X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=3b79f1200d6298b91017742d9a8deab340224e90;hb=483ecb5e4541537778844529cc93204f9124b68d;hp=35d73dedab23aae18855c66f2db96299d7427f3c;hpb=15662a256b76221299688fff94288d9bd37f8453;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 35d73de..3b79f12 100755
--- 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;
@@ -136,13 +137,6 @@ public class SeqCanvas extends Panel implements ViewportListenerI
               .visibleToAbsoluteColumn(endx);
     }
 
-    int maxwidth = av.getAlignment().getWidth();
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth) - 1;
-    }
-
     // WEST SCALE
     for (int i = 0; i < av.getAlignment().getHeight(); i++)
     {
@@ -418,71 +412,65 @@ public class SeqCanvas extends Panel implements ViewportListenerI
           int canvasHeight, int startRes)
   {
     AlignmentI al = av.getAlignment();
-  
+
     FontMetrics fm = getFontMetrics(av.getFont());
-  
+
     LABEL_EAST = 0;
     LABEL_WEST = 0;
-  
+
     if (av.getScaleRightWrapped())
     {
       LABEL_EAST = fm.stringWidth(getMask());
     }
-  
+
     if (av.getScaleLeftWrapped())
     {
       LABEL_WEST = fm.stringWidth(getMask());
     }
-  
+
     int hgap = avcharHeight;
     if (av.getScaleAboveWrapped())
     {
       hgap += avcharHeight;
     }
-  
+
     int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth;
     int cHeight = av.getAlignment().getHeight() * avcharHeight;
-  
+
     av.setWrappedWidth(cWidth);
-  
+
     av.getRanges().setViewportStartAndWidth(startRes, cWidth);
-  
+
     int endx;
     int ypos = hgap;
-  
-    int maxwidth = av.getAlignment().getWidth();
-  
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth);
-    }
-  
+
+    int maxwidth = av.getAlignment().getVisibleWidth();
+
     while ((ypos <= canvasHeight) && (startRes < maxwidth))
     {
       endx = startRes + cWidth - 1;
-  
+
       if (endx > maxwidth)
       {
         endx = maxwidth;
       }
-  
+
       g.setColor(Color.black);
-  
+
       if (av.getScaleLeftWrapped())
       {
         drawWestScale(g, startRes, endx, ypos);
       }
-  
+
       if (av.getScaleRightWrapped())
       {
         g.translate(canvasWidth - LABEL_EAST, 0);
         drawEastScale(g, startRes, endx, ypos);
         g.translate(-(canvasWidth - LABEL_EAST), 0);
       }
-  
+
       g.translate(LABEL_WEST, 0);
-  
+
       if (av.getScaleAboveWrapped())
       {
         drawNorthScale(g, startRes, endx, ypos);
@@ -499,20 +487,24 @@ public class SeqCanvas extends Panel implements ViewportListenerI
           res = it.next() - startRes;
           gg.fillPolygon(
                   new int[]
-                  { res * avcharWidth - avcharHeight / 4, res * avcharWidth + avcharHeight / 4, res * avcharWidth },
+                  { res * avcharWidth - avcharHeight / 4,
+                      res * avcharWidth + avcharHeight / 4,
+                      res * avcharWidth },
                   new int[]
-                  { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2), ypos - (avcharHeight / 2) + 8 }, 3);
+                  { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),
+                      ypos - (avcharHeight / 2) + 8 },
+                  3);
         }
       }
-  
+
       if (g.getClip() == null)
       {
         g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
       }
-  
+
       drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
       g.setClip(null);
-  
+
       if (av.isShowAnnotation())
       {
         g.translate(0, cHeight + ypos + 4);
@@ -520,17 +512,17 @@ public class SeqCanvas extends Panel implements ViewportListenerI
         {
           annotations = new AnnotationPanel(av);
         }
-  
+
         annotations.drawComponent(g, startRes, endx + 1);
         g.translate(0, -cHeight - ypos - 4);
       }
       g.translate(-LABEL_WEST, 0);
-  
+
       ypos += cHeight + getAnnotationHeight() + hgap;
-  
+
       startRes += cWidth;
     }
-  
+
   }
 
   AnnotationPanel annotations;
@@ -565,7 +557,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
       int blockEnd;
 
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-      VisibleContigsIterator regions = (VisibleContigsIterator) hidden
+      VisibleContigsIterator regions = hidden
               .getVisContigsIterator(startRes, endRes + 1, true);
 
       while (regions.hasNext())
@@ -918,4 +910,19 @@ 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;
+  }
+
 }