X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=30560d784268caf25ab788903c5a6ad9ac2c7299;hb=ee53965807b83bf93a21cbc341cee9a9e005b2cb;hp=399506ed1a9f73cc59981bcad81b8ff13cda77dc;hpb=0a2dcc2309a1fceb5e3ee8fe1dbbf89572e8e1f3;p=jalview.git

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 399506e..30560d7 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -177,23 +177,51 @@ public class IdCanvas
   {
     Color currentColor = Color.white;
     Color currentTextColor = Color.black;
+    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+                             av.getFont().getSize());
 
     if (av.getWrapAlignment())
     {
+      int annotationHeight = 0;
+      AnnotationLabels labels = null;
 
-      int rowSize = av.getEndRes() - av.getStartRes();
-      // Draw the rest of the panels
-
-      for (int ypos = 2 * av.charHeight, row = av.startRes;
-           ypos <= getSize().height && row < av.alignment.getWidth();
-           ypos += av.chunkHeight, row += rowSize)
+      if(av.showAnnotation)
       {
-        for (int i = starty; i < av.alignment.getHeight(); i++)
+        AnnotationPanel ap = new AnnotationPanel(av);
+        annotationHeight = ap.adjustPanelHeight();
+        labels = new AnnotationLabels(av);
+      }
+
+      int hgap = av.charHeight;
+      if (av.scaleAboveWrapped)
+        hgap += av.charHeight;
+
+      int cHeight = av.getAlignment().getHeight() * av.charHeight
+          + hgap
+          + annotationHeight;
+
+        int rowSize = av.getEndRes() - av.getStartRes();
+
+        // Draw the rest of the panels
+        for (int ypos = hgap, row = av.startRes;
+                (ypos <= getSize().height) && (row < av.alignment.getWidth());
+                ypos += cHeight, row += rowSize)
         {
-          SequenceI s = av.alignment.getSequenceAt(i);
-          drawIdString(gg, s, i, 0, ypos);
+            for (int i = starty; i < av.alignment.getHeight(); i++)
+            {
+                SequenceI s = av.alignment.getSequenceAt(i);
+                drawIdString(gg, s, i, 0, ypos);
+            }
+
+            if(labels!=null)
+            {
+              gg.setFont(av.getFont());
+              gg.translate(0, ypos+(av.getAlignment().getHeight() * av.charHeight));
+              labels.drawComponent(gg, getSize().width);
+              gg.translate(0, -ypos-(av.getAlignment().getHeight() * av.charHeight));
+              gg.setFont(italic);
+            }
         }
-      }
 
     }
     else