X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=7981634355f84715fae6cd55cf38188c3ffb3108;hb=006dda109bba6b7e6323c81d47d09f762ec1e205;hp=d2832f84f93305d101787cbc5974a6179c36c1fb;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index d2832f8..7981634 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,24 +1,28 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
 import java.awt.*;
 import java.awt.event.*;
+import java.util.List;
 import java.util.Vector;
 
 import jalview.datamodel.*;
@@ -72,10 +76,21 @@ public class IdPanel extends Panel implements MouseListener,
 
       }
     }
+    {
+      // upgrade old SRS link
+      int srsPos = links
+              .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      if (srsPos > -1)
+      {
+        links.setElementAt(
+                "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
+                srsPos);
+      }
+    }
     if (links.size() < 1)
     {
       links = new java.util.Vector();
-      links.addElement("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      links.addElement("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
     }
   }
 
@@ -198,7 +213,7 @@ public class IdPanel extends Panel implements MouseListener,
     // DEFAULT LINK IS FIRST IN THE LINK LIST
     int seq = alignPanel.seqPanel.findSeq(e);
     SequenceI sq = av.getAlignment().getSequenceAt(seq);
-    if (sq==null)
+    if (sq == null)
     {
       return;
     }
@@ -272,7 +287,7 @@ public class IdPanel extends Panel implements MouseListener,
     }
 
     if (mouseDragging && e.getY() >= getSize().height
-            && av.alignment.getHeight() > av.getEndSeq())
+            && av.getAlignment().getHeight() > av.getEndSeq())
     {
       scrollThread = new ScrollThread(false);
     }
@@ -296,7 +311,7 @@ public class IdPanel extends Panel implements MouseListener,
     if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
       Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
-      
+
       // build a new links menu based on the current links + any non-positional
       // features
       Vector nlinks = new Vector();
@@ -304,7 +319,7 @@ public class IdPanel extends Panel implements MouseListener,
       {
         nlinks.addElement(links.elementAt(l));
       }
-      SequenceFeature sf[] = sq==null ? null:sq.getSequenceFeatures();
+      SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
       for (int sl = 0; sf != null && sl < sf.length; sl++)
       {
         if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
@@ -331,7 +346,7 @@ public class IdPanel extends Panel implements MouseListener,
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
-      av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+      av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
     }
 
     if (e.isShiftDown() && lastid != -1)
@@ -350,7 +365,7 @@ public class IdPanel extends Panel implements MouseListener,
   {
     lastid = seq;
     SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
-    av.getSelectionGroup().addOrRemove(pickedSeq, false);
+    av.getSelectionGroup().addOrRemove(pickedSeq, true);
   }
 
   void selectSeqs(int start, int end)
@@ -377,7 +392,7 @@ public class IdPanel extends Panel implements MouseListener,
     for (int i = start; i <= end; i++)
     {
       av.getSelectionGroup().addSequence(
-              av.getAlignment().getSequenceAt(i), false);
+              av.getAlignment().getSequenceAt(i), i == end);
     }
 
   }
@@ -400,16 +415,16 @@ public class IdPanel extends Panel implements MouseListener,
     av.sendSelection();
   }
 
-  public void highlightSearchResults(java.util.Vector found)
+  public void highlightSearchResults(List<SequenceI> list)
   {
-    idCanvas.setHighlighted(found);
+    idCanvas.setHighlighted(list);
 
-    if (found == null)
+    if (list == null)
     {
       return;
     }
 
-    int index = av.alignment.findIndex((SequenceI) found.elementAt(0));
+    int index = av.getAlignment().findIndex(list.get(0));
 
     // do we need to scroll the panel?
     if (av.getStartSeq() > index || av.getEndSeq() < index)
@@ -454,7 +469,7 @@ public class IdPanel extends Panel implements MouseListener,
           {
             selectSeqs(lastid - 1, seq);
           }
-          else if (seq > lastid && seq < av.alignment.getHeight())
+          else if (seq > lastid && seq < av.getAlignment().getHeight())
           {
             selectSeqs(lastid + 1, seq);
           }