Merge branch 'documentation/JAL-2418_release2102' into develop

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

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index fb9bcbb..065f97e 100755 (executable)
--- 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;
@@ -108,8 +106,8 @@ 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,
+      StringBuilder tip = new StringBuilder(64);
+      seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
               av.isShowDBRefs(), av.isShowNPFeats(),
               sp.seqCanvas.fr.getMinMax());
       setToolTipText(JvSwingUtils.wrapTooltip(true,
@@ -140,7 +138,7 @@ public class IdPanel extends JPanel implements MouseListener,
     }
 
     lastid = seq;
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false);
   }
 
   /**
@@ -154,22 +152,22 @@ public class IdPanel extends JPanel implements MouseListener,
     {
       if (e.isShiftDown())
       {
-        alignPanel.scrollRight(true);
+        av.getRanges().scrollRight(true);
       }
       else
       {
-        alignPanel.scrollUp(false);
+        av.getRanges().scrollUp(false);
       }
     }
     else
     {
       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);
     }
@@ -314,7 +313,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
     av.isSelectionGroupChanged(true);
 
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false);
   }
 
   /**
@@ -328,7 +327,7 @@ public class IdPanel extends JPanel implements MouseListener,
     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();
+    List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
     SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
     if (sfs != null)
     {
@@ -340,7 +339,7 @@ public class IdPanel extends JPanel implements MouseListener,
           {
             for (int l = 0, lSize = sf.links.size(); l < lSize; l++)
             {
-              nlinks.addElement(sf.links.elementAt(l));
+              nlinks.add(sf.links.elementAt(l));
             }
           }
         }
@@ -444,9 +443,10 @@ 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 +485,14 @@ 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)