JAL-3581 no hidden sequence marker if hidden markers not shown

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

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 42376c7..10c0787 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -20,10 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.SequenceI;
-import jalview.viewmodel.ViewportListenerI;
-import jalview.viewmodel.ViewportRanges;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Font;
@@ -37,6 +33,10 @@ import java.util.List;
 
 import javax.swing.JPanel;
 
+import jalview.datamodel.SequenceI;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
 /**
  * DOCUMENT ME!
  * 
@@ -55,7 +55,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
 
   BufferedImage image;
 
-  Graphics2D gg;
+//  Graphics2D gg;
 
   int imgHeight = 0;
 
@@ -137,7 +137,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
     g.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
             (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
 
-    if (hiddenRows)
+    if (hiddenRows && av.getShowHiddenMarkers())
     {
       drawMarker(g, av, i, starty, ypos);
     }
@@ -152,10 +152,11 @@ public class IdCanvas extends JPanel implements ViewportListenerI
    */
   public void fastPaint(int vertical)
   {
+
     /*
      * for now, not attempting fast paint of wrapped ids...
      */
-    if (gg == null || av.getWrapAlignment())
+    if (image == null || av.getWrapAlignment())
     {
       repaint();
 
@@ -164,6 +165,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
 
     ViewportRanges ranges = av.getRanges();
 
+    Graphics2D gg = image.createGraphics();
     gg.copyArea(0, 0, getWidth(), imgHeight, 0,
             -vertical * av.getCharHeight());
 
@@ -200,6 +202,8 @@ public class IdCanvas extends JPanel implements ViewportListenerI
 
     gg.translate(0, -transY);
 
+    gg.dispose();
+    
     fastPaint = true;
 
     // Call repaint on alignment panel so that repaints from other alignment
@@ -217,8 +221,6 @@ public class IdCanvas extends JPanel implements ViewportListenerI
   @Override
   public void paintComponent(Graphics g)
   {
-    super.paintComponent(g);
-
     g.setColor(Color.white);
     g.fillRect(0, 0, getWidth(), getHeight());
     
@@ -246,13 +248,15 @@ public class IdCanvas extends JPanel implements ViewportListenerI
                 BufferedImage.TYPE_INT_RGB);
     }
     
-    gg = (Graphics2D) image.getGraphics();
+    Graphics2D gg = image.createGraphics();
     
     // Fill in the background
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getWidth(), imgHeight);
     
     drawIds(gg, av, av.getRanges().getStartSeq(), av.getRanges().getEndSeq(), searchResults);
+
+    gg.dispose();
     
     g.drawImage(image, 0, 0, this);
   }
@@ -359,7 +363,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
       g.drawString(string, xPos, (((i - startSeq) * charHeight) + charHeight)
               - (charHeight / 5));
 
-      if (hasHiddenRows)
+      if (hasHiddenRows && av.getShowHiddenMarkers())
       {
         drawMarker(g, alignViewport, i, startSeq, 0);
       }
@@ -380,33 +384,20 @@ public class IdCanvas extends JPanel implements ViewportListenerI
     int alignmentWidth = alignViewport.getAlignment().getWidth();
     final int alheight = alignViewport.getAlignment().getHeight();
 
-    int annotationHeight = 0;
+    /*
+     * assumption: SeqCanvas.calculateWrappedGeometry has been called
+     */
+    SeqCanvas seqCanvas = alignViewport.getAlignPanel()
+            .getSeqPanel().seqCanvas;
 
     final int charHeight = alignViewport.getCharHeight();
-    int hgap = charHeight;
-    if (alignViewport.getScaleAboveWrapped())
-    {
-      hgap += charHeight;
-    }
 
     AnnotationLabels labels = null;
     if (alignViewport.isShowAnnotation())
     {
-      hgap += SeqCanvas.SEQS_ANNOTATION_GAP;
-      if (ap == null)
-      {
-        ap = new AnnotationPanel(alignViewport);
-      }
-      annotationHeight = ap.adjustPanelHeight();
       labels = new AnnotationLabels(alignViewport);
     }
 
-    /*
-     * height of alignment + gap + annotations (if shown)
-     */
-    int cHeight = alheight * charHeight + hgap
-            + annotationHeight;
-
     ViewportRanges ranges = alignViewport.getRanges();
 
     int rowSize = ranges.getViewportWidth();
@@ -416,7 +407,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
      * out of visible space, whichever comes first
      */
     boolean hasHiddenRows = alignViewport.hasHiddenRows();
-    int ypos = hgap;
+    int ypos = seqCanvas.wrappedSpaceAboveAlignment;
     int rowStartRes = ranges.getStartRes();
     while ((ypos <= pageHeight) && (rowStartRes < alignmentWidth))
     {
@@ -441,7 +432,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
         g.translate(0, -ypos - (alheight * charHeight));
       }
 
-      ypos += cHeight;
+      ypos += seqCanvas.wrappedRepeatHeightPx;
       rowStartRes += rowSize;
     }
   }