X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=1a8e79fb6175eab09b01de632fea18b0931e1aef;hb=3b2dd110a9283ae50db9302c8cc22ab4aec7a199;hp=4057cef554e2601cb9fc3f8f4083e68795cdec68;hpb=42984135d36f8bb943fc4c20879359d1508bac0f;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 4057cef..1a8e79f 100755
--- 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!
  * 
@@ -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);
     }
@@ -324,6 +324,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
       if (hasHiddenRows || alignViewport.isDisplayReferenceSeq())
       {
         g.setFont(getHiddenFont(sequence, alignViewport));
+        fm = g.getFontMetrics();
       }
 
       // Selected sequence colours
@@ -363,7 +364,7 @@ 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);
       }
@@ -384,32 +385,20 @@ 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();
 
     AnnotationLabels labels = null;
     if (alignViewport.isShowAnnotation())
     {
-      if (ap == null)
-      {
-        ap = new AnnotationPanel(alignViewport);
-      }
-      annotationHeight = ap.adjustPanelHeight();
       labels = new AnnotationLabels(alignViewport);
     }
 
-    final int charHeight = alignViewport.getCharHeight();
-    int hgap = charHeight;
-    if (alignViewport.getScaleAboveWrapped())
-    {
-      hgap += charHeight;
-    }
-
-    /*
-     * height of alignment + gap + annotations (if shown)
-     */
-    int cHeight = alheight * charHeight + hgap
-            + annotationHeight;
-
     ViewportRanges ranges = alignViewport.getRanges();
 
     int rowSize = ranges.getViewportWidth();
@@ -419,7 +408,7 @@ 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))
     {
@@ -444,7 +433,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
         g.translate(0, -ypos - (alheight * charHeight));
       }
 
-      ypos += cHeight;
+      ypos += seqCanvas.wrappedRepeatHeightPx;
       rowStartRes += rowSize;
     }
   }