X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=735046ea57efb40fbf734b70f3241d02ee192c18;hb=cd669a0e8c7b91b379bca8fe6e702cf0fcbd1ce0;hp=2420cf7318a5feb0a6030622076bd9f1febf29f9;hpb=4650bd5a0ce2b7ef07bd91baa591fa5d0cadef4c;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 2420cf7..735046e 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -25,6 +25,7 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.VisibleContigsIterator;
 import jalview.renderer.ScaleRenderer;
 import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.viewmodel.AlignmentViewport;
@@ -37,8 +38,9 @@ import java.awt.Graphics;
 import java.awt.Image;
 import java.awt.Panel;
 import java.beans.PropertyChangeEvent;
-import java.util.List;
+import java.util.Iterator;
 
+@SuppressWarnings("serial")
 public class SeqCanvas extends Panel implements ViewportListenerI
 {
   FeatureRenderer fr;
@@ -130,16 +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
@@ -180,7 +175,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       endx = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(endx);
+              .visibleToAbsoluteColumn(endx);
     }
 
     SequenceI seq;
@@ -449,13 +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))
     {
@@ -491,16 +480,11 @@ public class SeqCanvas extends Panel implements ViewportListenerI
         HiddenColumns hidden = av.getAlignment().getHiddenColumns();
         g.setColor(Color.blue);
         int res;
-        List<Integer> positions = hidden.findHiddenRegionPositions();
-        for (int pos : positions)
+        Iterator<Integer> it = hidden.getStartRegionIterator(startRes,
+                endx + 1);
+        while (it.hasNext())
         {
-          res = pos - startRes;
-
-          if (res < 0 || res > endx - startRes)
-          {
-            continue;
-          }
-
+          res = it.next() - startRes;
           gg.fillPolygon(
                   new int[]
                   { res * avcharWidth - avcharHeight / 4,
@@ -510,7 +494,6 @@ public class SeqCanvas extends Panel implements ViewportListenerI
                   { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),
                       ypos - (avcharHeight / 2) + 8 },
                   3);
-
         }
       }
 
@@ -570,70 +553,44 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     else
     {
       int screenY = 0;
-      final int screenYMax = endRes - startRes;
-      int blockStart = startRes;
-      int blockEnd = endRes;
-
-      if (av.hasHiddenColumns())
-      {
-        HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-        for (int[] region : hidden.getHiddenColumnsCopy())
-        {
-          int hideStart = region[0];
-          int hideEnd = region[1];
-
-          if (hideStart <= blockStart)
-          {
-            blockStart += (hideEnd - hideStart) + 1;
-            continue;
-          }
+      int blockStart;
+      int blockEnd;
 
-          /*
-           * draw up to just before the next hidden region, or the end of
-           * the visible region, whichever comes first
-           */
-          blockEnd = Math.min(hideStart - 1, blockStart + screenYMax
-                  - screenY);
+      HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+      VisibleContigsIterator regions = hidden
+              .getVisContigsIterator(startRes, endRes + 1, true);
 
-          g1.translate(screenY * avcharWidth, 0);
-
-          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
-
-          /*
-           * draw the downline of the hidden column marker (ScalePanel draws the
-           * triangle on top) if we reached it
-           */
-          if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
-          {
-            g1.setColor(Color.blue);
-            g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
-                    0 + offset,
-                    (blockEnd - blockStart + 1) * avcharWidth - 1,
-                    (endSeq - startSeq + 1) * avcharHeight + offset);
-          }
-
-          g1.translate(-screenY * avcharWidth, 0);
-          screenY += blockEnd - blockStart + 1;
-          blockStart = hideEnd + 1;
-
-          if (screenY > screenYMax)
-          {
-            // already rendered last block
-            return;
-          }
-        }
-      }
-      if (screenY <= screenYMax)
+      while (regions.hasNext())
       {
-        // remaining visible region to render
-        blockEnd = blockStart + (endRes - startRes) - screenY;
+        int[] region = regions.next();
+        blockEnd = region[1];
+        blockStart = region[0];
+
+        /*
+         * draw up to just before the next hidden region, or the end of
+         * the visible region, whichever comes first
+         */
         g1.translate(screenY * avcharWidth, 0);
+
         draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
 
+        /*
+         * draw the downline of the hidden column marker (ScalePanel draws the
+         * triangle on top) if we reached it
+         */
+        if (av.getShowHiddenMarkers()
+                && (regions.hasNext() || regions.endsAtHidden()))
+        {
+          g1.setColor(Color.blue);
+          g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
+                  0 + offset, (blockEnd - blockStart + 1) * avcharWidth - 1,
+                  (endSeq - startSeq + 1) * avcharHeight + offset);
+        }
+
         g1.translate(-screenY * avcharWidth, 0);
+        screenY += blockEnd - blockStart + 1;
       }
     }
-
   }
 
   // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
@@ -687,7 +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));
       }
     }
@@ -953,4 +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;
+  }
+
 }