showinternal***dialog

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4707f3a..63ed59a 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -86,7 +86,6 @@ public class AlignFrame extends GAlignFrame
     public void run()\r
     {\r
       PrinterJob printJob = PrinterJob.getPrinterJob();\r
-    //  printJob.\r
       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
       printJob.setPrintable(alignPanel, pf);\r
       if (printJob.printDialog())\r
@@ -332,24 +331,36 @@ public class AlignFrame extends GAlignFrame
 \r
   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
   {\r
-    String thisChar = "-";\r
-    String nextChar = ".";\r
-    if(viewport.getGapCharacter().equals("-"))\r
+    char thisChar = '-';\r
+    char nextChar = '.';\r
+    if(viewport.getGapCharacter()=='-')\r
     {\r
-      thisChar = ".";\r
-      nextChar = "-";\r
+      thisChar = '.';\r
+      nextChar = '-';\r
     }\r
     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
     viewport.setGapCharacter(thisChar);\r
+    alignPanel.RefreshPanels();\r
   }\r
 \r
+  public void findMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+    JOptionPane op = new JOptionPane();\r
+    JInternalFrame frame =  op.createInternalFrame(this, "Find");\r
+    Finder finder = new Finder(viewport, alignPanel, frame);\r
+    frame.setContentPane(finder);\r
+    frame.setSize(300,110);\r
+    frame.setVisible(true);\r
+  }\r
+\r
+\r
 \r
   public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
   {\r
     String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
 \r
 \r
-    String selection = JOptionPane.showInputDialog(this,\r
+    String selection = JOptionPane.showInternalInputDialog(this,\r
                                 "Select font",\r
                                 "Font selection",\r
                                 JOptionPane.QUESTION_MESSAGE,\r
@@ -365,7 +376,7 @@ public class AlignFrame extends GAlignFrame
 \r
   public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
   {\r
-    String selection = JOptionPane.showInputDialog(this,\r
+    String selection = JOptionPane.showInternalInputDialog(this,\r
                                 "Select font size",\r
                                 "Font size",\r
                                 JOptionPane.QUESTION_MESSAGE,\r
@@ -380,7 +391,7 @@ public class AlignFrame extends GAlignFrame
 \r
   public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
   {\r
-    String selection = JOptionPane.showInputDialog(this,\r
+    String selection = JOptionPane.showInternalInputDialog(this,\r
                                 "Select font style",\r
                                 "Font style",\r
                                 JOptionPane.QUESTION_MESSAGE,\r
@@ -430,6 +441,14 @@ public class AlignFrame extends GAlignFrame
      updateResidueView();\r
   }\r
 \r
+\r
+  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
+    alignPanel.RefreshPanels();\r
+  }\r
+\r
+\r
   void updateResidueView()\r
   {\r
     if (viewport.getSelection().size() == 0)\r
@@ -493,7 +512,7 @@ public class AlignFrame extends GAlignFrame
 \r
   }catch(java.lang.OutOfMemoryError ex)\r
    {\r
-     JOptionPane.showMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
+     JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
                                    +"\nTry reducing the font size.",\r
                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
    }\r
@@ -647,7 +666,7 @@ public class AlignFrame extends GAlignFrame
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
   {\r
     if(viewport.getSelection().size()<2)\r
-      JOptionPane.showMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
+      JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
     else\r
     {\r
       JInternalFrame frame = new JInternalFrame();\r
@@ -661,7 +680,7 @@ public class AlignFrame extends GAlignFrame
     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
        || viewport.getAlignment().getHeight()<4)\r
     {\r
-      JOptionPane.showMessageDialog(this, "Principal component analysis must take\n"\r
+      JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
                                     +"at least 4 input sequences.",\r
                                     "Sequence selection insufficient",\r
                                     JOptionPane.WARNING_MESSAGE);\r
@@ -675,7 +694,7 @@ public class AlignFrame extends GAlignFrame
       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
    }catch(java.lang.OutOfMemoryError ex)\r
    {\r
-     JOptionPane.showMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
+     JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
    }\r
 \r
@@ -727,7 +746,7 @@ public class AlignFrame extends GAlignFrame
 \r
   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
   {\r
-    JOptionPane.showMessageDialog(this, "Jalview is currently being reengineered"\r
+    JOptionPane.showInternalMessageDialog(this, "Jalview is currently being reengineered"\r
                                   +"\nwithin the Barton Group, Dundee University."\r
                                   +"\nThis will be available as a web service 2005",\r
                                   "Web service", JOptionPane.INFORMATION_MESSAGE);\r
@@ -735,7 +754,7 @@ public class AlignFrame extends GAlignFrame
 \r
   public void pdbTest_actionPerformed(ActionEvent e)\r
   {\r
-   String reply = JOptionPane.showInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE);\r
+   String reply = JOptionPane.showInternalInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE);\r
 \r
    String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";\r
    if (reply.length()>1)\r
@@ -763,4 +782,15 @@ public class AlignFrame extends GAlignFrame
 \r
   }\r
 \r
+\r
+  public void doKeyPressed(KeyEvent evt)\r
+  {\r
+\r
+    System.out.println(evt.getKeyChar());\r
+    if(evt.isControlDown() && evt.getKeyChar()=='f')\r
+      findMenuItem_actionPerformed(null);\r
+\r
+  }\r
+\r
+\r
 }\r