Merge branch 'features/JAL-2608closeOverview' into develop

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index b45ddef..07c65fe 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -97,9 +97,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   private AnnotationLabels alabels;
 
-  // this value is set false when selection area being dragged
-  boolean fastPaint = true;
-
   private int hextent = 0;
 
   private int vextent = 0;
@@ -214,7 +211,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     alignFrame.updateEditMenuBar();
 
-    paintAlignment(true);
+    // no idea if we need to update structure
+    paintAlignment(true, true);
 
   }
 
@@ -231,7 +229,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
             new Dimension(10, av.getCharHeight() + fm.getDescent()));
     idSpaceFillerPanel1.setPreferredSize(
             new Dimension(10, av.getCharHeight() + fm.getDescent()));
-
+    idwidthAdjuster.invalidate();
+    scalePanelHolder.invalidate();
     getIdPanel().getIdCanvas().gg = null;
     getSeqPanel().seqCanvas.img = null;
     getAnnotationPanel().adjustPanelHeight();
@@ -242,11 +241,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
     getIdPanel().getIdCanvas().setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(d);
 
-    if (this.alignFrame.getSplitViewContainer() != null)
-    {
-      ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
-    }
-
     repaint();
   }
 
@@ -485,7 +479,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       scrollNeeded = vpRanges.scrollToWrappedVisible(start);
     }
 
-    paintAlignment(redrawOverview);
+    paintAlignment(redrawOverview, false);
 
     return scrollNeeded;
   }
@@ -542,7 +536,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     validateAnnotationDimensions(true);
     addNotify();
-    paintAlignment(true);
+    // TODO: many places call this method and also paintAlignment with various
+    // different settings. this means multiple redraws are triggered...
+    paintAlignment(true, false);
   }
 
   /**
@@ -636,9 +632,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       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);
@@ -772,10 +768,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       vpRanges.setViewportStartAndHeight(y, height);
     }
-    if (!fastPaint)
-    {
-      repaint();
-    }
+    repaint();
   }
 
   /**
@@ -841,12 +834,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
     repaint();
   }
 
-  /**
-   * Repaint the alignment including the annotations and overview panels (if
-   * shown).
+  /* (non-Javadoc)
+   * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
    */
   @Override
-  public void paintAlignment(boolean updateOverview)
+  public void paintAlignment(boolean updateOverview,
+          boolean updateStructures)
   {
     final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
             av.isShowAutocalculatedAbove());
@@ -854,10 +847,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
             av.getSortAnnotationsBy());
     repaint();
 
-    if (updateOverview)
+    if (updateStructures)
     {
-      // TODO: determine if this paintAlignment changed structure colours
       av.getStructureSelectionManager().sequenceColoursChanged(this);
+    }
+    if (updateOverview)
+    {
 
       if (overviewPanel != null)
       {
@@ -1100,7 +1095,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * single graphics context), then reset to (0, scale height)
      */
     alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
-    getSeqPanel().seqCanvas.drawPanelForPrint(alignmentGraphics, startRes,
+    getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
             endRes, startSeq, endSeq);
     alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
 
@@ -1228,7 +1223,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     pg.translate(idWidth, 0);
 
-    getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
+    getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth,
             totalHeight, 0);
 
     if ((pi * pheight) < totalHeight)
@@ -1609,6 +1604,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (annotationPanel != null)
     {
       annotationPanel.dispose();
+      annotationPanel = null;
     }
 
     if (av != null)
@@ -1638,9 +1634,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected void closeChildFrames()
   {
+    if (overviewPanel != null)
+    {
+      overviewPanel.dispose();
+      overviewPanel = null;
+    }
     if (calculationDialog != null)
     {
       calculationDialog.closeFrame();
+      calculationDialog = null;
     }
   }
 
@@ -1870,7 +1872,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (adjustHeight)
     {
       // sort, repaint, update overview
-      paintAlignment(true);
+      paintAlignment(true, false);
     }
     else
     {