merge from 2_4_Release branch

[jalview.git] / src / jalview / appletgui / IdPanel.java

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 44a03ec..9bf2374 100755 (executable)
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program 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 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program 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 this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.awt.*;
@@ -25,19 +24,26 @@ import java.awt.event.*;
 import jalview.datamodel.*;
 import jalview.util.UrlLink;
 
-public class IdPanel
-    extends Panel implements MouseListener, MouseMotionListener
+public class IdPanel extends Panel implements MouseListener,
+        MouseMotionListener
 {
 
   protected IdCanvas idCanvas;
+
   protected AlignViewport av;
+
   protected AlignmentPanel alignPanel;
+
   ScrollThread scrollThread = null;
 
   int offy;
+
   int width;
+
   int lastid = -1;
+
   boolean mouseDragging = false;
+
   java.util.Vector links = new java.util.Vector();
 
   public IdPanel(AlignViewport av, AlignmentPanel parent)
@@ -68,11 +74,13 @@ public class IdPanel
     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("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
     }
   }
 
   Tooltip tooltip;
+
   public void mouseMoved(MouseEvent e)
   {
     int seq = alignPanel.seqPanel.findSeq(e);
@@ -91,14 +99,13 @@ public class IdPanel
 
     if (tooltip == null)
     {
-      tooltip = new Tooltip(
-          sequence.getDisplayId(true)
-          + "\n" + sequence.getDescription(), idCanvas);
+      tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
+              + sequence.getDescription(), idCanvas);
     }
     else
     {
-      tooltip.setTip(sequence.getDisplayId(true)
-                     + "\n" + sequence.getDescription());
+      tooltip.setTip(sequence.getDisplayId(true) + "\n"
+              + sequence.getDescription());
     }
   }
 
@@ -128,13 +135,13 @@ public class IdPanel
       return;
     }
 
-    //DEFAULT LINK IS FIRST IN THE LINK LIST
+    // DEFAULT LINK IS FIRST IN THE LINK LIST
     int seq = alignPanel.seqPanel.findSeq(e);
     String id = av.getAlignment().getSequenceAt(seq).getName();
-    
+
     String target = null;
     String url = null;
-    int i=0;
+    int i = 0;
     while (url == null && i < links.size())
     {
       // DEFAULT LINK IS FIRST IN THE LINK LIST
@@ -161,7 +168,7 @@ public class IdPanel
       }
 
       String urls[] = urlLink.makeUrls(id, true);
-      if (urls == null || urls[0]==null || urls[0].length()<1)
+      if (urls == null || urls[0] == null || urls[0].length() < 1)
       {
         url = null;
         continue;
@@ -173,8 +180,7 @@ public class IdPanel
     {
 
       alignPanel.alignFrame.showURL(url, target);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -200,8 +206,8 @@ public class IdPanel
       scrollThread = new ScrollThread(true);
     }
 
-    if (mouseDragging && e.getY() >= getSize().height &&
-        av.alignment.getHeight() > av.getEndSeq())
+    if (mouseDragging && e.getY() >= getSize().height
+            && av.alignment.getHeight() > av.getEndSeq())
     {
       scrollThread = new ScrollThread(false);
     }
@@ -222,19 +228,18 @@ public class IdPanel
 
     int seq = alignPanel.seqPanel.findSeq(e);
 
-    if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) ==
-        InputEvent.BUTTON3_MASK)
+    if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
-      APopupMenu popup = new APopupMenu(alignPanel,
-                                        (Sequence) av.getAlignment().
-                                        getSequenceAt(seq), links);
+      APopupMenu popup = new APopupMenu(alignPanel, (Sequence) av
+              .getAlignment().getSequenceAt(seq), links);
       this.add(popup);
       popup.show(this, e.getX(), e.getY());
       return;
     }
 
-    if ( (av.getSelectionGroup() == null) ||
-        ( (!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))
+    if ((av.getSelectionGroup() == null)
+            || ((!e.isControlDown() && !e.isShiftDown()) && av
+                    .getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
@@ -280,7 +285,8 @@ public class IdPanel
 
     for (int i = start; i <= end; i++)
     {
-      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), false);
+      av.getSelectionGroup().addSequence(
+              av.getAlignment().getSequenceAt(i), false);
     }
 
   }
@@ -310,7 +316,7 @@ public class IdPanel
       return;
     }
 
-    int index = av.alignment.findIndex( (SequenceI) found.elementAt(0));
+    int index = av.alignment.findIndex((SequenceI) found.elementAt(0));
 
     // do we need to scroll the panel?
     if (av.getStartSeq() > index || av.getEndSeq() < index)
@@ -320,11 +326,12 @@ public class IdPanel
   }
 
   // this class allows scrolling off the bottom of the visible alignment
-  class ScrollThread
-      extends Thread
+  class ScrollThread extends Thread
   {
     boolean running = false;
+
     boolean up = true;
+
     public ScrollThread(boolean up)
     {
       this.up = up;
@@ -370,9 +377,9 @@ public class IdPanel
         try
         {
           Thread.sleep(100);
+        } catch (Exception ex)
+        {
         }
-        catch (Exception ex)
-        {}
       }
     }
   }