JAL-2727 ensure ViewportRanges (and gapcounts) are nulled when viewport

is closed

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 13b715e..1ae733e 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -163,8 +163,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   AlignViewport viewport;
 
-  ViewportRanges vpRanges;
-
   public AlignViewControllerI avc;
 
   List<AlignmentPanel> alignPanels = new ArrayList<>();
@@ -336,7 +334,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
     }
 
-    vpRanges = viewport.getRanges();
     avc = new jalview.controller.AlignViewController(this, viewport,
             alignPanel);
     if (viewport.getAlignmentConservationAnnotation() == null)
@@ -654,9 +651,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   { (viewport.cursorMode ? "on" : "off") }));
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
+            ViewportRanges ranges = viewport.getRanges();
+            alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
                     .getStartRes();
-            alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
+            alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
                     .getStartSeq();
           }
           alignPanel.getSeqPanel().seqCanvas.repaint();
@@ -689,10 +687,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           break;
         }
         case KeyEvent.VK_PAGE_UP:
-          vpRanges.pageUp();
+          viewport.getRanges().pageUp();
           break;
         case KeyEvent.VK_PAGE_DOWN:
-          vpRanges.pageDown();
+          viewport.getRanges().pageDown();
           break;
         }
       }
@@ -2147,7 +2145,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
 
         // propagate alignment changed.
-        vpRanges.setEndSeq(alignment.getHeight());
+        viewport.getRanges().setEndSeq(alignment.getHeight());
         if (annotationAdded)
         {
           // Duplicate sequence annotation in all views.
@@ -2548,7 +2546,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
                 column, viewport.getAlignment());
-        vpRanges.setStartRes(0);
+        viewport.getRanges().setStartRes(0);
       }
       else
       {
@@ -2613,13 +2611,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // This is to maintain viewport position on first residue
     // of first sequence
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(vpRanges.getStartRes());
+    ViewportRanges ranges = viewport.getRanges();
+    int startRes = seq.findPosition(ranges.getStartRes());
     // ShiftList shifts;
     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
     // edit.alColumnChanges=shifts.getInverse();
     // if (viewport.hasHiddenColumns)
     // viewport.getColumnSelection().compensateForEdits(shifts);
-    vpRanges.setStartRes(seq.findIndex(startRes) - 1);
+    ranges.setStartRes(seq.findIndex(startRes) - 1);
     viewport.firePropertyChange("alignment", null,
             viewport.getAlignment().getSequences());
 
@@ -2652,12 +2651,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // This is to maintain viewport position on first residue
     // of first sequence
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(vpRanges.getStartRes());
+    int startRes = seq.findPosition(viewport.getRanges().getStartRes());
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
             viewport.getAlignment()));
 
-    vpRanges.setStartRes(seq.findIndex(startRes) - 1);
+    viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
 
     viewport.firePropertyChange("alignment", null,
             viewport.getAlignment().getSequences());

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 76368ed..9b74007 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -76,8 +76,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
 {
   public AlignViewport av;
 
-  ViewportRanges vpRanges;
-
   OverviewPanel overviewPanel;
 
   private SeqPanel seqPanel;
@@ -124,7 +122,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     alignFrame = af;
     this.av = av;
-    vpRanges = av.getRanges();
     setSeqPanel(new SeqPanel(av, this));
     setIdPanel(new IdPanel(av, this));
 
@@ -156,11 +153,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
         // reset the viewport ranges when the alignment panel is resized
         // in particular, this initialises the end residue value when Jalview
         // is initialised
+        ViewportRanges ranges = av.getRanges();
         if (av.getWrapAlignment())
         {
           int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth(
                   getSeqPanel().seqCanvas.getWidth());
-          vpRanges.setViewportWidth(widthInRes);
+          ranges.setViewportWidth(widthInRes);
         }
         else
         {
@@ -169,8 +167,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
           int heightInSeq = getSeqPanel().seqCanvas.getHeight()
                   / av.getCharHeight();
 
-          vpRanges.setViewportWidth(widthInRes);
-          vpRanges.setViewportHeight(heightInSeq);
+          ranges.setViewportWidth(widthInRes);
+          ranges.setViewportHeight(heightInSeq);
         }
       }
 
@@ -384,6 +382,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           int verticalOffset, boolean redrawOverview, boolean centre)
   {
     int startv, endv, starts, ends;
+    ViewportRanges ranges = av.getRanges();
 
     if (results == null || results.isEmpty() || av == null
             || av.getAlignment() == null)
@@ -411,7 +410,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
      */
     if (centre)
     {
-      int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
+      int offset = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1;
       start = Math.max(start - offset, 0);
       end = end + offset - 1;
     }
@@ -447,33 +446,33 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     if (!av.getWrapAlignment())
     {
-      if ((startv = vpRanges.getStartRes()) >= start)
+      if ((startv = ranges.getStartRes()) >= start)
       {
         /*
          * Scroll left to make start of search results visible
          */
         setScrollValues(start, seqIndex);
       }
-      else if ((endv = vpRanges.getEndRes()) <= end)
+      else if ((endv = ranges.getEndRes()) <= end)
       {
         /*
          * Scroll right to make end of search results visible
          */
         setScrollValues(startv + end - endv, seqIndex);
       }
-      else if ((starts = vpRanges.getStartSeq()) > seqIndex)
+      else if ((starts = ranges.getStartSeq()) > seqIndex)
       {
         /*
          * Scroll up to make start of search results visible
          */
-        setScrollValues(vpRanges.getStartRes(), seqIndex);
+        setScrollValues(ranges.getStartRes(), seqIndex);
       }
-      else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
+      else if ((ends = ranges.getEndSeq()) <= seqIndex)
       {
         /*
          * Scroll down to make end of search results visible
          */
-        setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
+        setScrollValues(ranges.getStartRes(), starts + seqIndex - ends
                 + 1);
       }
       /*
@@ -483,7 +482,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     else
     {
-      scrollNeeded = vpRanges.scrollToWrappedVisible(start);
+      scrollNeeded = ranges.scrollToWrappedVisible(start);
     }
 
     paintAlignment(redrawOverview);
@@ -610,7 +609,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     fontChanged();
     setAnnotationVisible(av.isShowAnnotation());
     boolean wrap = av.getWrapAlignment();
-    vpRanges.setStartSeq(0);
+    ViewportRanges ranges = av.getRanges();
+    ranges.setStartSeq(0);
     scalePanelHolder.setVisible(!wrap);
     hscroll.setVisible(!wrap);
     idwidthAdjuster.setVisible(!wrap);
@@ -633,7 +633,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         int widthInRes = getSeqPanel().seqCanvas
                 .getWrappedCanvasWidth(canvasWidth);
-        vpRanges.setViewportWidth(widthInRes);
+        ranges.setViewportWidth(widthInRes);
       }
       else
       {
@@ -641,8 +641,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
         int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
                 / av.getCharHeight()) - 1;
 
-        vpRanges.setViewportWidth(widthInRes);
-        vpRanges.setViewportHeight(heightInSeq);
+        ranges.setViewportWidth(widthInRes);
+        ranges.setViewportHeight(heightInSeq);
       }
     }
 
@@ -741,10 +741,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
       return;
     }
 
+    ViewportRanges ranges = av.getRanges();
+
     if (evt.getSource() == hscroll)
     {
-      int oldX = vpRanges.getStartRes();
-      int oldwidth = vpRanges.getViewportWidth();
+      int oldX = ranges.getStartRes();
+      int oldwidth = ranges.getViewportWidth();
       int x = hscroll.getValue();
       int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
 
@@ -755,12 +757,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         return;
       }
-      vpRanges.setViewportStartAndWidth(x, width);
+      ranges.setViewportStartAndWidth(x, width);
     }
     else if (evt.getSource() == vscroll)
     {
-      int oldY = vpRanges.getStartSeq();
-      int oldheight = vpRanges.getViewportHeight();
+      int oldY = ranges.getStartSeq();
+      int oldheight = ranges.getViewportHeight();
       int y = vscroll.getValue();
       int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
 
@@ -771,7 +773,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         return;
       }
-      vpRanges.setViewportStartAndHeight(y, height);
+      ranges.setViewportStartAndHeight(y, height);
     }
     if (!fastPaint)
     {
@@ -791,6 +793,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       return; // no horizontal scroll when wrapped
     }
+    final ViewportRanges ranges = av.getRanges();
+
     if (evt.getSource() == vscroll)
     {
       int newY = vscroll.getValue();
@@ -800,8 +804,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
        * this prevents infinite recursion of events when the scroll/viewport
        * ranges values are the same
        */
-      int oldX = vpRanges.getStartRes();
-      int oldY = vpRanges.getWrappedScrollPosition(oldX);
+      int oldX = ranges.getStartRes();
+      int oldY = ranges.getWrappedScrollPosition(oldX);
       if (oldY == newY)
       {
         return;
@@ -811,9 +815,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
         /*
          * limit page up/down to one width's worth of positions
          */
-        int rowSize = vpRanges.getViewportWidth();
+        int rowSize = ranges.getViewportWidth();
         int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
-        vpRanges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
+        ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
       }
     }
     else
@@ -834,8 +838,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
                   "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
 
           // scroll to start of panel
-          vpRanges.setStartRes(0);
-          vpRanges.setStartSeq(0);
+          ranges.setStartRes(0);
+          ranges.setStartSeq(0);
         }
       });
     }
@@ -886,7 +890,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     /*
      * set scroll bar positions
      */
-    setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
+    ViewportRanges ranges = av.getRanges();
+    setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
   }
 
   /**
@@ -898,8 +903,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   private void setScrollingForWrappedPanel(int topLeftColumn)
   {
-    int scrollPosition = vpRanges.getWrappedScrollPosition(topLeftColumn);
-    int maxScroll = vpRanges.getWrappedMaxScroll(topLeftColumn);
+    ViewportRanges ranges = av.getRanges();
+    int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn);
+    int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn);
 
     /*
      * a scrollbar's value can be set to at most (maximum-extent)
@@ -1888,8 +1894,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public void propertyChange(PropertyChangeEvent evt)
   {
     // update this panel's scroll values based on the new viewport ranges values
-    int x = vpRanges.getStartRes();
-    int y = vpRanges.getStartSeq();
+    ViewportRanges ranges = av.getRanges();
+    int x = ranges.getStartRes();
+    int y = ranges.getStartSeq();
     setScrollValues(x, y);
 
     // now update any complementary alignment (its viewport ranges object

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 3702cd0..a66855e 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -80,7 +80,7 @@ import java.util.Map;
 public abstract class AlignmentViewport
         implements AlignViewportI, CommandListener, VamsasSource
 {
-  final protected ViewportRanges ranges;
+  protected ViewportRanges ranges;
 
   protected ViewStyleI viewStyle = new ViewStyle();
 
@@ -949,10 +949,12 @@ public abstract class AlignmentViewport
     groupConservation = null;
     hconsensus = null;
     hcomplementConsensus = null;
+    gapcounts = null;
     // colour scheme may hold reference to consensus
     residueShading = null;
     // TODO remove listeners from changeSupport?
     changeSupport = null;
+    ranges = null;
     setAlignment(null);
   }