X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPopupMenu.java;fp=src%2Fjalview%2Fgui%2FPopupMenu.java;h=7576173302b6b4a047bede07c19d114b9dcbfc3a;hb=588042b69abf8e60bcc950b24c283933c7dd422f;hp=7133e44472a6fdb6ca5da12c2a5881f4f8865834;hpb=5cd8e373c75fb348ecda4d94d8a46468fb92756d;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 7133e44..7576173 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,41 +1,43 @@
 /*
-* 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.gui;
 
-import jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.schemes.*;
 import java.awt.*;
-import javax.swing.*;
 import java.awt.event.*;
-import jalview.io.*;
+import javax.swing.*;
+
 import MCview.*;
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.schemes.*;
 
-public class PopupMenu extends JPopupMenu
+public class PopupMenu
+    extends JPopupMenu
 {
   JMenu groupMenu = new JMenu();
   JMenuItem groupName = new JMenuItem();
   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem hydrophobicityColour = new
+      JRadioButtonMenuItem();
   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
@@ -46,8 +48,6 @@ public class PopupMenu extends JPopupMenu
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
-
-
   AlignmentPanel ap;
   JMenu sequenceMenu = new JMenu();
   JMenuItem sequenceName = new JMenuItem();
@@ -69,7 +69,6 @@ public class PopupMenu extends JPopupMenu
     //
     // If from the IDPanel, we must display the sequence menu
     //////////////////////////////////////////////////////////
-
     this.ap = ap;
     sequence = seq;
 
@@ -89,57 +88,96 @@ public class PopupMenu extends JPopupMenu
     colours.add(BLOSUM62Colour);
 
     try
-    {     jbInit();   }
-    catch(Exception e)
-    {    e.printStackTrace();    }
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
 
     SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg!=null)
+
+    if (sg != null)
     {
       groupName.setText(sg.getName());
-      if(sg.cs instanceof ZappoColourScheme)
+
+      if (sg.cs instanceof ZappoColourScheme)
+      {
         zappoColour.setSelected(true);
-      else if(sg.cs instanceof TaylorColourScheme)
+      }
+      else if (sg.cs instanceof TaylorColourScheme)
+      {
         taylorColour.setSelected(true);
+      }
       else if (sg.cs instanceof PIDColourScheme)
+      {
         PIDColour.setSelected(true);
+      }
       else if (sg.cs instanceof Blosum62ColourScheme)
+      {
         BLOSUM62Colour.setSelected(true);
+      }
       else if (sg.cs instanceof UserColourScheme)
+      {
         userDefinedColour.setSelected(true);
+      }
       else if (sg.cs instanceof HydrophobicColourScheme)
+      {
         hydrophobicityColour.setSelected(true);
+      }
       else if (sg.cs instanceof HelixColourScheme)
+      {
         helixColour.setSelected(true);
+      }
       else if (sg.cs instanceof StrandColourScheme)
+      {
         strandColour.setSelected(true);
+      }
       else if (sg.cs instanceof TurnColourScheme)
+      {
         turnColour.setSelected(true);
+      }
       else if (sg.cs instanceof BuriedColourScheme)
+      {
         buriedColour.setSelected(true);
+      }
       else if (sg.cs instanceof ClustalxColourScheme)
+      {
         clustalColour.setSelected(true);
+      }
       else
+      {
         noColourmenuItem.setSelected(true);
+      }
 
       if (sg.cs instanceof ConservationColourScheme)
+      {
         conservationMenuItem.setSelected(true);
+      }
 
       showText.setSelected(sg.getDisplayText());
       showColourText.setSelected(sg.getColourText());
       showBoxes.setSelected(sg.getDisplayBoxes());
     }
 
-    if( !ap.av.alignment.getGroups().contains(sg))
+    if (!ap.av.alignment.getGroups().contains(sg))
+    {
       unGroupMenuItem.setVisible(false);
+    }
     else
+    {
       groupMenu.insertSeparator(3);
+    }
 
-    if(seq==null)
-       sequenceMenu.setVisible(false);
-
+    if (seq == null)
+    {
+      sequenceMenu.setVisible(false);
+    }
   }
-  private void jbInit() throws Exception
+
+  private void jbInit()
+      throws Exception
   {
     groupMenu.setText("Group");
     groupMenu.setText("Define");
@@ -356,24 +394,24 @@ public class PopupMenu extends JPopupMenu
       }
     });
     conservationMenuItem.setText("Conservation");
-   conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
-   {
-     public void actionPerformed(ActionEvent e)
-     {
-       conservationMenuItem_actionPerformed(e);
-     }
-   });
-
-
-
+    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        conservationMenuItem_actionPerformed(e);
+      }
+    });
   }
 
   void refresh()
   {
     SequenceGroup sg = getGroup();
-    SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
-    if( superG !=null)
-      superG.setSuperGroupProperties( sg );
+    SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
+
+    if (superG != null)
+    {
+      superG.setSuperGroupProperties(sg);
+    }
 
     ap.seqPanel.repaint();
   }
@@ -381,7 +419,8 @@ public class PopupMenu extends JPopupMenu
   protected void clustalColour_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
+    sg.cs = new ClustalxColourScheme(sg.sequences,
+                                     ap.av.alignment.getWidth());
     refresh();
   }
 
@@ -397,7 +436,6 @@ public class PopupMenu extends JPopupMenu
     refresh();
   }
 
-
   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
     getGroup().cs = new HydrophobicColourScheme();
@@ -434,24 +472,28 @@ public class PopupMenu extends JPopupMenu
     refresh();
   }
 
-
-
   protected void abovePIDColour_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = getGroup();
+
     if (abovePIDColour.isSelected())
     {
       sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
                                                ap.av.alignment.getWidth()));
-      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
+
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+          getGroup().getName());
+
       if (sg.cs instanceof ResidueColourScheme)
-        ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
+      {
+        ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
+      }
       else if (sg.cs instanceof ScoreColourScheme)
+      {
         ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
+      }
 
       SliderPanel.showPIDSlider();
-
-
     }
     else // remove PIDColouring
     {
@@ -461,13 +503,11 @@ public class PopupMenu extends JPopupMenu
     }
 
     refresh();
-
   }
 
-
   protected void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    new UserDefinedColours( ap, getGroup());
+    new UserDefinedColours(ap, getGroup());
   }
 
   protected void PIDColour_actionPerformed(ActionEvent e)
@@ -475,7 +515,7 @@ public class PopupMenu extends JPopupMenu
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                               ap.av.alignment.getWidth()));
+                                             ap.av.alignment.getWidth()));
     refresh();
   }
 
@@ -486,34 +526,32 @@ public class PopupMenu extends JPopupMenu
     sg.cs = new Blosum62ColourScheme();
 
     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                               ap.av.alignment.getWidth()));
+                                             ap.av.alignment.getWidth()));
 
     refresh();
   }
 
-
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
     getGroup().cs = null;
     refresh();
   }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  protected void conservationMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = getGroup();
 
-    if(conservationMenuItem.isSelected())
+    if (conservationMenuItem.isSelected())
     {
+      Conservation c = new Conservation("Group",
+                                        ResidueProperties.propHash, 3,
+                                        sg.sequences, 0,
+                                        ap.av.alignment.getWidth());
 
-        Conservation c = new Conservation("Group",
-                                          ResidueProperties.propHash, 3,
-                                          sg.sequences, 0,
-                                          ap.av.alignment.getWidth());
-
-        c.calculate();
-        c.verdict(false, ap.av.ConsPercGaps);
-        ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
+      c.calculate();
+      c.verdict(false, ap.av.ConsPercGaps);
 
+      ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
       sg.cs = ccs;
 
@@ -522,45 +560,48 @@ public class PopupMenu extends JPopupMenu
     }
     else // remove ConservationColouring
     {
-        ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-        sg.cs = ccs.cs;
+      ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
+      sg.cs = ccs.cs;
     }
 
-     refresh();
+    refresh();
   }
 
-
   protected void groupName_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = getGroup();
-    String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);
-    if(reply==null)
+    String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
+        "Enter new group name", "Edit group name",
+        JOptionPane.QUESTION_MESSAGE);
+
+    if (reply == null)
+    {
       return;
+    }
 
     sg.setName(reply);
     groupName.setText(reply);
   }
 
-
   protected void analyze_actionPerformed(ActionEvent e)
   {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer();
-     JInternalFrame frame = new JInternalFrame();
-     frame.setContentPane(cap);
-     Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
-     SequenceGroup sg = getGroup();
-     StringBuffer sb = new StringBuffer();
-
-     for(int i=0; i<sg.sequences.size(); i++)
-     {
-       Sequence tmp = (Sequence)sg.sequences.get(i);
-       sb.append(  tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));
-       sb.append("\n");
-     }
-
-     sb.append("Something amazing will happen soon");
-     cap.setText( sb.toString() );
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    JInternalFrame frame = new JInternalFrame();
+    frame.setContentPane(cap);
+    Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
+
+    SequenceGroup sg = getGroup();
+    StringBuffer sb = new StringBuffer();
 
+    for (int i = 0; i < sg.sequences.size(); i++)
+    {
+      Sequence tmp = (Sequence) sg.sequences.get(i);
+      sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
+      sb.append("\n");
+    }
+
+    sb.append("Something amazing will happen soon");
+    cap.setText(sb.toString());
   }
 
   SequenceGroup getGroup()
@@ -576,47 +617,47 @@ public class PopupMenu extends JPopupMenu
   void sequenceName_actionPerformed(ActionEvent e)
   {
     String id = sequence.getName();
-    String s = (String)JOptionPane.showInternalInputDialog(
-                ap,
-                "Edit sequence name",
-                "Edit sequence name ("+sequence.getName()+")",
-                JOptionPane.PLAIN_MESSAGE,
-                null,
-                null,
-                id);
+    String s = (String) JOptionPane.showInternalInputDialog(ap,
+        "Edit sequence name",
+        "Edit sequence name (" + sequence.getName() + ")",
+        JOptionPane.PLAIN_MESSAGE, null, null, id);
 
-    if(s!=null)
+    if (s != null)
     {
       sequence.setName(s);
       ap.repaint();
     }
-
   }
 
   void unGroupMenuItem_actionPerformed(ActionEvent e)
   {
-     SequenceGroup sg = ap.av.getSelectionGroup();
-     ap.av.alignment.deleteGroup(sg);
-     ap.av.setSelectionGroup(null);
-     ap.repaint();
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    ap.av.alignment.deleteGroup(sg);
+    ap.av.setSelectionGroup(null);
+    ap.repaint();
   }
 
   void pdbMenuItem_actionPerformed(ActionEvent e)
   {
-    if(sequence.getPDBId()==null)
+    if (sequence.getPDBId() == null)
+    {
       return;
+    }
 
     try
     {
       EBIFetchClient ebi = new EBIFetchClient();
-      String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);
+      String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,
+                                      null);
 
       PDBfile pdb = new PDBfile(result);
 
       rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);
       JInternalFrame frame = new JInternalFrame();
       frame.setContentPane(rc);
-      Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);
+      Desktop.addInternalFrame(frame,
+                               sequence.getName() + " " + sequence.getPDBId(),
+                               400, 400);
     }
     catch (Exception ex)
     {
@@ -627,9 +668,14 @@ public class PopupMenu extends JPopupMenu
   protected void outline_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = getGroup();
-    Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);
-    if(col!=null)
+    Color col = JColorChooser.showDialog(this, "Select Outline Colour",
+                                         Color.BLUE);
+
+    if (col != null)
+    {
       sg.setOutlineColour(col);
+    }
+
     ap.repaint();
   }
 
@@ -650,5 +696,4 @@ public class PopupMenu extends JPopupMenu
     getGroup().setColourText(showColourText.isSelected());
     refresh();
   }
-
 }