added placeholder indicators and menu item

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 80533f2..a8f8456 100755 (executable)
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -106,6 +106,9 @@ public class IdCanvas extends Panel
     imgHeight = getSize().height;\r
     imgHeight -= imgHeight % av.charHeight;\r
 \r
+    if (imgHeight<1)\r
+      return;\r
+\r
     if(image==null || imgHeight!=image.getHeight(this))\r
     {\r
       image = createImage(getSize().width, imgHeight);\r

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index db91d08..e028819 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -184,12 +184,13 @@ public void fastPaint(int horizontal, int vertical)
     // this draws the whole of the alignment\r
       imgWidth  = this.getSize().width;\r
       imgHeight = this.getSize().height;\r
-      if(imgWidth<1 || imgHeight<1)\r
-        return;\r
 \r
       imgWidth -= imgWidth%av.charWidth;\r
       imgHeight-= imgHeight%av.charHeight;\r
 \r
+      if(imgWidth<1 || imgHeight<1)\r
+              return;\r
+\r
       if(img==null || imgWidth!=img.getWidth(this) || imgHeight!=img.getHeight(this))\r
       {\r
         img = createImage(imgWidth, imgHeight);\r

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 882ed7a..4f5288d 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -105,6 +105,10 @@ public class IdCanvas extends JPanel
 \r
     imgHeight = getHeight();\r
     imgHeight -= imgHeight % av.charHeight;\r
+\r
+    if (imgHeight<1)\r
+      return;\r
+\r
     image = new BufferedImage(getWidth(), imgHeight, BufferedImage.TYPE_INT_RGB);\r
     gg = (Graphics2D) image.getGraphics();\r
     //Fill in the background\r

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 12659a8..b2e9d3e 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -188,12 +188,13 @@ public void fastPaint(int horizontal, int vertical)
     // this draws the whole of the alignment\r
       imgWidth  = getWidth();\r
       imgHeight = getHeight();\r
-      if(imgWidth<1 || imgHeight<1)\r
-        return;\r
 \r
       imgWidth -= imgWidth%av.charWidth;\r
       imgHeight-= imgHeight%av.charHeight;\r
 \r
+      if(imgWidth<1 || imgHeight<1)\r
+        return;\r
+\r
       img = new BufferedImage(imgWidth,imgHeight,BufferedImage.TYPE_INT_RGB);\r
       gg  = (Graphics2D)img.getGraphics();\r
       gg.setFont(av.getFont());\r

diff --git a/src/jalview/jbgui/GTreePanel.java b/src/jalview/jbgui/GTreePanel.java
index 27b5c5c..e7030b8 100755 (executable)
--- a/src/jalview/jbgui/GTreePanel.java
+++ b/src/jalview/jbgui/GTreePanel.java
@@ -17,6 +17,7 @@ public class GTreePanel extends JInternalFrame
   protected JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();\r
   protected JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();\r
   protected JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();\r
+  protected JCheckBoxMenuItem placeholdersMenu = new JCheckBoxMenuItem();\r
   JMenuItem pngTree = new JMenuItem();\r
   JMenuItem epsTree = new JMenuItem();\r
   JMenu saveAsMenu = new JMenu();\r
@@ -108,6 +109,16 @@ public class GTreePanel extends JInternalFrame
       }\r
     });\r
     saveAsMenu.setText("Save as");\r
+    placeholdersMenu.setToolTipText(\r
+        "Marks leaves of tree not associated with a sequence");\r
+    placeholdersMenu.setText("Mark unlinked leaves");\r
+    placeholdersMenu.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        placeholdersMenu_actionPerformed(e);\r
+      }\r
+    });\r
     this.getContentPane().add(scrollPane, BorderLayout.CENTER);\r
     jMenuBar1.add(jMenu1);\r
     jMenuBar1.add(jMenu2);\r
@@ -117,6 +128,7 @@ public class GTreePanel extends JInternalFrame
     jMenu2.add(fontSize);\r
     jMenu2.add(distanceMenu);\r
     jMenu2.add(bootstrapMenu);\r
+    jMenu2.add(placeholdersMenu);\r
     saveAsMenu.add(saveAsNewick);\r
     saveAsMenu.add(epsTree);\r
     saveAsMenu.add(pngTree);\r
@@ -158,7 +170,12 @@ public class GTreePanel extends JInternalFrame
 \r
   }\r
 \r
-  public void saveAsNewick_actionPerformed(ActionEvent e)\r
+  protected void saveAsNewick_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  protected void placeholdersMenu_actionPerformed(ActionEvent e)\r
   {\r
 \r
   }\r