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removeGaps method can record changes in alignment columns to pass to ColumnSelection
[jalview.git] / src / jalview / gui / IdPanel.java
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index d1dc11d..47f43d5 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -69,15 +69,8 @@ public class IdPanel extends JPanel implements MouseListener,
      */\r
     public void mouseMoved(MouseEvent e)\r
     {\r
-      int y = e.getY();\r
-\r
-      if (av.getWrapAlignment())\r
-      {\r
-        y = getWrappedY(y);\r
-      }\r
-\r
-      final int seq = av.getIndex(y);\r
-      if(seq!=-1)\r
+      int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));\r
+      if(seq>-1 && seq<av.alignment.getHeight())\r
       {\r
         SequenceI sequence = av.alignment.getSequenceAt(seq);\r
         StringBuffer tip = new StringBuffer("<html>");\r
@@ -100,25 +93,28 @@ public class IdPanel extends JPanel implements MouseListener,
               }\r
             }\r
           }\r
-\r
           tip.append("</i></td></tr></table>");\r
         }\r
+\r
+        DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef();\r
+        if (dbrefs != null)\r
+        {\r
+          tip.append("<i>");\r
+          for (int i = 0; i < dbrefs.length; i++)\r
+          {\r
+            tip.append("<br>");\r
+            tip.append(dbrefs[i].getSource() + " "\r
+                       + dbrefs[i].getAccessionId());\r
+          }\r
+          tip.append("</i>");\r
+        }\r
+\r
         tip.append("</html>");\r
         setToolTipText(tip.toString());\r
       }\r
     }\r
 \r
 \r
-    int getWrappedY(int y)\r
-    {\r
-      int hgap = av.charHeight;\r
-      if (av.scaleAboveWrapped)\r
-        hgap += av.charHeight;\r
-\r
-      return y - hgap;\r
-    }\r
-\r
-\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -128,19 +124,7 @@ public class IdPanel extends JPanel implements MouseListener,
     {\r
         mouseDragging = true;\r
 \r
-        int y = e.getY();\r
-\r
-        if (av.getWrapAlignment())\r
-        {\r
-            y = getWrappedY(y);\r
-        }\r
-\r
-        int seq = av.getIndex(y);\r
-\r
-        if (seq < 0)\r
-        {\r
-            return;\r
-        }\r
+        int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));\r
 \r
         if (seq < lastid)\r
         {\r
@@ -170,17 +154,9 @@ public class IdPanel extends JPanel implements MouseListener,
       if (links == null || links.size() < 1)\r
         return;\r
 \r
-      int y = e.getY();\r
-\r
-      if (av.getWrapAlignment())\r
-      {\r
-         y = getWrappedY(y);\r
-      }\r
+      int seq = alignPanel.seqPanel.findSeq(e);\r
 \r
       //DEFAULT LINK IS FIRST IN THE LINK LIST\r
-      int seq = av.getIndex(y);\r
-      if(seq==-1)\r
-        return;\r
 \r
       String id = av.getAlignment().getSequenceAt(seq).getName();\r
       if (id.indexOf("|") > -1)\r
@@ -256,49 +232,20 @@ public class IdPanel extends JPanel implements MouseListener,
             return;\r
         }\r
 \r
-        int y = e.getY();\r
-\r
-        if (av.getWrapAlignment())\r
-        {\r
-            y = getWrappedY(y);\r
-        }\r
+        int seq = alignPanel.seqPanel.findSeq(e);\r
 \r
-        int seq = av.getIndex(y);\r
-\r
-        if (seq == -1)\r
-        {\r
-            return;\r
-        }\r
 \r
         if (javax.swing.SwingUtilities.isRightMouseButton(e))\r
         {\r
             jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,\r
                     (Sequence) av.getAlignment().getSequenceAt(seq),\r
                     Preferences.sequenceURLLinks);\r
-            pop.show(this, e.getX(), y);\r
+            pop.show(this, e.getX(), e.getY());\r
 \r
             return;\r
         }\r
 \r
-      /*  if (!e.isControlDown() && !e.isShiftDown() &&\r
-                (av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null))\r
-        {\r
-          System.out.println("no modifiers");\r
-            SequenceGroup selection = new SequenceGroup();\r
-            SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(\r
-                        seq));\r
-            selection.setStartRes(0);\r
-            selection.setEndRes(av.alignment.getWidth() - 1);\r
-\r
-            for (int i = 0; i < sg.getSize(); i++)\r
-            {\r
-                selection.addSequence(sg.getSequenceAt(i), true);\r
-            }\r
-\r
-            av.setSelectionGroup(selection);\r
 \r
-            return;\r
-        }*/\r
 \r
         if ((av.getSelectionGroup() == null) ||\r
                 ((!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))\r
@@ -309,7 +256,6 @@ public class IdPanel extends JPanel implements MouseListener,
         }\r
 \r
 \r
-\r
         if (e.isShiftDown() && (lastid != -1))\r
         {\r
             selectSeqs(lastid, seq);\r