X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=1a83b0900a0645d0827378c262df7ccb0bd1e891;hb=3ca1aeccca8d3adfd55d1ff8bd447f8bf0d4ac2f;hp=095377d9fe9e4b8d881e659c397c73f0e6854b2c;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 095377d..1a83b09 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,40 +1,41 @@
-
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 
 package jalview.appletgui;
 
-import java.awt.event.*;
 import java.awt.*;
+import java.awt.event.*;
+
 import jalview.datamodel.*;
 
-public class AnnotationLabels extends Panel implements ActionListener
+public class AnnotationLabels
+    extends Panel implements ActionListener
 {
   boolean active = false;
-  AlignmentPanel ap ;
+  AlignmentPanel ap;
   boolean resizing = false;
   int oldY, mouseX;
   static String ADDNEW = "Add new row";
   static String HIDE = "Hide this row";
   static String DELETE = "Delete this row";
-  static String SHOWALL="Show all hidden rows";
-  static String OUTPUT_TEXT="Show Values In Textbox";
+  static String SHOWALL = "Show all hidden rows";
+  static String OUTPUT_TEXT = "Show Values In Textbox";
   int selectedRow = 0;
   int scrollOffset = 0;
 
@@ -43,7 +44,8 @@ public class AnnotationLabels extends Panel implements ActionListener
     this.ap = ap;
     setLayout(null);
     addMouseListener(new MouseAdapter()
-    {public void mousePressed(MouseEvent evt)
+    {
+      public void mousePressed(MouseEvent evt)
       {
         doMousePressed(evt);
       }
@@ -60,30 +62,32 @@ public class AnnotationLabels extends Panel implements ActionListener
   {
     AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
-   if(evt.getActionCommand().equals(HIDE))
-   {
-     aa[selectedRow].visible = false;
-   }
-   else if(evt.getActionCommand().equals(SHOWALL))
-   {
-       for(int i=0; i<aa.length; i++)
-         aa[i].visible = true;
-   }
-   else if (evt.getActionCommand().equals(OUTPUT_TEXT))
-   {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
-     Frame frame = new Frame();
-     frame.add(cap);
-     jalview.bin.JalviewLite.addFrame(frame,
-                                      ap.alignFrame.getTitle() + " - " +
-                                      aa[selectedRow].label, 500, 100);
-     cap.setText(aa[selectedRow].toString());
-   }
-
-   ap.annotationPanel.adjustPanelHeight();
-   setSize(getSize().width,ap.annotationPanel.getSize().height);
-   ap.validate();
-   ap.repaint();
+    if (evt.getActionCommand().equals(HIDE))
+    {
+      aa[selectedRow].visible = false;
+    }
+    else if (evt.getActionCommand().equals(SHOWALL))
+    {
+      for (int i = 0; i < aa.length; i++)
+      {
+        aa[i].visible = true;
+      }
+    }
+    else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+    {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+      Frame frame = new Frame();
+      frame.add(cap);
+      jalview.bin.JalviewLite.addFrame(frame,
+                                       ap.alignFrame.getTitle() + " - " +
+                                       aa[selectedRow].label, 500, 100);
+      cap.setText(aa[selectedRow].toString());
+    }
+
+    ap.annotationPanel.adjustPanelHeight();
+    setSize(getSize().width, ap.annotationPanel.getSize().height);
+    ap.validate();
+    ap.repaint();
   }
 
   public void doMousePressed(MouseEvent evt)
@@ -94,7 +98,9 @@ public class AnnotationLabels extends Panel implements ActionListener
     for (int i = 0; i < aa.length; i++)
     {
       if (!aa[i].visible)
+      {
         continue;
+      }
 
       height += aa[i].height;
       if (y < height)
@@ -115,7 +121,26 @@ public class AnnotationLabels extends Panel implements ActionListener
     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 calculation",
+          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());
 
   }
 
@@ -128,33 +153,43 @@ public class AnnotationLabels extends Panel implements ActionListener
   {
     FontMetrics fm = g.getFontMetrics(g.getFont());
     g.setColor(Color.white);
-    g.fillRect(0,0, getSize().width, getSize().height);
+    g.fillRect(0, 0, getSize().width, getSize().height);
 
     g.translate(0, scrollOffset);
     g.setColor(Color.black);
 
-   AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-   int y = g.getFont().getSize();
-   int x = 0;
-
-   if(aa!=null)
-   for(int i=0; i<aa.length; i++)
-   {
-     if(!aa[i].visible)
-       continue;
-
-     x = getSize().width - fm.stringWidth(aa[i].label)-3;
-
-     if(aa[i].isGraph)
-       y+=(aa[i].height/3);
-
-     g.drawString(aa[i].label, x, y);
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    int y = g.getFont().getSize();
+    int x = 0;
 
-     if(aa[i].isGraph)
-       y+=(2*aa[i].height/3);
-    else
-       y+=aa[i].height;
-   }
+    if (aa != null)
+    {
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (!aa[i].visible)
+        {
+          continue;
+        }
+
+        x = getSize().width - fm.stringWidth(aa[i].label) - 3;
+
+        if (aa[i].isGraph)
+        {
+          y += (aa[i].height / 3);
+        }
+
+        g.drawString(aa[i].label, x, y);
+
+        if (aa[i].isGraph)
+        {
+          y += (2 * aa[i].height / 3);
+        }
+        else
+        {
+          y += aa[i].height;
+        }
+      }
+    }
   }
 
 }