X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=e07dae61814c4b8848c374ba717b32bf63644761;hb=8956fdfd008d0d949814c4680a7b3a55969e39e1;hp=fc7c46efe45fd7bcee134a31dbf41bced285c318;hpb=be762d8d9c71a7aa3121e845c45911c7192b7827;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index fc7c46e..e07dae6 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -43,7 +43,6 @@ import jalview.util.Comparison;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Font;
@@ -148,13 +147,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   void setCursorRow()
   {
     seqCanvas.cursorY = getKeyboardNo1() - 1;
-    scrollToVisible();
+    scrollToVisible(true);
   }
 
   void setCursorColumn()
   {
     seqCanvas.cursorX = getKeyboardNo1() - 1;
-    scrollToVisible();
+    scrollToVisible(true);
   }
 
   void setCursorRowAndColumn()
@@ -167,7 +166,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       seqCanvas.cursorX = getKeyboardNo1() - 1;
       seqCanvas.cursorY = getKeyboardNo2() - 1;
-      scrollToVisible();
+      scrollToVisible(true);
     }
   }
 
@@ -176,7 +175,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
 
     seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
-    scrollToVisible();
+    scrollToVisible(true);
   }
 
   void moveCursor(int dx, int dy)
@@ -202,10 +201,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         seqCanvas.cursorX = original;
       }
     }
-    scrollToVisible();
+    scrollToVisible(false);
   }
 
-  void scrollToVisible()
+  /**
+   * Scroll to make the cursor visible in the viewport.
+   * 
+   * @param jump
+   *          just jump to the location rather than scrolling
+   */
+  void scrollToVisible(boolean jump)
   {
     if (seqCanvas.cursorX < 0)
     {
@@ -226,44 +231,34 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
 
     endEditing();
-    if (av.getWrapAlignment())
+
+    boolean repaintNeeded = true;
+    if (jump)
     {
-      av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
+      // only need to repaint if the viewport did not move, as otherwise it will
+      // get a repaint
+      repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX,
+              seqCanvas.cursorY);
     }
     else
     {
-      ViewportRanges ranges = av.getRanges();
-      HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-      while (seqCanvas.cursorY < ranges.getStartSeq())
-      {
-        ranges.scrollUp(true);
-      }
-      while (seqCanvas.cursorY > ranges.getEndSeq())
+      if (av.getWrapAlignment())
       {
-        ranges.scrollUp(false);
-      }
-      while (seqCanvas.cursorX < hidden
-              .adjustForHiddenColumns(ranges.getStartRes()))
-      {
-
-        if (!ranges.scrollRight(false))
-        {
-          break;
-        }
+        av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
       }
-      while (seqCanvas.cursorX > hidden
-              .adjustForHiddenColumns(ranges.getEndRes()))
+      else
       {
-        if (!ranges.scrollRight(true))
-        {
-          break;
-        }
+        av.getRanges().scrollToVisible(seqCanvas.cursorX,
+                seqCanvas.cursorY);
       }
     }
     setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
             seqCanvas.cursorX, seqCanvas.cursorY);
 
-    seqCanvas.repaint();
+    if (repaintNeeded)
+    {
+      seqCanvas.repaint();
+    }
   }
 
   void setSelectionAreaAtCursor(boolean topLeft)
@@ -335,7 +330,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
     }
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
@@ -417,7 +412,6 @@ public class SeqPanel extends Panel implements MouseMotionListener,
    *          alignment column
    * @param seq
    *          index of sequence in alignment
-   * @return position of column in sequence or -1 if at gap
    */
   void setStatusMessage(SequenceI sequence, int column, int seq)
   {
@@ -653,7 +647,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     if (av.hasHiddenColumns())
     {
       res = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(res);
+              .visibleToAbsoluteColumn(res);
     }
 
     return res;
@@ -983,7 +977,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
       lastMousePress = evt.getPoint();
 
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
       ap.annotationPanel.image = null;
       return;
     }
@@ -1129,9 +1123,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       fixedColumns = true;
       int y1 = av.getAlignment().getHiddenColumns()
-              .getHiddenBoundaryLeft(startres);
+              .getNextHiddenBoundary(true, startres);
       int y2 = av.getAlignment().getHiddenColumns()
-              .getHiddenBoundaryRight(startres);
+              .getNextHiddenBoundary(false, startres);
 
       if ((insertGap && startres > y1 && lastres < y1)
               || (!insertGap && startres < y2 && lastres > y2))
@@ -1203,7 +1197,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           if (sg.getSize() == av.getAlignment().getHeight())
           {
             if ((av.hasHiddenColumns() && startres < av.getAlignment()
-                    .getHiddenColumns().getHiddenBoundaryRight(startres)))
+                    .getHiddenColumns()
+                    .getNextHiddenBoundary(false, startres)))
             {
               endEditing();
               return;
@@ -1402,7 +1397,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     if (scrollThread != null)
     {
-      scrollThread.running = false;
+      scrollThread.threadRunning = false;
       scrollThread = null;
     }
 
@@ -1450,7 +1445,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         {
           if (links == null)
           {
-            links = new Vector<String>();
+            links = new Vector<>();
           }
           links.addAll(sf.links);
         }
@@ -1524,7 +1519,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
     }
     PaintRefresher.Refresh(ap, av.getSequenceSetId());
-    ap.paintAlignment(needOverviewUpdate);
+    ap.paintAlignment(needOverviewUpdate, needOverviewUpdate);
     needOverviewUpdate = false;
     changeEndRes = false;
     changeStartRes = false;
@@ -1649,7 +1644,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       mouseExited(evt);
     }
 
-    if (scrollThread != null)
+    if ((scrollThread != null) && (scrollThread.isRunning()))
     {
       scrollThread.setEvent(evt);
     }
@@ -1665,9 +1660,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       oldSeq = 0;
     }
 
-    if (scrollThread != null)
+    if ((scrollThread != null) && (scrollThread.isRunning()))
     {
-      scrollThread.running = false;
+      scrollThread.stopScrolling();
       scrollThread = null;
     }
   }
@@ -1690,9 +1685,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     if (evt == null)
     {
-      if (scrollThread != null)
+      if ((scrollThread != null) && (scrollThread.isRunning()))
       {
-        scrollThread.running = false;
+        scrollThread.stopScrolling();
         scrollThread = null;
       }
       mouseDragging = false;
@@ -1715,7 +1710,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     MouseEvent evt;
 
-    boolean running = false;
+    private volatile boolean threadRunning = true;
 
     public ScrollThread()
     {
@@ -1729,14 +1724,18 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     public void stopScrolling()
     {
-      running = false;
+      threadRunning = false;
+    }
+
+    public boolean isRunning()
+    {
+      return threadRunning;
     }
 
     @Override
     public void run()
     {
-      running = true;
-      while (running)
+      while (threadRunning)
       {
 
         if (evt != null)
@@ -1745,23 +1744,23 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           if (mouseDragging && evt.getY() < 0
                   && av.getRanges().getStartSeq() > 0)
           {
-            running = av.getRanges().scrollUp(true);
+            av.getRanges().scrollUp(true);
           }
 
           if (mouseDragging && evt.getY() >= getSize().height && av
                   .getAlignment().getHeight() > av.getRanges().getEndSeq())
           {
-            running = av.getRanges().scrollUp(false);
+            av.getRanges().scrollUp(false);
           }
 
           if (mouseDragging && evt.getX() < 0)
           {
-            running = av.getRanges().scrollRight(false);
+            av.getRanges().scrollRight(false);
           }
 
           else if (mouseDragging && evt.getX() >= getSize().width)
           {
-            running = av.getRanges().scrollRight(true);
+            av.getRanges().scrollRight(true);
           }
         }