X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=1f1dd2f30bf072a6fcebfdc51a5a22a98fd0f9e9;hb=2672f9a72ffb8ffaf4b48a08e64de7f3d83ce061;hp=cce2ee0880e97b4c68e6467b6da71e1da75748ed;hpb=7ecacfd7a5977fdc69d4e81d5ec24b049ff927e0;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index cce2ee0..1f1dd2f 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
@@ -54,11 +55,12 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.event.MouseWheelEvent;
 import java.awt.event.MouseWheelListener;
+import java.util.ArrayList;
 import java.util.List;
-import java.util.Vector;
 
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 
 /**
@@ -509,6 +511,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   void insertNucAtCursor(boolean group, String nuc)
   {
+    // TODO not called - delete?
     groupEditing = group;
     startseq = seqCanvas.cursorY;
     lastres = seqCanvas.cursorX;
@@ -599,7 +602,7 @@ public class SeqPanel extends JPanel implements MouseListener,
   {
     lastMousePress = evt.getPoint();
 
-    if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
+    if (SwingUtilities.isMiddleMouseButton(evt))
     {
       mouseWheelPressed = true;
       return;
@@ -1171,8 +1174,7 @@ public class SeqPanel extends JPanel implements MouseListener,
           {
             for (int j = 0; j < startres - lastres; j++)
             {
-              if (!jalview.util.Comparison.isGap(groupSeqs[g]
-                      .getCharAt(fixedRight - j)))
+              if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
               {
                 blank = false;
                 break;
@@ -1234,7 +1236,7 @@ public class SeqPanel extends JPanel implements MouseListener,
               continue;
             }
 
-            if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
+            if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
             {
               // Not a gap, block edit not valid
               endEditing();
@@ -1366,7 +1368,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
       {
-        if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
+        if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
         {
           // Theres a space, so break and insert the gap
           break;
@@ -1597,24 +1599,24 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     }
 
-    if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+    if (SwingUtilities.isRightMouseButton(evt))
     {
       List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
               .findFeaturesAtRes(sequence.getDatasetSequence(),
                       sequence.findPosition(res));
-      Vector links = new Vector();
+      List<String> links = new ArrayList<String>();
       for (SequenceFeature sf : allFeatures)
       {
         if (sf.links != null)
         {
-          for (int j = 0; j < sf.links.size(); j++)
+          for (String link : sf.links)
           {
-            links.addElement(sf.links.elementAt(j));
+            links.add(link);
           }
         }
       }
 
-      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
+      PopupMenu pop = new PopupMenu(ap, null, links);
       pop.show(this, evt.getX(), evt.getY());
       return;
     }
@@ -1955,7 +1957,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       if (av.getAlignment() == null)
       {
-        jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
+        Cache.log.warn("alignviewport av SeqSetId="
                 + av.getSequenceSetId() + " ViewId=" + av.getViewId()
                 + " 's alignment is NULL! returning immediately.");
         return;