Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 9a408e3..1246d23 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -22,14 +22,14 @@ package jalview.datamodel;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
 
 import java.awt.Color;
 import java.util.ArrayList;
-import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
-import java.util.Vector;
 
 /**
  * Collects a set contiguous ranges on a set of sequences
@@ -45,8 +45,6 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   Conservation conserve;
 
-  Vector aaFrequency;
-
   boolean displayBoxes = true;
 
   boolean displayText = true;
@@ -73,7 +71,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * Colourscheme applied to group if any
    */
-  public ColourSchemeI cs;
+  public ResidueShaderI cs;
 
   // start column (base 0)
   int startRes = 0;
@@ -120,6 +118,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   public SequenceGroup()
   {
     groupName = "JGroup:" + this.hashCode();
+    cs = new ResidueShader();
   }
 
   /**
@@ -140,12 +139,13 @@ public class SequenceGroup implements AnnotatedCollectionI
           ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
           boolean colourText, int start, int end)
   {
+    this();
     this.sequences = sequences;
     this.groupName = groupName;
     this.displayBoxes = displayBoxes;
     this.displayText = displayText;
     this.colourText = colourText;
-    this.cs = scheme;
+    this.cs = new ResidueShader(scheme);
     startRes = start;
     endRes = end;
     recalcConservation();
@@ -158,6 +158,7 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public SequenceGroup(SequenceGroup seqsel)
   {
+    this();
     if (seqsel != null)
     {
       sequences = new ArrayList<SequenceI>();
@@ -531,7 +532,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     boolean upd = false;
     try
     {
-      Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
+      ProfilesI cnsns = AAFrequency.calculate(sequences, startRes,
               endRes + 1, showSequenceLogo);
       if (consensus != null)
       {
@@ -547,8 +548,8 @@ public class SequenceGroup implements AnnotatedCollectionI
       if ((conservation != null)
               || (cs != null && cs.conservationApplied()))
       {
-        Conservation c = new Conservation(groupName, 3, sequences,
-                startRes, endRes + 1);
+        Conservation c = new Conservation(groupName, sequences, startRes,
+                endRes + 1);
         c.calculate();
         c.verdict(false, consPercGaps);
         if (conservation != null)
@@ -603,9 +604,9 @@ public class SequenceGroup implements AnnotatedCollectionI
     c.completeAnnotations(conservation, null, startRes, endRes + 1);
   }
 
-  public Hashtable[] consensusData = null;
+  public ProfilesI consensusData = null;
 
-  private void _updateConsensusRow(Hashtable[] cnsns, long nseq)
+  private void _updateConsensusRow(ProfilesI cnsns, long nseq)
   {
     if (consensus == null)
     {
@@ -1273,10 +1274,14 @@ public class SequenceGroup implements AnnotatedCollectionI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    if (calcId == null)
+    {
+      return aa;
+    }
     for (AlignmentAnnotation a : getAlignmentAnnotation())
     {
-      if (a.getCalcId() == calcId)
+      if (calcId.equals(a.getCalcId()))
       {
         aa.add(a);
       }
@@ -1342,13 +1347,25 @@ public class SequenceGroup implements AnnotatedCollectionI
   private AnnotatedCollectionI context;
 
   /**
-   * set the alignment or group context for this group
+   * Sets the alignment or group context for this group
    * 
-   * @param context
+   * @param ctx
+   * @throws IllegalArgumentException
+   *           if setting the context would result in a circular reference chain
    */
-  public void setContext(AnnotatedCollectionI context)
+  public void setContext(AnnotatedCollectionI ctx)
   {
-    this.context = context;
+    AnnotatedCollectionI ref = ctx;
+    while (ref != null)
+    {
+      if (ref == this || ref.getContext() == ctx)
+      {
+        throw new IllegalArgumentException(
+                "Circular reference in SequenceGroup.context");
+      }
+      ref = ref.getContext();
+    }
+    this.context = ctx;
   }
 
   /*
@@ -1361,4 +1378,57 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     return context;
   }
+
+  public void setColourScheme(ColourSchemeI scheme)
+  {
+    if (cs == null)
+    {
+      cs = new ResidueShader();
+    }
+    cs.setColourScheme(scheme);
+  }
+
+  public void setGroupColourScheme(ResidueShaderI scheme)
+  {
+    cs = scheme;
+  }
+
+  public ColourSchemeI getColourScheme()
+  {
+    return cs == null ? null : cs.getColourScheme();
+  }
+
+  public ResidueShaderI getGroupColourScheme()
+  {
+    return cs;
+  }
+
+  @Override
+  public boolean isNucleotide()
+  {
+    if (context != null) {
+      return context.isNucleotide();
+    }
+    return false;
+  }
+
+  /**
+   * @param seq
+   * @return true if seq is a member of the group
+   */
+
+  public boolean contains(SequenceI seq1)
+  {
+    return sequences.contains(seq1);
+  }
+
+  /**
+   * @param seq
+   * @param apos
+   * @return true if startRes<=apos and endRes>=apos and seq is in the group
+   */
+  public boolean contains(SequenceI seq, int apos)
+  {
+    return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
+  }
 }