JAL-4259 construct a new SequenceRenderer when rendering an MSA to an exporter

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

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 076b0a3..735046e 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;
@@ -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()
-              .findColumnPosition(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);
@@ -492,27 +480,31 @@ 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())
         {
           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;
@@ -565,8 +557,8 @@ public class SeqCanvas extends Panel implements ViewportListenerI
       int blockEnd;
 
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-      VisibleContigsIterator regions = (VisibleContigsIterator) hidden
-              .getVisContigsIterator(startRes, endRes, true);
+      VisibleContigsIterator regions = hidden
+              .getVisContigsIterator(startRes, endRes + 1, true);
 
       while (regions.hasNext())
       {
@@ -652,7 +644,9 @@ public class SeqCanvas extends Panel implements ViewportListenerI
       if (av.cursorMode && cursorY == i && cursorX >= startRes
               && cursorX <= endRes)
       {
-        sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * avcharWidth,
+        char s = nextSeq.getCharAt(cursorX);
+
+        sr.drawCursor(g,s, (cursorX - startRes) * avcharWidth,
                 offset + ((i - startSeq) * avcharHeight));
       }
     }
@@ -918,4 +912,19 @@ 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;
+  }
+
 }