JAL-3253 temporary branch SwingJS upgrade with testNG fixes Java 8

[jalview.git] / src / jalview / appletgui / SeqCanvas.java

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 2c90047..ecb0888 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -40,6 +40,7 @@ import java.awt.Panel;
 import java.beans.PropertyChangeEvent;
 import java.util.Iterator;
 
+@SuppressWarnings("serial")
 public class SeqCanvas extends Panel implements ViewportListenerI
 {
   FeatureRenderer fr;
@@ -131,16 +132,9 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       startx = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(startx);
+              .visibleToAbsoluteColumn(startx);
       endx = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(endx);
-    }
-
-    int maxwidth = av.getAlignment().getWidth();
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth) - 1;
+              .visibleToAbsoluteColumn(endx);
     }
 
     // WEST SCALE
@@ -181,7 +175,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       endx = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(endx);
+              .visibleToAbsoluteColumn(endx);
     }
 
     SequenceI seq;
@@ -450,13 +444,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     int endx;
     int ypos = hgap;
   
-    int maxwidth = av.getAlignment().getWidth();
-  
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth);
-    }
+    int maxwidth = av.getAlignment().getVisibleWidth();
   
     while ((ypos <= canvasHeight) && (startRes < maxwidth))
     {
@@ -492,7 +480,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
         HiddenColumns hidden = av.getAlignment().getHiddenColumns();
         g.setColor(Color.blue);
         int res;
-        Iterator<Integer> it = hidden.getBoundedStartIterator(startRes,
+        Iterator<Integer> it = hidden.getStartRegionIterator(startRes,
                 endx + 1);
         while (it.hasNext())
         {
@@ -504,15 +492,17 @@ public class SeqCanvas extends Panel implements ViewportListenerI
                   { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2), ypos - (avcharHeight / 2) + 8 }, 3);
         }
       }
-  
+      // BH 2020.03.19 avoiding g.setClip at all costs
+      g = g.create();
       if (g.getClip() == null)
       {
-        g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
+        g.clipRect(0, 0, cWidth * avcharWidth, canvasHeight);
       }
   
       drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
-      g.setClip(null);
+      // g.setClip(null);
   
+      g.dispose();
       if (av.isShowAnnotation())
       {
         g.translate(0, cHeight + ypos + 4);
@@ -565,8 +555,8 @@ public class SeqCanvas extends Panel implements ViewportListenerI
       int blockEnd;
 
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-      VisibleContigsIterator regions = (VisibleContigsIterator) hidden
-              .getVisibleBlocksIterator(startRes, endRes, true);
+      VisibleContigsIterator regions = hidden
+              .getVisContigsIterator(startRes, endRes + 1, true);
 
       while (regions.hasNext())
       {
@@ -918,4 +908,19 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     }
   }
 
+  /**
+   * Ensure that a full paint is done next, for whatever reason. This was
+   * necessary for JavaScript; apparently in Java the timing is just right on
+   * multiple threads (EventQueue-0, Consensus, Conservation) that we can get
+   * away with one fast paint before the others, but this ensures that in the
+   * end we get a full paint. Problem arose in relation to copy/paste, where the
+   * paste was not finalized with a full paint.
+   * 
+   * @author hansonr 2019.04.17
+   */
+  public void clearFastPaint()
+  {
+    fastPaint = false;
+  }
+
 }