Merge branch 'improvement/JAL-4023_snotation_for_trees' into develop

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

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index fc8ac49..5e33229 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -88,7 +88,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * group members
    */
-  private List<SequenceI> sequences = new ArrayList<>();
+  private List<SequenceI> sequences;
 
   /**
    * representative sequence for this group (if any)
@@ -108,7 +108,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   private int startRes = 0;
 
   /**
-   *  end column (base 0)
+   * end column (base 0)
    */
   private int endRes = 0;
 
@@ -162,6 +162,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     groupName = "JGroup:" + this.hashCode();
     cs = new ResidueShader();
+    sequences = new ArrayList<>();
   }
 
   /**
@@ -213,7 +214,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       displayBoxes = seqsel.displayBoxes;
       displayText = seqsel.displayText;
       colourText = seqsel.colourText;
-      
+
       startRes = seqsel.startRes;
       endRes = seqsel.endRes;
       cs = new ResidueShader((ResidueShader) seqsel.cs);
@@ -243,6 +244,17 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
   }
 
+  /**
+   * Constructor that copies the given list of sequences
+   * 
+   * @param seqs
+   */
+  public SequenceGroup(List<SequenceI> seqs)
+  {
+    this();
+    this.sequences.addAll(seqs);
+  }
+
   public boolean isShowSequenceLogo()
   {
     return showSequenceLogo;
@@ -257,16 +269,16 @@ public class SequenceGroup implements AnnotatedCollectionI
     for (int i = 0, ipos = 0; i < inorder.length; i++)
     {
       SequenceI seq = inorder[i];
-
-      seqs[ipos] = seq.getSubSequence(startRes, endRes + 1);
-      if (seqs[ipos] != null)
+      SequenceI seqipos = seqs[ipos] = seq.getSubSequence(startRes,
+              endRes + 1);
+      if (seqipos != null)
       {
-        seqs[ipos].setDescription(seq.getDescription());
-        seqs[ipos].setDBRefs(seq.getDBRefs());
-        seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
+        seqipos.setDescription(seq.getDescription());
+        seqipos.setDBRefs(seq.getDBRefs());
+        seqipos.setSequenceFeatures(seq.getSequenceFeatures());
         if (seq.getDatasetSequence() != null)
         {
-          seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
+          seqipos.setDatasetSequence(seq.getDatasetSequence());
         }
 
         if (seq.getAnnotation() != null)
@@ -280,7 +292,7 @@ public class SequenceGroup implements AnnotatedCollectionI
             if (alann != null)
             {
               boolean found = false;
-              for (int pos = 0; pos < alann.length; pos++)
+              for (int pos = 0, np = alann.length; pos < np; pos++)
               {
                 if (alann[pos] == tocopy)
                 {
@@ -298,7 +310,7 @@ public class SequenceGroup implements AnnotatedCollectionI
             newannot.restrict(startRes, endRes);
             newannot.setSequenceRef(seqs[ipos]);
             newannot.adjustForAlignment();
-            seqs[ipos].addAlignmentAnnotation(newannot);
+            seqipos.addAlignmentAnnotation(newannot);
           }
         }
         ipos++;
@@ -762,10 +774,9 @@ public class SequenceGroup implements AnnotatedCollectionI
   public void setStartRes(int newStart)
   {
     int before = startRes;
-   startRes= Math.max(0,newStart); // sanity check for negative start column positions
-   changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
-    
-
+    startRes = Math.max(0, newStart); // sanity check for negative start column
+                                      // positions
+    changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
 
   }