X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=8f24f119390027cc8e9c1f0981f502dbfdc0b9c7;hb=ce26ffcae5e876cf4127173c92f0eddffc9830da;hp=8a0efc3ddeb0feb8b1f42ae974c16a8ecc09de79;hpb=48b925b3dd950c86b1add0f2a90a2d0f8b6e316e;p=jalview.git

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 8a0efc3..8f24f11 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,46 +1,53 @@
 /*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.UrlLink;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.Panel;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
 import java.util.List;
 import java.util.Vector;
 
-import jalview.datamodel.*;
-import jalview.util.UrlLink;
-
 public class IdPanel extends Panel implements MouseListener,
         MouseMotionListener
 {
 
   protected IdCanvas idCanvas;
 
-  protected AlignViewport av;
+  protected AlignmentViewport av;
 
   protected AlignmentPanel alignPanel;
 
   ScrollThread scrollThread = null;
 
-  int offy;
-
-  int width;
-
   int lastid = -1;
 
   boolean mouseDragging = false;
@@ -73,10 +80,21 @@ 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=$SEQUENCE_ID$");
     }
   }
 
@@ -124,7 +142,7 @@ public class IdPanel extends Panel implements MouseListener,
             nl = true;
           }
           ;
-          if (sf[sl].getScore() != Float.NaN && sf[sl].getScore() != 0f)
+          if (!Float.isNaN(sf[sl].getScore()) && sf[sl].getScore() != 0f)
           {
             tooltiptext.append(" Score = ");
             tooltiptext.append(sf[sl].getScore());
@@ -199,7 +217,7 @@ 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;
     }
@@ -289,7 +307,7 @@ public class IdPanel extends Panel implements MouseListener,
     int y = e.getY();
     if (av.getWrapAlignment())
     {
-      y -= 2 * av.charHeight;
+      y -= 2 * av.getCharHeight();
     }
 
     int seq = alignPanel.seqPanel.findSeq(e);
@@ -297,7 +315,7 @@ 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();
@@ -305,7 +323,7 @@ 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)
@@ -351,7 +369,7 @@ 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)
@@ -378,7 +396,7 @@ public class IdPanel extends Panel implements MouseListener,
     for (int i = start; i <= end; i++)
     {
       av.getSelectionGroup().addSequence(
-              av.getAlignment().getSequenceAt(i), i==end);
+              av.getAlignment().getSequenceAt(i), i == end);
     }
 
   }
@@ -477,5 +495,4 @@ public class IdPanel extends Panel implements MouseListener,
       }
     }
   }
-
 }