X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=182f20eb5138ab4adbf8072b2936080933fe70f6;hb=8b5ec42b22c5f0cd5e8b34823c60c84a27a9763b;hp=070004f1f7263718f78aebced1828c8b7554f576;hpb=12045b681611d64529bdaf35f05d8cb0d9a2b054;p=jalview.git

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 070004f..182f20e 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,29 +1,43 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 java.util.List;
-import java.util.Vector;
+import static jalview.util.UrlConstants.EMBLEBI_STRING;
+import static jalview.util.UrlConstants.SRS_STRING;
 
-import jalview.datamodel.*;
+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;
 
 public class IdPanel extends Panel implements MouseListener,
         MouseMotionListener
@@ -31,16 +45,12 @@ public class IdPanel extends Panel implements MouseListener,
 
   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;
@@ -75,24 +85,22 @@ 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");
+      int srsPos = links.indexOf(SRS_STRING);
       if (srsPos > -1)
       {
-        links.setElementAt(
-                "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
-                srsPos);
+        links.setElementAt(EMBLEBI_STRING, srsPos);
       }
     }
     if (links.size() < 1)
     {
       links = new java.util.Vector();
-      links.addElement("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
+      links.addElement(EMBLEBI_STRING);
     }
   }
 
   Tooltip tooltip;
 
+  @Override
   public void mouseMoved(MouseEvent e)
   {
     int seq = alignPanel.seqPanel.findSeq(e);
@@ -135,7 +143,7 @@ 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());
@@ -181,6 +189,7 @@ public class IdPanel extends Panel implements MouseListener,
     tooltiptext = null;
   }
 
+  @Override
   public void mouseDragged(MouseEvent e)
   {
     mouseDragging = true;
@@ -200,6 +209,7 @@ public class IdPanel extends Panel implements MouseListener,
     alignPanel.paintAlignment(false);
   }
 
+  @Override
   public void mouseClicked(MouseEvent e)
   {
     if (e.getClickCount() < 2)
@@ -236,7 +246,14 @@ public class IdPanel extends Panel implements MouseListener,
         url = null;
         continue;
       }
-      ;
+
+      if (urlLink.usesDBAccession())
+      {
+        // this URL requires an accession id, not the name of a sequence
+        url = null;
+        continue;
+      }
+
       if (!urlLink.isValid())
       {
         System.err.println(urlLink.getInvalidMessage());
@@ -263,6 +280,7 @@ public class IdPanel extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mouseEntered(MouseEvent e)
   {
     if (scrollThread != null)
@@ -271,6 +289,7 @@ public class IdPanel extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mouseExited(MouseEvent e)
   {
     if (av.getWrapAlignment())
@@ -290,6 +309,7 @@ public class IdPanel extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mousePressed(MouseEvent e)
   {
     if (e.getClickCount() > 1)
@@ -300,7 +320,7 @@ 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);
@@ -338,8 +358,8 @@ public class IdPanel extends Panel implements MouseListener,
     }
 
     if ((av.getSelectionGroup() == null)
-            || ((!e.isControlDown() && !e.isShiftDown()) && av
-                    .getSelectionGroup() != null))
+            || ((!jalview.util.Platform.isControlDown(e) && !e
+                    .isShiftDown()) && av.getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
@@ -394,6 +414,7 @@ public class IdPanel extends Panel implements MouseListener,
 
   }
 
+  @Override
   public void mouseReleased(MouseEvent e)
   {
     if (scrollThread != null)
@@ -448,6 +469,7 @@ public class IdPanel extends Panel implements MouseListener,
       running = false;
     }
 
+    @Override
     public void run()
     {
       running = true;
@@ -488,5 +510,4 @@ public class IdPanel extends Panel implements MouseListener,
       }
     }
   }
-
 }