X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=a1831440d65413baf57742d2725e619f8a8dd7fb;hb=bb620cae1e4c44ae9efaf975c7bbbc63b0558db3;hp=fb9bcbbb14cc9ba0288fc53f83d6dd3fe53948ff;hpb=a889a61789f15e79ecde7043cddfdea18ad00166;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index fb9bcbb..a183144 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -36,9 +36,7 @@ import java.awt.event.MouseMotionListener;
 import java.awt.event.MouseWheelEvent;
 import java.awt.event.MouseWheelListener;
 import java.util.List;
-import java.util.Vector;
 
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
@@ -50,8 +48,8 @@ import javax.swing.ToolTipManager;
  * @author $author$
  * @version $Revision$
  */
-public class IdPanel extends JPanel implements MouseListener,
-        MouseMotionListener, MouseWheelListener
+public class IdPanel extends JPanel
+        implements MouseListener, MouseMotionListener, MouseWheelListener
 {
   private IdCanvas idCanvas;
 
@@ -108,10 +106,9 @@ public class IdPanel extends JPanel implements MouseListener,
     if (seq > -1 && seq < av.getAlignment().getHeight())
     {
       SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-      StringBuffer tip = new StringBuffer(64);
-      seqAnnotReport.createSequenceAnnotationReport(tip, sequence,
-              av.isShowDBRefs(), av.isShowNPFeats(),
-              sp.seqCanvas.fr.getMinMax());
+      StringBuilder tip = new StringBuilder(64);
+      seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
+              av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr);
       setToolTipText(JvSwingUtils.wrapTooltip(true,
               sequence.getDisplayId(true) + " " + tip.toString()));
     }
@@ -140,7 +137,7 @@ public class IdPanel extends JPanel implements MouseListener,
     }
 
     lastid = seq;
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -150,26 +147,27 @@ public class IdPanel extends JPanel implements MouseListener,
   public void mouseWheelMoved(MouseWheelEvent e)
   {
     e.consume();
-    if (e.getWheelRotation() > 0)
+    double wheelRotation = e.getPreciseWheelRotation();
+    if (wheelRotation > 0)
     {
       if (e.isShiftDown())
       {
-        alignPanel.scrollRight(true);
+        av.getRanges().scrollRight(true);
       }
       else
       {
-        alignPanel.scrollUp(false);
+        av.getRanges().scrollUp(false);
       }
     }
-    else
+    else if (wheelRotation < 0)
     {
       if (e.isShiftDown())
       {
-        alignPanel.scrollRight(false);
+        av.getRanges().scrollRight(false);
       }
       else
       {
-        alignPanel.scrollUp(true);
+        av.getRanges().scrollUp(true);
       }
     }
   }
@@ -200,17 +198,17 @@ public class IdPanel extends JPanel implements MouseListener,
 
     int seq = alignPanel.getSeqPanel().findSeq(e);
     String id = av.getAlignment().getSequenceAt(seq).getName();
-    String url = Preferences.sequenceUrlLinks.getDefaultUrl(id);
+    String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id);
 
     try
     {
       jalview.util.BrowserLauncher.openURL(url);
     } catch (Exception ex)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
               MessageManager.getString("label.web_browser_not_found_unix"),
               MessageManager.getString("label.web_browser_not_found"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
       ex.printStackTrace();
     }
   }
@@ -244,13 +242,14 @@ public class IdPanel extends JPanel implements MouseListener,
       return;
     }
 
-    if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
+    if (mouseDragging && (e.getY() < 0)
+            && (av.getRanges().getStartSeq() > 0))
     {
       scrollThread = new ScrollThread(true);
     }
 
     if (mouseDragging && (e.getY() >= getHeight())
-            && (av.getAlignment().getHeight() > av.getEndSeq()))
+            && (av.getAlignment().getHeight() > av.getRanges().getEndSeq()))
     {
       scrollThread = new ScrollThread(false);
     }
@@ -294,8 +293,8 @@ public class IdPanel extends JPanel implements MouseListener,
     }
 
     if ((av.getSelectionGroup() == null)
-            || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown() && av
-                    .getSelectionGroup() != null))
+            || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown()
+                    && av.getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
@@ -314,7 +313,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
     av.isSelectionGroupChanged(true);
 
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -326,28 +325,25 @@ public class IdPanel extends JPanel implements MouseListener,
   {
     int seq2 = alignPanel.getSeqPanel().findSeq(e);
     Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
-    // build a new links menu based on the current links + any non-positional
-    // features
-    Vector<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
-    SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
-    if (sfs != null)
+
+    /*
+     *  build a new links menu based on the current links
+     *  and any non-positional features
+     */
+    List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
+    List<SequenceFeature> features = sq.getFeatures().getNonPositionalFeatures();
+    for (SequenceFeature sf : features)
     {
-      for (SequenceFeature sf : sfs)
+      if (sf.links != null)
       {
-        if (sf.begin == sf.end && sf.begin == 0)
+        for (String link : sf.links)
         {
-          if (sf.links != null && sf.links.size() > 0)
-          {
-            for (int l = 0, lSize = sf.links.size(); l < lSize; l++)
-            {
-              nlinks.addElement(sf.links.elementAt(l));
-            }
-          }
+          nlinks.add(link);
         }
       }
     }
 
-    PopupMenu pop = new PopupMenu(alignPanel, sq, nlinks,
+    PopupMenu pop = new PopupMenu(alignPanel, sq, features,
             Preferences.getGroupURLLinks());
     pop.show(this, e.getX(), e.getY());
   }
@@ -396,8 +392,8 @@ public class IdPanel extends JPanel implements MouseListener,
 
     for (int i = start; i <= end; i++)
     {
-      av.getSelectionGroup().addSequence(
-              av.getAlignment().getSequenceAt(i), i == end);
+      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+              i == end);
     }
   }
 
@@ -444,9 +440,10 @@ public class IdPanel extends JPanel implements MouseListener,
     int index = av.getAlignment().findIndex(list.get(0));
 
     // do we need to scroll the panel?
-    if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
+    if ((av.getRanges().getStartSeq() > index)
+            || (av.getRanges().getEndSeq() < index))
     {
-      alignPanel.setScrollValues(av.getStartRes(), index);
+      av.getRanges().setStartSeq(index);
     }
   }
 
@@ -485,14 +482,14 @@ public class IdPanel extends JPanel implements MouseListener,
 
       while (running)
       {
-        if (alignPanel.scrollUp(up))
+        if (av.getRanges().scrollUp(up))
         {
           // scroll was ok, so add new sequence to selection
-          int seq = av.getStartSeq();
+          int seq = av.getRanges().getStartSeq();
 
           if (!up)
           {
-            seq = av.getEndSeq();
+            seq = av.getRanges().getEndSeq();
           }
 
           if (seq < lastid)
@@ -511,7 +508,7 @@ public class IdPanel extends JPanel implements MouseListener,
           running = false;
         }
 
-        alignPanel.paintAlignment(false);
+        alignPanel.paintAlignment(false, false);
 
         try
         {