Jalview.isJS() --> Platform.isJS(), DBRefEntry[] --> List<DBRefEntry>

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

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 944f263..1e579ec 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -25,6 +25,7 @@ import jalview.analysis.Conservation;
 import jalview.renderer.ResidueShader;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
+import jalview.ws.params.InvalidArgumentException;
 
 import java.awt.Color;
 import java.beans.PropertyChangeListener;
@@ -102,11 +103,15 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public ResidueShaderI cs;
 
-  // start column (base 0)
-  int startRes = 0;
+  /**
+   * start column (base 0)
+   */
+  private int startRes = 0;
 
-  // end column (base 0)
-  int endRes = 0;
+  /**
+   *  end column (base 0)
+   */
+  private int endRes = 0;
 
   public Color outlineColour = Color.black;
 
@@ -209,6 +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);
@@ -252,16 +258,15 @@ 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.getDBRefsFrom(seq);
+        seqipos.setSequenceFeatures(seq.getSequenceFeatures());
         if (seq.getDatasetSequence() != null)
         {
-          seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
+          seqipos.setDatasetSequence(seq.getDatasetSequence());
         }
 
         if (seq.getAnnotation() != null)
@@ -275,7 +280,7 @@ 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)
                 {
@@ -293,7 +298,7 @@ public class SequenceGroup implements AnnotatedCollectionI
             newannot.restrict(startRes, endRes);
             newannot.setSequenceRef(seqs[ipos]);
             newannot.adjustForAlignment();
-            seqs[ipos].addAlignmentAnnotation(newannot);
+            seqipos.addAlignmentAnnotation(newannot);
           }
         }
         ipos++;
@@ -752,13 +757,16 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * Set the first column selected by this group. Runs from 0<=i<N_cols
    * 
-   * @param i
+   * @param newStart
    */
-  public void setStartRes(int i)
+  public void setStartRes(int newStart)
   {
     int before = startRes;
-    startRes = i;
-    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);
+    
+
+
   }
 
   /**