ForegroundColor is darker.darker.darker

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a41491a..1d6cbf4 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -202,6 +202,13 @@ public class AlignFrame extends GAlignFrame
     frame.setResizable(false);\r
   }\r
 \r
+  protected void deleteGroups_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.alignment.deleteAllGroups();\r
+    alignPanel.RefreshPanels();\r
+  }\r
+\r
+\r
 \r
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
   {\r
@@ -312,8 +319,9 @@ public class AlignFrame extends GAlignFrame
     JOptionPane op = new JOptionPane();\r
     JInternalFrame frame =  op.createInternalFrame(this, "Find");\r
     Finder finder = new Finder(viewport, alignPanel, frame);\r
+    frame.setClosable(true);\r
     frame.setContentPane(finder);\r
-    frame.setSize(300,110);\r
+    frame.setSize(340,110);\r
     frame.setVisible(true);\r
   }\r
 \r
@@ -518,6 +526,13 @@ public class AlignFrame extends GAlignFrame
     changeColour();\r
   }\r
 \r
+  public void nucleotideColour_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setGlobalColourScheme( new NucleotideColourScheme() );\r
+    changeColour();\r
+  }\r
+\r
+\r
   void changeColour()\r
   {\r
     if(abovePIDThreshold.isSelected())\r
@@ -802,28 +817,107 @@ public class AlignFrame extends GAlignFrame
 \r
   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
   {\r
-    // JBPNote\r
-    // Should check to see if the server settings are valid\r
-    // Need visual-delay indication here.\r
-     jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
+    JInternalFrame frame = new JInternalFrame();\r
+    ClustalThread ct = new ClustalThread(frame);\r
+    Thread t = new Thread(ct);\r
+    t.start();\r
+    frame.setContentPane(ct);\r
+     Desktop.addInternalFrame(frame, title, 300, 80);\r
 \r
-    Vector sv = viewport.getAlignment().getSequences();\r
-    SequenceI[] seqs = new SequenceI[sv.size()];\r
+  }\r
 \r
-    int i=0;\r
-    do\r
+  class ClustalThread extends JPanel implements Runnable\r
+  {\r
+    Image [] image;\r
+    int imageIndex = 0;\r
+    boolean webServiceRunning = false;\r
+    JInternalFrame frame;\r
+    public ClustalThread(JInternalFrame frame)\r
     {\r
-      seqs[i] = (SequenceI) sv.elementAt(i);\r
-    } while (++i<sv.size());\r
-\r
-    SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
+      this.frame = frame;\r
+      image = new Image[9];\r
+      for(int i=0; i<9; i++)\r
+      {\r
+        java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");\r
+        if (url != null)\r
+        {\r
+          image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
+          MediaTracker mt = new MediaTracker(this);\r
+          mt.addImage(image[i], i);\r
+          try{mt.waitForID(i);}\r
+          catch(Exception ex){}\r
+        }\r
+      }\r
+      DNATwirler twirler = new DNATwirler();\r
+      twirler.start();\r
+      webServiceRunning = true;\r
+    }\r
 \r
-    if (alignment != null)\r
+    class DNATwirler extends Thread\r
     {\r
-      AlignFrame af = new AlignFrame(new Alignment(alignment));\r
-      Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
-                               700, 500); // JBPNote - is there a new window geom. property ?\r
+      public void run()\r
+      {\r
+        while(webServiceRunning)\r
+        {\r
+          try{\r
+            Thread.sleep(100);\r
+            imageIndex++;\r
+            imageIndex %=9;\r
+            repaint();\r
+          }\r
+          catch(Exception ex){}\r
+        }\r
+      }\r
     }\r
+\r
+    // JBPNote\r
+    // Should check to see if the server settings are valid\r
+    // Need visual-delay indication here.\r
+    public void run()\r
+       {\r
+         jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
+         Vector sv = viewport.getAlignment().getSequences();\r
+         SequenceI[] seqs = new SequenceI[sv.size()];\r
+\r
+         int i = 0;\r
+         do\r
+         {\r
+           seqs[i] = (SequenceI) sv.elementAt(i);\r
+         }\r
+         while (++i < sv.size());\r
+\r
+         SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
+\r
+         if (alignment != null)\r
+         {\r
+           AlignFrame af = new AlignFrame(new Alignment(alignment));\r
+           Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
+                                    700, 500); // JBPNote - is there a new window geom. property ?\r
+         }\r
+         else\r
+           JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
+                                         JOptionPane.WARNING_MESSAGE);\r
+\r
+         webServiceRunning = false;\r
+         try{\r
+           frame.setClosed(true);\r
+         }catch(Exception ex){}\r
+       }\r
+\r
+       public void paintComponent(Graphics g)\r
+       {\r
+         g.setColor(Color.white);\r
+         g.fillRect(0,0,getWidth(), getHeight());\r
+         if(image!=null)\r
+         {\r
+           g.drawImage(image[imageIndex],10,10,this);\r
+         }\r
+         g.setFont(new Font("Arial", Font.BOLD, 12));\r
+         g.setColor(Color.black);\r
+         g.drawString("Clustal Alignment Web Service running", 30,30);\r
+       }\r
+\r
+\r
   }\r
 \r
 \r