JAL-2418 source formatting

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

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 6ae19f0..4ccfb2f 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -48,8 +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;
 
@@ -138,7 +138,7 @@ public class IdPanel extends JPanel implements MouseListener,
     }
 
     lastid = seq;
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false);
   }
 
   /**
@@ -152,22 +152,22 @@ public class IdPanel extends JPanel implements MouseListener,
     {
       if (e.isShiftDown())
       {
-        alignPanel.scrollRight(true);
+        av.getRanges().scrollRight(true);
       }
-      else
+      else if (!av.getWrapAlignment())
       {
-        alignPanel.scrollUp(false);
+        av.getRanges().scrollUp(false);
       }
     }
     else
     {
       if (e.isShiftDown())
       {
-        alignPanel.scrollRight(false);
+        av.getRanges().scrollRight(false);
       }
-      else
+      else if (!av.getWrapAlignment())
       {
-        alignPanel.scrollUp(true);
+        av.getRanges().scrollUp(true);
       }
     }
   }
@@ -242,13 +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);
     }
@@ -292,8 +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);
@@ -312,7 +313,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
     av.isSelectionGroupChanged(true);
 
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false);
   }
 
   /**
@@ -394,8 +395,8 @@ 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);
     }
   }
 
@@ -442,9 +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);
     }
   }
 
@@ -483,14 +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)