X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=8b3a503ce83f644b2ce8e3a599743f023e093a9b;hb=32c056ffe34e60a1fde83bf4061af6e82d41f958;hp=38013d1a0804a379dd864484bfb1bef1389edfad;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 38013d1..8b3a503 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -29,6 +29,7 @@ public class AnnotationLabels
 {
   boolean active = false;
   AlignmentPanel ap;
+  AlignViewport av;
   boolean resizing = false;
   int oldY, mouseX;
   static String ADDNEW = "Add new row";
@@ -42,6 +43,7 @@ public class AnnotationLabels
   public AnnotationLabels(AlignmentPanel ap)
   {
     this.ap = ap;
+    this.av = ap.av;
     setLayout(null);
     addMouseListener(new MouseAdapter()
     {
@@ -52,6 +54,12 @@ public class AnnotationLabels
     });
   }
 
+  public AnnotationLabels(AlignViewport av)
+{
+  this.av = av;
+}
+
+
   public void setScrollOffset(int y)
   {
     scrollOffset = y;
@@ -60,7 +68,7 @@ public class AnnotationLabels
 
   public void actionPerformed(ActionEvent evt)
   {
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
     if (evt.getActionCommand().equals(HIDE))
     {
@@ -75,7 +83,7 @@ public class AnnotationLabels
     }
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
       Frame frame = new Frame();
       frame.add(cap);
       jalview.bin.JalviewLite.addFrame(frame,
@@ -121,25 +129,45 @@ public class AnnotationLabels
     item = new MenuItem(OUTPUT_TEXT);
     item.addActionListener(this);
     pop.add(item);
-    pop.show(this, evt.getX(), evt.getY());
+
+    if (aa[selectedRow].label.equals("Consensus"))
+    {
+      pop.addSeparator();
+      final CheckboxMenuItem cbmi = new CheckboxMenuItem(
+          "Ignore Gaps In Consensus",
+          ap.av.getIgnoreGapsConsensus());
+
+      cbmi.addItemListener(new ItemListener()
+      {
+        public void itemStateChanged(ItemEvent e)
+        {
+          ap.av.setIgnoreGapsConsensus(cbmi.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(cbmi);
+    }
+
+     pop.show(this, evt.getX(), evt.getY());
 
   }
 
   public void paint(Graphics g)
   {
-    drawComponent(g);
+    drawComponent(g, getSize().width);
   }
 
-  public void drawComponent(Graphics g)
+  public void drawComponent(Graphics g, int width)
   {
-    FontMetrics fm = g.getFontMetrics(g.getFont());
+    g.setFont(av.getFont());
+    FontMetrics fm = g.getFontMetrics(av.getFont());
     g.setColor(Color.white);
     g.fillRect(0, 0, getSize().width, getSize().height);
 
     g.translate(0, scrollOffset);
     g.setColor(Color.black);
 
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
     int y = g.getFont().getSize();
     int x = 0;
 
@@ -152,16 +180,16 @@ public class AnnotationLabels
           continue;
         }
 
-        x = getSize().width - fm.stringWidth(aa[i].label) - 3;
+        x = width - fm.stringWidth(aa[i].label) - 3;
 
-        if (aa[i].isGraph)
+        if (aa[i].graph>0)
         {
           y += (aa[i].height / 3);
         }
 
         g.drawString(aa[i].label, x, y);
 
-        if (aa[i].isGraph)
+        if (aa[i].graph>0)
         {
           y += (2 * aa[i].height / 3);
         }