From 5e9a8519d84c8f2b6fa6adec6620f2ccf87cf4a4 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 16 Nov 2004 15:16:41 +0000
Subject: [PATCH] New Class

---
 src/jalview/gui/GroupEditor.java |  316 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 316 insertions(+)
 create mode 100755 src/jalview/gui/GroupEditor.java

diff --git a/src/jalview/gui/GroupEditor.java b/src/jalview/gui/GroupEditor.java
new file mode 100755
index 0000000..3c58df3
--- /dev/null
+++ b/src/jalview/gui/GroupEditor.java
@@ -0,0 +1,316 @@
+package jalview.gui;
+
+import jalview.jbgui.GGroupEditor;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import java.awt.event.*;
+import java.util.*;
+import javax.swing.*;
+
+
+public class GroupEditor extends GGroupEditor
+{
+  AlignViewport av;
+  AlignmentPanel ap;
+  Vector groups;
+  Vector unassignedVector;
+  Vector assignedVector=new Vector();
+  boolean updating=false;
+  int selectedGroupIndex = 0;
+  Hashtable sequenceHash = new Hashtable();
+
+  public GroupEditor(AlignViewport av, AlignmentPanel ap)
+  {
+    this.av = av;
+    this.ap = ap;
+    groups = av.getAlignment().getGroups();
+
+    updateUnassigned();
+    for (int i=0; i < ColourProperties.getColourSchemeNames().size(); i++)
+       colourCombo.addItem(ColourProperties.getColourSchemeNames().elementAt(i));
+
+    showGroup();
+    updateGroupcombo();
+
+    assignedList.addMouseListener( new MouseAdapter()
+    {
+      public void mouseClicked(MouseEvent e)
+      {
+        if (e.getClickCount() == 2)
+        {    remove_actionPerformed(null);      }
+      }
+    });
+
+    unassignedList.addMouseListener( new MouseAdapter()
+    {
+      public void mouseClicked(MouseEvent e)
+      {
+        if (e.getClickCount() == 2)
+        { add_actionPerformed(null);    }
+      }
+    });
+  }
+
+
+  void updateGui()
+  {
+    unassignedList.setListData(unassignedVector);
+    assignedList.setListData(assignedVector);
+    updateGroupcombo();
+    ap.RefreshPanels();
+  }
+
+
+  void updateGroupcombo()
+  {
+    updating=true;
+
+    if(groupsCombo.getItemCount()>0)
+      groupsCombo.removeAllItems();
+
+    for (int i = 0; i < groups.size(); i++) {
+      SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+      groupsCombo.addItem( sg.getName() + " (" + sg.getSize() + " sequences)");
+    }
+    groupsCombo.setSelectedIndex(selectedGroupIndex);
+    updating=false;
+  }
+
+  void updateUnassigned()
+  {
+    unassignedVector=new Vector();
+    AlignmentI align = av.getAlignment();
+
+    for (int i = 0; i < align.getHeight();i++)
+    {
+      sequenceHash.put( align.getSequenceAt(i).getDisplayId(), align.getSequenceAt(i) );
+      boolean assigned = false;
+      for(int j=0; j<groups.size(); j++)
+      {
+        SequenceGroup sg = (SequenceGroup)groups.elementAt(j);
+        for(int k=0; k<sg.getSize(); k++)
+        {
+          if(sg.getSequenceAt(k).getDisplayId().equals( align.getSequenceAt(i).getDisplayId() ) )
+          {
+            assigned = true; break;
+          }
+        }
+
+        if(assigned)
+          break;
+      }
+
+      if(!assigned)
+          unassignedVector.add(align.getSequenceAt(i).getDisplayId());
+
+    }
+
+    unassignedList.setListData(unassignedVector);
+  }
+
+
+  void showGroup()
+  {
+    assignedVector = new Vector();
+    if(selectedGroupIndex!=-1)
+    {
+      SequenceGroup sg = (SequenceGroup) groups.elementAt(selectedGroupIndex);
+      for (int j = 0; j < sg.getSize(); j++)
+      {
+        Sequence s = (Sequence) sg.getSequenceAt(j);
+        assignedVector.addElement(s.getDisplayId());
+      }
+      int num = ColourProperties.indexOfClass(sg.cs);
+      colourCombo.setSelectedIndex(num);
+
+      boxesCheck.setSelected(sg.getDisplayBoxes());
+      textCheck.setSelected(sg.getDisplayText());
+      colourTextCheck.setSelected(sg.getColourText());
+    }
+
+
+    assignedList.setListData( assignedVector );
+  }
+
+
+  protected void groupsCombo_actionPerformed(ActionEvent e)
+  {
+    if( !updating )
+    {
+      selectedGroupIndex = groupsCombo.getSelectedIndex();
+      showGroup();
+    }
+  }
+
+  protected void groupName_actionPerformed(ActionEvent e)
+  {
+    String reply = JOptionPane.showInputDialog(this, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);
+    if(reply==null)
+      return;
+
+    SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);
+    sg.setName(reply);
+    updateGroupcombo();
+  }
+
+  protected void colourCombo_actionPerformed(ActionEvent e)
+  {
+     SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);
+
+     sg.cs = ColourSchemeFactory.get( (String)colourCombo.getSelectedItem() );
+     //ColourProperties.getColourScheme( colourCombo.getSelectedIndex() );
+     ap.RefreshPanels();
+  }
+
+  protected void boxesCheck_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);
+    sg.setDisplayBoxes( boxesCheck.isSelected());
+        ap.RefreshPanels();
+  }
+
+  protected void textCheck_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);
+    sg.setDisplayText( textCheck.isSelected() );
+        ap.RefreshPanels();
+  }
+
+  protected void colourTextCheck_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);
+    sg.setColourText( colourTextCheck.isSelected());
+        ap.RefreshPanels();
+  }
+
+  protected void addSelectedIds_actionPerformed(ActionEvent e)
+  {
+    if(selectedGroupIndex==-1)
+      return;
+
+    SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);
+    Selection sel = av.getSelection();
+    for(int i=0; i<sel.size(); i++)
+    {
+      int index = unassignedVector.indexOf( sel.sequenceAt(i).getDisplayId() );
+      if(index!=-1)
+      {
+        sg.addSequence( (SequenceI) sequenceHash.get( unassignedVector.elementAt(index) ));
+        assignedVector.addElement( unassignedVector.elementAt(index));
+        unassignedVector.removeElementAt( index );
+      }
+
+    }
+    updateGui();
+  }
+
+  protected void add_actionPerformed(ActionEvent e)
+  {
+    if(selectedGroupIndex==-1)
+      return;
+
+    int [] indices  = unassignedList.getSelectedIndices();
+    if(indices.length<1)
+      return;
+
+    SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);
+
+    for(int i=0; i<indices.length; i++)
+    {
+      assignedVector.addElement(unassignedVector.elementAt(indices[i]-i));
+      sg.addSequence( (SequenceI)sequenceHash.get( unassignedVector.elementAt(indices[i]-i) ));
+      unassignedVector.removeElementAt(indices[i]-i);
+    }
+    updateGui();
+  }
+
+  protected void addAll_actionPerformed(ActionEvent e)
+  {
+    if(selectedGroupIndex==-1)
+      return;
+
+    SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);
+    Enumeration enum = unassignedVector.elements();
+    while(enum.hasMoreElements())
+    {
+      String id = (String)enum.nextElement();
+      assignedVector.addElement( id );
+      sg.addSequence( (SequenceI)sequenceHash.get( id ));
+    }
+
+    unassignedVector.clear();
+    updateGui();
+  }
+
+  protected void remove_actionPerformed(ActionEvent e)
+  {
+    if(selectedGroupIndex==-1)
+      return;
+
+    SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);
+
+    int [] indices = assignedList.getSelectedIndices();
+    if(indices.length<1)
+      return;
+
+    for(int i=0; i<indices.length; i++)
+    {
+
+      unassignedVector.addElement(assignedVector.elementAt(indices[i]-i));
+      sg.deleteSequence( (SequenceI)sequenceHash.get( assignedVector.elementAt(indices[i]-i) ));
+      assignedVector.removeElementAt(indices[i]-i);
+
+    }
+
+    updateGui();
+  }
+
+  protected void removeAll_actionPerformed(ActionEvent e)
+  {
+    if(selectedGroupIndex==-1)
+      return;
+
+    SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);
+    Enumeration enum = assignedVector.elements();
+    while(enum.hasMoreElements())
+    {
+      String id = (String)enum.nextElement();
+      unassignedVector.addElement( id );
+      sg.deleteSequence( (SequenceI)sequenceHash.get( id ));
+    }
+
+    assignedVector.clear();
+    updateGui();
+  }
+
+  protected void addGroup_actionPerformed(ActionEvent e)
+  {
+
+   ColourSchemeI cs = ColourSchemeFactory.get( (String)colourCombo.getSelectedItem() );
+    //   ColourProperties.getColourScheme( colourCombo.getSelectedIndex() );
+
+   groups.add(
+      new SequenceGroup("Group "+(groups.size()+1),
+                        cs,
+                        false,
+                        boxesCheck.isSelected(),
+                        textCheck.isSelected(),
+                        colourTextCheck.isSelected(),
+                        true) );
+
+   updateGroupcombo();
+   groupsCombo.setSelectedIndex( groupsCombo.getItemCount()-1 );
+   showGroup();
+  }
+
+  protected void deleteGroup_actionPerformed(ActionEvent e)
+  {
+    removeAll_actionPerformed(null);
+    groups.remove( selectedGroupIndex );
+    selectedGroupIndex=-1;
+    updateGroupcombo();
+    groupsCombo.setSelectedIndex( groupsCombo.getItemCount()-1 );
+    showGroup();
+  }
+
+}
-- 
1.7.10.2