X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=7686e8ab549b82217600e3b8ddb89488d8423e76;hb=a28c9340eeadfdaa551a21b9dea1d0f1530126e3;hp=8b6939e4e53605be6bbeb4ae26a05b714b1f209a;hpb=6e71f42b0a3713ddbc3054e7ea9d8f5088130ec9;p=jalview.git

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 8b6939e..7686e8a 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
@@ -55,7 +54,7 @@ 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);
     }
@@ -63,26 +62,22 @@ public class IdCanvas
              av.getSelectionGroup().sequences.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();
-    }
+    String string = s.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());
 
     gg.drawString(string, 0,
-                  AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos +
+                  ((i - starty) * charHeight) + ypos +
                   charHeight - (charHeight / 5));
 
   }
@@ -162,6 +157,12 @@ public class IdCanvas
       gg.setFont(av.getFont());
     }
 
+    if(!jalview.bin.JalviewLite.AWT1)
+    {
+      MyGraphics.AntiAlias(gg);
+    }
+
+
     //Fill in the background
     gg.setColor(Color.white);
     Font italic = new Font(av.getFont().getName(), Font.ITALIC,
@@ -177,23 +178,51 @@ 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
@@ -228,18 +257,16 @@ 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();
-        }
+        String string = av.alignment.getSequenceAt(i)
+            .getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());
+
         gg.drawString(string, 0,
-                      AlignmentUtil.getPixelHeight(starty, i, av.charHeight) +
+                      ((i - starty) * av.charHeight) +
                       av.charHeight - (av.charHeight / 5));
       }