boolean isConservationColourSelected()
   {
     return viewStyle.isConservationColourSelected();
@@ -2151,6 +2217,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isRenderGaps()
    */
+  @Override
   public boolean isRenderGaps()
   {
     return viewStyle.isRenderGaps();
@@ -2160,6 +2227,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isShowColourText()
    */
+  @Override
   public boolean isShowColourText()
   {
     return viewStyle.isShowColourText();
@@ -2169,6 +2237,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param conservationColourSelected
    * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
    */
+  @Override
   public void setConservationColourSelected(
           boolean conservationColourSelected)
   {
@@ -2179,6 +2248,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param showColourText
    * @see jalview.api.ViewStyleI#setShowColourText(boolean)
    */
+  @Override
   public void setShowColourText(boolean showColourText)
   {
     viewStyle.setShowColourText(showColourText);
@@ -2188,6 +2258,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param textColour
    * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
    */
+  @Override
   public void setTextColour(Color textColour)
   {
     viewStyle.setTextColour(textColour);
@@ -2197,6 +2268,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param thresholdTextColour
    * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
    */
+  @Override
   public void setThresholdTextColour(int thresholdTextColour)
   {
     viewStyle.setThresholdTextColour(thresholdTextColour);
@@ -2206,6 +2278,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param textColour2
    * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
    */
+  @Override
   public void setTextColour2(Color textColour2)
   {
     viewStyle.setTextColour2(textColour2);
@@ -2233,6 +2306,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getIdWidth()
    */
+  @Override
   public int getIdWidth()
   {
     return viewStyle.getIdWidth();
@@ -2242,6 +2316,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param i
    * @see jalview.api.ViewStyleI#setIdWidth(int)
    */
+  @Override
   public void setIdWidth(int i)
   {
     viewStyle.setIdWidth(i);
@@ -2251,6 +2326,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isCentreColumnLabels()
    */
+  @Override
   public boolean isCentreColumnLabels()
   {
     return viewStyle.isCentreColumnLabels();
@@ -2260,6 +2336,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param centreColumnLabels
    * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
    */
+  @Override
   public void setCentreColumnLabels(boolean centreColumnLabels)
   {
     viewStyle.setCentreColumnLabels(centreColumnLabels);
@@ -2269,6 +2346,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param showdbrefs
    * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
    */
+  @Override
   public void setShowDBRefs(boolean showdbrefs)
   {
     viewStyle.setShowDBRefs(showdbrefs);
@@ -2278,6 +2356,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isShowDBRefs()
    */
+  @Override
   public boolean isShowDBRefs()
   {
     return viewStyle.isShowDBRefs();
@@ -2287,6 +2366,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isShowNPFeats()
    */
+  @Override
   public boolean isShowNPFeats()
   {
     return viewStyle.isShowNPFeats();
@@ -2296,6 +2376,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param shownpfeats
    * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
    */
+  @Override
   public void setShowNPFeats(boolean shownpfeats)
   {
     viewStyle.setShowNPFeats(shownpfeats);
@@ -2428,6 +2509,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return startRes;
   }
 
+  @Override
   public int getEndRes()
   {
     return endRes;
@@ -2503,7 +2585,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       return 0;
     }
-    final Set<AlignedCodonFrame> mappings = proteinAlignment
+    final List<AlignedCodonFrame> mappings = proteinAlignment
             .getCodonFrames();
 
     /*

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index ad1d3bf..75c6485 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -32,8 +32,9 @@ import jalview.io.FormatAdapter;
 import jalview.util.MapList;
 
 import java.io.IOException;
-import java.util.Collections;
+import java.util.Arrays;
 import java.util.Iterator;
+import java.util.List;
 
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
@@ -397,7 +398,9 @@ public class AlignmentTest
     // create sequence and alignment datasets
     protein.setDataset(null);
     AlignedCodonFrame acf = new AlignedCodonFrame();
-    protein.getDataset().setCodonFrames(Collections.singleton(acf));
+    List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
+    { acf });
+    protein.getDataset().setCodonFrames(acfList);
     AlignmentI copy = new Alignment(protein);
 
     /*
@@ -468,4 +471,26 @@ public class AlignmentTest
     // prove the codon frames are indeed on the dataset:
     assertTrue(ds.getCodonFrames().contains(acf));
   }
+
+  @Test(groups = "Functional")
+  public void testAddCodonFrame()
+  {
+    AlignmentI align = new Alignment(new SequenceI[] {});
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    align.addCodonFrame(acf);
+    assertEquals(1, align.getCodonFrames().size());
+    assertTrue(align.getCodonFrames().contains(acf));
+    // can't add the same object twice:
+    align.addCodonFrame(acf);
+    assertEquals(1, align.getCodonFrames().size());
+
+    // create dataset alignment - mappings move to dataset
+    ((Alignment) align).createDatasetAlignment();
+    assertSame(align.getCodonFrames(), align.getDataset().getCodonFrames());
+    assertEquals(1, align.getCodonFrames().size());
+
+    AlignedCodonFrame acf2 = new AlignedCodonFrame();
+    align.addCodonFrame(acf2);
+    assertTrue(align.getDataset().getCodonFrames().contains(acf));
+  }
 }

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 0a53f10..b39b2bd 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -37,8 +37,8 @@ import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.structure.StructureSelectionManager;
 
-import java.util.LinkedHashSet;
-import java.util.Set;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
@@ -136,7 +136,7 @@ public class AlignViewportTest
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
 
-    Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
     mappings.add(acf1);
     mappings.add(acf2);
     af1.getViewport().getAlignment().setCodonFrames(mappings);
@@ -148,18 +148,18 @@ public class AlignViewportTest
      */
     StructureSelectionManager ssm = StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance);
-    assertEquals(2, ssm.seqmappings.size());
-    assertTrue(ssm.seqmappings.contains(acf1));
-    assertTrue(ssm.seqmappings.contains(acf2));
+    assertEquals(2, ssm.getSequenceMappings().size());
+    assertTrue(ssm.getSequenceMappings().contains(acf1));
+    assertTrue(ssm.getSequenceMappings().contains(acf2));
 
     /*
      * Close the second view. Verify that mappings are not removed as the first
      * view still holds a reference to them.
      */
     af1.closeMenuItem_actionPerformed(false);
-    assertEquals(2, ssm.seqmappings.size());
-    assertTrue(ssm.seqmappings.contains(acf1));
-    assertTrue(ssm.seqmappings.contains(acf2));
+    assertEquals(2, ssm.getSequenceMappings().size());
+    assertTrue(ssm.getSequenceMappings().contains(acf1));
+    assertTrue(ssm.getSequenceMappings().contains(acf2));
   }
 
   /**
@@ -183,11 +183,11 @@ public class AlignViewportTest
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
     AlignedCodonFrame acf3 = new AlignedCodonFrame();
 
-    Set<AlignedCodonFrame> mappings1 = new LinkedHashSet<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
     mappings1.add(acf1);
     af1.getViewport().getAlignment().setCodonFrames(mappings1);
 
-    Set<AlignedCodonFrame> mappings2 = new LinkedHashSet<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
     mappings2.add(acf2);
     mappings2.add(acf3);
     af2.getViewport().getAlignment().setCodonFrames(mappings2);
@@ -196,7 +196,7 @@ public class AlignViewportTest
      * AlignFrame1 has mapping acf1, AlignFrame2 has acf2 and acf3
      */
 
-    Set<AlignedCodonFrame> ssmMappings = ssm.seqmappings;
+    List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
     assertEquals(0, ssmMappings.size());
     ssm.registerMapping(acf1);
     assertEquals(1, ssmMappings.size());
@@ -236,12 +236,12 @@ public class AlignViewportTest
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
     AlignedCodonFrame acf3 = new AlignedCodonFrame();
 
-    Set<AlignedCodonFrame> mappings1 = new LinkedHashSet<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
     mappings1.add(acf1);
     mappings1.add(acf2);
     af1.getViewport().getAlignment().setCodonFrames(mappings1);
 
-    Set<AlignedCodonFrame> mappings2 = new LinkedHashSet<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
     mappings2.add(acf2);
     mappings2.add(acf3);
     af2.getViewport().getAlignment().setCodonFrames(mappings2);
@@ -250,7 +250,7 @@ public class AlignViewportTest
      * AlignFrame1 has mappings acf1 and acf2, AlignFrame2 has acf2 and acf3
      */
 
-    Set<AlignedCodonFrame> ssmMappings = ssm.seqmappings;
+    List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
     assertEquals(0, ssmMappings.size());
     ssm.registerMapping(acf1);
     assertEquals(1, ssmMappings.size());