X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=f7f1b203b5f237c149edfcad4bb7dc4e677b2693;hb=7bc213bae5828287329a3490faba291706599b03;hp=3c3c52c896d2cfabc41ddeb24582c2a34e8d645b;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 3c3c52c..f7f1b20 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -21,7 +21,6 @@ package jalview.appletgui;
 
 import java.awt.*;
 
-import jalview.analysis.*;
 import jalview.datamodel.*;
 
 public class IdCanvas
@@ -44,7 +43,7 @@ public class IdCanvas
   {
     setLayout(null);
     this.av = av;
-    PaintRefresher.Register(this);
+    PaintRefresher.Register(this, av.alignment);
   }
 
   public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
@@ -55,34 +54,29 @@ public class IdCanvas
     if (searchResults != null && searchResults.contains(s))
     {
       gg.setColor(Color.black);
-      gg.fillRect(0, AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos,
                   getSize().width, charHeight);
       gg.setColor(Color.white);
     }
     else if (av.getSelectionGroup() != null &&
-             av.getSelectionGroup().sequences.contains(s))
+             av.getSelectionGroup().getSequences(false).contains(s))
     {
       gg.setColor(Color.lightGray);
-      gg.fillRect(0, AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos,
                   getSize().width, charHeight);
       gg.setColor(Color.white);
     }
     else
     {
       gg.setColor(s.getColor());
-      gg.fillRect(0, AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos,
                   getSize().width, charHeight);
       gg.setColor(Color.black);
     }
 
-    String string = s.getName();
-    if (av.getShowFullId())
-    {
-      string = s.getDisplayId();
-    }
 
-    gg.drawString(string, 0,
-                  AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos +
+    gg.drawString( s.getDisplayId(av.getShowJVSuffix()), 0,
+                  ((i - starty) * charHeight) + ypos +
                   charHeight - (charHeight / 5));
 
   }
@@ -177,23 +171,50 @@ 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);
+                gg.setFont(italic);
+                drawIdString(gg, s, i, 0, ypos);
+            }
+
+            if(labels!=null)
+            {
+              gg.translate(0, ypos+(av.getAlignment().getHeight() * av.charHeight));
+              labels.drawComponent(gg, getSize().width);
+              gg.translate(0, -ypos-(av.getAlignment().getHeight() * av.charHeight));
+            }
         }
-      }
 
     }
     else
@@ -213,7 +234,7 @@ public class IdCanvas
         }
         else if (av.getSelectionGroup() != null
                  &&
-                 av.getSelectionGroup().sequences.contains(av.alignment.
+                 av.getSelectionGroup().getSequences(false).contains(av.alignment.
             getSequenceAt(i)))
         {
           currentColor = Color.lightGray;
@@ -228,18 +249,15 @@ public class IdCanvas
         gg.setColor(currentColor);
 
         gg.fillRect(0,
-                    AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
+                    ((i - starty) * av.charHeight),
                     getSize().width,
                     av.charHeight);
 
         gg.setColor(currentTextColor);
-        String string = av.alignment.getSequenceAt(i).getName();
-        if (av.getShowFullId())
-        {
-          string = av.alignment.getSequenceAt(i).getDisplayId();
-        }
-        gg.drawString(string, 0,
-                      AlignmentUtil.getPixelHeight(starty, i, av.charHeight) +
+
+        gg.drawString(av.alignment.getSequenceAt(i)
+            .getDisplayId(av.getShowJVSuffix()), 0,
+                      ((i - starty) * av.charHeight) +
                       av.charHeight - (av.charHeight / 5));
       }