formatting

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

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 9a6d022..693291f 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -18,6 +18,7 @@
 package jalview.datamodel;
 
 import java.util.*;
+import java.util.List;
 
 import java.awt.*;
 
@@ -54,7 +55,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * group members
    */
-  private Vector sequences = new Vector();
+  private Vector<SequenceI> sequences = new Vector<SequenceI>();
 
   /**
    * representative sequence for this group (if any)
@@ -91,12 +92,12 @@ public class SequenceGroup implements AnnotatedCollectionI
    * consensus calculation property
    */
   private boolean showSequenceLogo = false;
+
   /**
    * flag indicating if logo should be rendered normalised
    */
   private boolean normaliseSequenceLogo;
 
-
   /**
    * @return the includeAllConsSymbols
    */
@@ -152,7 +153,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     if (seqsel != null)
     {
       sequences = new Vector();
-      Enumeration sq = seqsel.sequences.elements();
+      Enumeration<SequenceI> sq = seqsel.sequences.elements();
       while (sq.hasMoreElements())
       {
         sequences.addElement(sq.nextElement());
@@ -285,7 +286,13 @@ public class SequenceGroup implements AnnotatedCollectionI
     return eres;
   }
 
-  public Vector getSequences(Hashtable hiddenReps)
+  public List<SequenceI> getSequences()
+  {
+    return sequences;
+  }
+
+  public List<SequenceI> getSequences(
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
     if (hiddenReps == null)
     {
@@ -294,17 +301,16 @@ public class SequenceGroup implements AnnotatedCollectionI
     else
     {
       Vector allSequences = new Vector();
-      SequenceI seq, seq2;
+      SequenceI seq;
       for (int i = 0; i < sequences.size(); i++)
       {
         seq = (SequenceI) sequences.elementAt(i);
         allSequences.addElement(seq);
         if (hiddenReps.containsKey(seq))
         {
-          SequenceGroup hsg = (SequenceGroup) hiddenReps.get(seq);
-          for (int h = 0; h < hsg.getSize(); h++)
+          SequenceCollectionI hsg = hiddenReps.get(seq);
+          for (SequenceI seq2 : hsg.getSequences())
           {
-            seq2 = hsg.getSequenceAt(h);
             if (seq2 != seq && !allSequences.contains(seq2))
             {
               allSequences.addElement(seq2);
@@ -317,20 +323,15 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
   }
 
-  public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
+  public SequenceI[] getSequencesAsArray(
+          Map<SequenceI, SequenceCollectionI> map)
   {
-    Vector tmp = getSequences(hiddenReps);
+    List<SequenceI> tmp = getSequences(map);
     if (tmp == null)
     {
       return null;
     }
-    SequenceI[] result = new SequenceI[tmp.size()];
-    for (int i = 0; i < result.length; i++)
-    {
-      result[i] = (SequenceI) tmp.elementAt(i);
-    }
-
-    return result;
+    return tmp.toArray(new SequenceI[tmp.size()]);
   }
 
   /**
@@ -482,9 +483,9 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       return;
     }
-    if (cs!=null)
+    if (cs != null)
     {
-      cs.alignmentChanged(this);
+      cs.alignmentChanged(this, null);
     }
     try
     {
@@ -497,11 +498,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       if (cs != null)
       {
         cs.setConsensus(cnsns);
-
-        if (cs instanceof ClustalxColourScheme)
-        {
-          ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
-        }
+        cs.alignmentChanged(this, null);
       }
 
       if ((conservation != null)
@@ -521,12 +518,7 @@ public class SequenceGroup implements AnnotatedCollectionI
           if (cs.conservationApplied())
           {
             cs.setConservation(c);
-
-            if (cs instanceof ClustalxColourScheme)
-            {
-              ((ClustalxColourScheme) cs).resetClustalX(sequences,
-                      getWidth());
-            }
+            cs.alignmentChanged(this, null);
           }
         }
       }
@@ -956,18 +948,19 @@ public class SequenceGroup implements AnnotatedCollectionI
    * 
    * @param alignment
    *          (may not be null)
-   * @param hashtable
+   * @param map
    *          (may be null)
    * @return new group containing sequences common to this group and alignment
    */
-  public SequenceGroup intersect(AlignmentI alignment, Hashtable hashtable)
+  public SequenceGroup intersect(AlignmentI alignment,
+          Map<SequenceI, SequenceCollectionI> map)
   {
     SequenceGroup sgroup = new SequenceGroup(this);
     SequenceI[] insect = getSequencesInOrder(alignment);
     sgroup.sequences = new Vector();
     for (int s = 0; insect != null && s < insect.length; s++)
     {
-      if (hashtable == null || hashtable.containsKey(insect[s]))
+      if (map == null || map.containsKey(insect[s]))
       {
         sgroup.sequences.addElement(insect[s]);
       }
@@ -1178,55 +1171,65 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   /**
    * set flag indicating if logo should be normalised when rendered
+   * 
    * @param norm
    */
   public void setNormaliseSequenceLogo(boolean norm)
   {
-    normaliseSequenceLogo=norm;
+    normaliseSequenceLogo = norm;
   }
+
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
   }
+
   @Override
   /**
    * returns a new array with all annotation involving this group
    */
   public AlignmentAnnotation[] getAlignmentAnnotation()
   {
-    // TODO add in other methods like 'getAlignmentAnnotation(String label), etc'
+    // TODO add in other methods like 'getAlignmentAnnotation(String label),
+    // etc'
     ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
-    for (SequenceI seq:(Vector<SequenceI>)sequences)
+    for (SequenceI seq : (Vector<SequenceI>) sequences)
     {
-      for (AlignmentAnnotation al: seq.getAnnotation())
+      for (AlignmentAnnotation al : seq.getAnnotation())
       {
-        if (al.groupRef==this)
+        if (al.groupRef == this)
         {
           annot.add(al);
         }
       }
     }
-    if (consensus!=null)
+    if (consensus != null)
     {
       annot.add(consensus);
     }
-    if (conservation!=null)
+    if (conservation != null)
     {
       annot.add(conservation);
     }
     return annot.toArray(new AlignmentAnnotation[0]);
   }
+
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    ArrayList<AlignmentAnnotation> aa=new ArrayList<AlignmentAnnotation>();
-    for (AlignmentAnnotation a:getAlignmentAnnotation())
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    for (AlignmentAnnotation a : getAlignmentAnnotation())
     {
-      if (a.getCalcId()==calcId)
+      if (a.getCalcId() == calcId)
       {
         aa.add(a);
       }
     }
     return aa;
   }
+
+  public void clear()
+  {
+    sequences.clear();
+  }
 }