JAL-3493 fix patch for 2.11.1_js (nb - these changes should not be merged to 2.11.2!)

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index cb2b3ed..277e11d 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -123,6 +123,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
+    setName("AligmentPanel");
     // setBackground(Color.white); // BH 2019
     alignFrame = af;
     this.av = av;
@@ -568,17 +569,24 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     // BH 2018.04.18 comment: addNotify() is not appropriate here. We
     // are not changing ancestors, and keyboard action listeners do
-    // not need to be reset. addNotify() is a very expensive operation,
+    // not need to be reset, and most importantly, we can't be sure we are actually
+    // connected to resources. 
+    
+    // addNotify() is a very expensive operation,
     // requiring a full re-layout of all parents and children.
+    
     // Note in JComponent:
+    
     // This method is called by the toolkit internally and should
     // not be called directly by programs.
+    
     // I note that addNotify() is called in several areas of Jalview.
 
     int annotationHeight = getAnnotationPanel().adjustPanelHeight();
     annotationHeight = getAnnotationPanel()
             .adjustForAlignFrame(adjustPanelHeight, annotationHeight);
 
+    // BH no!!
     hscroll.addNotify();
     annotationScroller.setPreferredSize(
             new Dimension(annotationScroller.getWidth(), annotationHeight));
@@ -594,9 +602,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   /**
    * update alignment layout for viewport settings
-   * 
-   * @param wrap
-   *          DOCUMENT ME!
    */
   public void updateLayout()
   {
@@ -618,9 +623,24 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       annotationScroller.setVisible(true);
       annotationSpaceFillerHolder.setVisible(true);
-      validateAnnotationDimensions(false);
     }
 
+    idSpaceFillerPanel1.setVisible(!wrap);
+
+    /*
+     * defer dimension calculations if panel not yet added to a Window
+     * BH 2020.06.09
+     */
+    if (getTopLevelAncestor() == null)
+    {
+      repaint();
+      return;
+    }
+
+    if (!wrap && av.isShowAnnotation())
+    {
+      validateAnnotationDimensions(false);
+    }
     int canvasWidth = getSeqPanel().seqCanvas.getWidth();
     if (canvasWidth > 0)
     { // may not yet be laid out
@@ -641,7 +661,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
     }
 
-    idSpaceFillerPanel1.setVisible(!wrap);
+    // System.out.println("ap dim = " + getSize());
+    // these values will go negative if getSize() returns (0,0):
+    // System.out.println("seqpan dim = " + getSeqPanel().getSize());
+    // System.out.println("seqcan dim = " + getSeqPanel().seqCanvas.getSize());
 
     repaint();
   }
@@ -655,10 +678,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
    *          visible row to scroll to
    * 
    */
-  public void setScrollValues(int xpos, int ypos)
+  public void setScrollValues(int x, int y)
   {
-    int x = xpos;
-    int y = ypos;
 
     if (av == null || av.getAlignment() == null)
     {
@@ -673,40 +694,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       int width = av.getAlignment().getVisibleWidth();
       int height = av.getAlignment().getHeight();
-
-      hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
-      vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
-
-      if (hextent > width)
-      {
-        hextent = width;
-      }
-
-      if (vextent > height)
-      {
-        vextent = height;
-      }
-
-      if ((hextent + x) > width)
-      {
-        x = width - hextent;
-      }
-
-      if ((vextent + y) > height)
-      {
-        y = height - vextent;
-      }
-
-      if (y < 0)
-      {
-        y = 0;
-      }
-
-      if (x < 0)
-      {
-        x = 0;
-      }
-
+      
+      hextent = Math.min(getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(),  width);
+      vextent = Math.min(getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(),  height);
+  
+      x = Math.max(0, Math.min(x,  width - hextent));
+      y = Math.max(0, Math.min(y,  height - vextent));
+      
       updateRanges(x, y);
       updateScrollBars(x, y, width, height);
     }
@@ -868,12 +862,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (updateOverview)
     {
       alignFrame.repaint();
-
       if (overviewPanel != null)
       {
         overviewPanel.updateOverviewImage();
       }
     } else {
+      invalidate(); // needed so that the id width adjuster works correctly
       repaint();
     }
   }
@@ -881,6 +875,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   @Override
   public void paintComponent(Graphics g)
   {
+    // BH OUCH!
     invalidate(); // needed so that the id width adjuster works correctly
 
     Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
@@ -1947,7 +1942,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     av.setSelectionGroup(null);
     av.getColumnSelection().clear();
-    av.setSelectionGroup(null);
+    av.setSearchResults(null);
     getIdPanel().getIdCanvas().searchResults = null;
     av.sendSelection();
     // JAL-2034 - should delegate to