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[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 6592399..08cbb9a 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -110,6 +110,8 @@ public class AlignFrame extends Frame implements ActionListener,
    this.addKeyListener(this);\r
    alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
    alignPanel.idPanel.idCanvas.addKeyListener(this);\r
+   alignPanel.scalePanel.addKeyListener(this);\r
+   alignPanel.annotationPanel.addKeyListener(this);\r
 \r
     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
     {\r
@@ -327,6 +329,28 @@ public class AlignFrame extends Frame implements ActionListener,
           findMenuItem_actionPerformed();\r
         }\r
         break;\r
+      case KeyEvent.VK_H:\r
+      {\r
+        SequenceGroup sg = viewport.getSelectionGroup();\r
+        if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())\r
+        {\r
+          hideSelectedSeqs();\r
+        }\r
+        else\r
+          viewport.showAllHiddenSeqs();\r
+\r
+        if (viewport.colSel.getSelected().size() > 0)\r
+        {\r
+          viewport.hideSelectedColumns();\r
+        }\r
+        else\r
+         {\r
+           viewport.showAllHiddenColumns();\r
+         }\r
+        alignPanel.repaint();\r
+        break;\r
+      }\r
+\r
     }\r
   }\r
   public void keyReleased(KeyEvent evt)\r
@@ -415,7 +439,7 @@ public void itemStateChanged(ItemEvent evt)
     else if(source==invertSequenceMenuItem)\r
             invertSequenceMenuItem_actionPerformed();\r
     else if(source==invertColSel)\r
-    { viewport.invertColumnSelection(); repaint(); }\r
+    { viewport.invertColumnSelection(); alignPanel.repaint(); }\r
     else if(source==remove2LeftMenuItem)\r
             remove2LeftMenuItem_actionPerformed();\r
     else if(source==remove2RightMenuItem)\r
@@ -430,28 +454,19 @@ public void itemStateChanged(ItemEvent evt)
             font_actionPerformed();\r
     else if(source==showColumns)\r
     {\r
-      viewport.showAllHiddenColumns(); repaint();\r
+      viewport.showAllHiddenColumns(); alignPanel.repaint();\r
     }\r
     else if(source==showSeqs)\r
     {\r
-      viewport.showAllHiddenSeqs(); repaint();\r
+      viewport.showAllHiddenSeqs(); alignPanel.repaint();\r
     }\r
     else if(source == hideColumns)\r
     {\r
-      viewport.hideSelectedColumns(); repaint();\r
+      viewport.hideSelectedColumns(); alignPanel.repaint();\r
     }\r
     else if(source == hideSequences && viewport.getSelectionGroup()!=null)\r
     {\r
-      SequenceI[] seqs = viewport.getSelectionGroup().getSequencesInOrder(\r
-          viewport.alignment\r
-          );\r
-\r
-      for (int i = 0; i < seqs.length; i++)\r
-      {\r
-        viewport.hideSequence(seqs[i]);\r
-      }\r
-\r
-      alignPanel.repaint();\r
+      hideSelectedSeqs();\r
     }\r
     else if(source==featureSettings)\r
             featureSettings_actionPerformed();\r
@@ -1257,6 +1272,20 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.repaint();\r
   }\r
 \r
+  void hideSelectedSeqs()\r
+  {\r
+    SequenceI[] seqs = viewport.getSelectionGroup().getSequencesInOrder(\r
+        viewport.alignment\r
+        );\r
+\r
+    for (int i = 0; i < seqs.length; i++)\r
+    {\r
+      viewport.hideSequence(seqs[i]);\r
+    }\r
+\r
+    alignPanel.repaint();\r
+  }\r
+\r
   protected void scaleAbove_actionPerformed()\r
   {\r
     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
@@ -1597,7 +1626,8 @@ public void itemStateChanged(ItemEvent evt)
 \r
   public void pairwiseAlignmentMenuItem_actionPerformed()\r
   {\r
-    if (viewport.getSelectionGroup().getSize(false) > 1)\r
+    if (viewport.getSelectionGroup()!=null\r
+        && viewport.getSelectionGroup().getSize(false) > 1)\r
     {\r
       Frame frame = new Frame();\r
       frame.add(new PairwiseAlignPanel(alignPanel));\r
@@ -1686,13 +1716,19 @@ public void itemStateChanged(ItemEvent evt)
 \r
     }\r
 \r
-    final TreePanel tp = new TreePanel(viewport,\r
-                         type,\r
-                         pwType);\r
+    if ( (viewport.getSelectionGroup() != null &&\r
+          viewport.getSelectionGroup().getSize(false) > 1)\r
+      || (viewport.getSelectionGroup() == null\r
+          && viewport.alignment.getHeight() > 1))\r
+    {\r
+      final TreePanel tp = new TreePanel(viewport,\r
+                                         type,\r
+                                         pwType);\r
 \r
-    addTreeMenuItem(tp, title);\r
+      addTreeMenuItem(tp, title);\r
 \r
-    jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
+      jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
+    }\r
   }\r
 \r
   void loadTree_actionPerformed()\r
@@ -1930,12 +1966,11 @@ public void itemStateChanged(ItemEvent evt)
       MenuItem item;\r
 \r
       // dynamically fill save as menu with available formats\r
-      for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)\r
+      for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
       {\r
 \r
-        item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r
-                            elementAt(\r
-                                i));\r
+        item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
+\r
         item.addActionListener(new java.awt.event.ActionListener()\r
         {\r
           public void actionPerformed(ActionEvent e)\r