X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=2c5684a8a168c5ccd0876b20f2614d83447a66a2;hb=95d7a34b009144b172d60bbb5827df2fbb43524e;hp=e7e1202e9bd7b8ba2f95e9767fd9320ac9e62f82;hpb=fee8c0ba299ae67650716b8ebb85bd0fc51fb15a;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index e7e1202..2c5684a 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -48,7 +48,6 @@ import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
-import java.awt.Insets;
 import java.awt.event.AdjustmentEvent;
 import java.awt.event.AdjustmentListener;
 import java.awt.event.ComponentAdapter;
@@ -76,8 +75,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
 {
   public AlignViewport av;
 
-  ViewportRanges vpRanges;
-
   OverviewPanel overviewPanel;
 
   private SeqPanel seqPanel;
@@ -121,7 +118,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     alignFrame = af;
     this.av = av;
-    vpRanges = av.getRanges();
     setSeqPanel(new SeqPanel(av, this));
     setIdPanel(new IdPanel(av, this));
 
@@ -153,11 +149,12 @@ 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
         {
@@ -166,8 +163,8 @@ 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);
         }
       }
 
@@ -377,6 +374,7 @@ 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)
@@ -404,7 +402,7 @@ 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;
     }
@@ -420,8 +418,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-      start = hidden.findColumnPosition(start);
-      end = hidden.findColumnPosition(end);
+      start = hidden.absoluteToVisibleColumn(start);
+      end = hidden.absoluteToVisibleColumn(end);
       if (start == end)
       {
         if (!hidden.isVisible(r[0]))
@@ -440,33 +438,33 @@ 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);
       }
       /*
@@ -476,7 +474,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     else
     {
-      scrollNeeded = vpRanges.scrollToWrappedVisible(start);
+      scrollNeeded = ranges.scrollToWrappedVisible(start);
     }
 
     paintAlignment(redrawOverview, false);
@@ -557,13 +555,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
       /*
        * Estimate available height in the AlignFrame for alignment +
        * annotations. Deduct an estimate for title bar, menu bar, scale panel,
-       * hscroll, status bar (as these are not laid out we can't inspect their
-       * actual heights). Insets gives frame borders.
+       * hscroll, status bar, insets. 
        */
-      int stuff = Platform.isAMac() ? 80 : 100;
-      Insets insets = alignFrame.getInsets();
-      int availableHeight = alignFrame.getHeight() - stuff - insets.top
-              - insets.bottom;
+      int stuff = Platform.isAMac() ? 120 : 140;
+      int availableHeight = alignFrame.getHeight() - stuff;
 
       /*
        * If not enough vertical space, maximize annotation height while keeping
@@ -605,7 +600,8 @@ 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);
@@ -628,16 +624,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         int widthInRes = getSeqPanel().seqCanvas
                 .getWrappedCanvasWidth(canvasWidth);
-        vpRanges.setViewportWidth(widthInRes);
+        ranges.setViewportWidth(widthInRes);
       }
       else
       {
-        int widthInRes = (canvasWidth / av.getCharWidth()) - 1;
+        int widthInRes = (canvasWidth / av.getCharWidth());
         int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
-                / av.getCharHeight()) - 1;
+                / av.getCharHeight());
 
-        vpRanges.setViewportWidth(widthInRes);
-        vpRanges.setViewportHeight(heightInSeq);
+        ranges.setViewportWidth(widthInRes);
+        ranges.setViewportHeight(heightInSeq);
       }
     }
 
@@ -678,7 +674,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         // reset the width to exclude hidden columns
         width = av.getAlignment().getHiddenColumns()
-                .findColumnPosition(width);
+                .absoluteToVisibleColumn(width);
       }
 
       hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
@@ -736,10 +732,12 @@ 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();
 
@@ -750,12 +748,12 @@ 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();
 
@@ -766,7 +764,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         return;
       }
-      vpRanges.setViewportStartAndHeight(y, height);
+      ranges.setViewportStartAndHeight(y, height);
     }
     repaint();
   }
@@ -783,6 +781,8 @@ 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();
@@ -792,8 +792,8 @@ 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;
@@ -803,9 +803,9 @@ 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
@@ -826,8 +826,8 @@ 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);
         }
       });
     }
@@ -870,17 +870,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
   @Override
   public void paintComponent(Graphics g)
   {
-    invalidate();
+    invalidate(); // needed so that the id width adjuster works correctly
 
     Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
     idPanelHolder.setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
-    validate();
+
+    validate(); // needed so that the id width adjuster works correctly
 
     /*
-     * set scroll bar positions
+     * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
+     * though I still think this call should be elsewhere.
      */
-    setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
+    ViewportRanges ranges = av.getRanges();
+    setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
   }
 
   /**
@@ -892,8 +895,9 @@ 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)
@@ -1168,7 +1172,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth) - 1;
+              .absoluteToVisibleColumn(maxwidth) - 1;
     }
 
     int resWidth = getSeqPanel().seqCanvas
@@ -1360,7 +1364,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth);
+              .absoluteToVisibleColumn(maxwidth);
     }
 
     int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
@@ -1578,7 +1582,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth) - 1;
+              .absoluteToVisibleColumn(maxwidth) - 1;
     }
 
     int height = ((maxwidth / chunkWidth) + 1) * cHeight;
@@ -1604,13 +1608,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (annotationPanel != null)
     {
       annotationPanel.dispose();
+      annotationPanel = null;
     }
 
     if (av != null)
     {
       av.removePropertyChangeListener(propertyChangeListener);
-      jalview.structure.StructureSelectionManager ssm = av
-              .getStructureSelectionManager();
+      propertyChangeListener = null;
+      StructureSelectionManager ssm = av.getStructureSelectionManager();
       ssm.removeStructureViewerListener(getSeqPanel(), null);
       ssm.removeSelectionListener(getSeqPanel());
       ssm.removeCommandListener(av);
@@ -1633,9 +1638,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected void closeChildFrames()
   {
+    if (overviewPanel != null)
+    {
+      overviewPanel.dispose();
+      overviewPanel = null;
+    }
     if (calculationDialog != null)
     {
       calculationDialog.closeFrame();
+      calculationDialog = null;
     }
   }
 
@@ -1800,35 +1811,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
   {
-    /*
-     * To avoid jumpy vertical scrolling (if some sequences are gapped or not
-     * mapped), we can make the scroll-to location a sequence above the one
-     * actually mapped.
-     */
-    SequenceI mappedTo = sr.getResults().get(0).getSequence();
-    List<SequenceI> seqs = av.getAlignment().getSequences();
-
-    /*
-     * This is like AlignmentI.findIndex(seq) but here we are matching the
-     * dataset sequence not the aligned sequence
-     */
-    boolean matched = false;
-    for (SequenceI seq : seqs)
-    {
-      if (mappedTo == seq.getDatasetSequence())
-      {
-        matched = true;
-        break;
-      }
-    }
-    if (!matched)
-    {
-      return; // failsafe, shouldn't happen
-    }
-
-    /*
-     * Scroll to position but centring the target residue.
-     */
     scrollToPosition(sr, verticalOffset, true, true);
   }
 
@@ -1882,8 +1864,9 @@ 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