src/jalview/gui/GroupEditor.java

   1 package jalview.gui;\r
   2 \r
   3 import jalview.jbgui.GGroupEditor;\r
   4 import jalview.datamodel.*;\r
   5 import jalview.schemes.*;\r
   6 import java.awt.event.*;\r
   7 import java.util.*;\r
   8 import javax.swing.*;\r
   9 \r
  10 \r
  11 public class GroupEditor extends GGroupEditor\r
  12 {\r
  13   AlignViewport av;\r
  14   AlignmentPanel ap;\r
  15   Vector groups;\r
  16   Vector unassignedVector;\r
  17   Vector assignedVector=new Vector();\r
  18   boolean updating=false;\r
  19   int selectedGroupIndex = 0;\r
  20   Hashtable sequenceHash = new Hashtable();\r
  21 \r
  22   public GroupEditor(AlignViewport av, AlignmentPanel ap)\r
  23   {\r
  24     this.av = av;\r
  25     this.ap = ap;\r
  26     groups = av.getAlignment().getGroups();\r
  27 \r
  28     updateUnassigned();\r
  29     for (int i=0; i < ColourProperties.getColourSchemeNames().size(); i++)\r
  30        colourCombo.addItem(ColourProperties.getColourSchemeNames().elementAt(i));\r
  31 \r
  32      if(groups.size()>0)\r
  33      {\r
  34        showGroup();\r
  35        updateGroupcombo();\r
  36      }\r
  37 \r
  38     assignedList.addMouseListener( new MouseAdapter()\r
  39     {\r
  40       public void mouseClicked(MouseEvent e)\r
  41       {\r
  42         if (e.getClickCount() == 2)\r
  43         {    remove_actionPerformed(null);      }\r
  44       }\r
  45     });\r
  46 \r
  47     unassignedList.addMouseListener( new MouseAdapter()\r
  48     {\r
  49       public void mouseClicked(MouseEvent e)\r
  50       {\r
  51         if (e.getClickCount() == 2)\r
  52         { add_actionPerformed(null);    }\r
  53       }\r
  54     });\r
  55   }\r
  56 \r
  57 \r
  58   void updateGui()\r
  59   {\r
  60     unassignedList.setListData(unassignedVector);\r
  61     assignedList.setListData(assignedVector);\r
  62     updateGroupcombo();\r
  63     ap.RefreshPanels();\r
  64   }\r
  65 \r
  66 \r
  67   void updateGroupcombo()\r
  68   {\r
  69     updating=true;\r
  70 \r
  71     if(groupsCombo.getItemCount()>0)\r
  72       groupsCombo.removeAllItems();\r
  73 \r
  74     for (int i = 0; i < groups.size(); i++) {\r
  75       SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
  76       groupsCombo.addItem( sg.getName() + " (" + sg.getSize() + " sequences)");\r
  77     }\r
  78     groupsCombo.setSelectedIndex(selectedGroupIndex);\r
  79     updating=false;\r
  80   }\r
  81 \r
  82   void updateUnassigned()\r
  83   {\r
  84     unassignedVector=new Vector();\r
  85     AlignmentI align = av.getAlignment();\r
  86 \r
  87     for (int i = 0; i < align.getHeight();i++)\r
  88     {\r
  89       sequenceHash.put( align.getSequenceAt(i).getDisplayId(), align.getSequenceAt(i) );\r
  90       boolean assigned = false;\r
  91       for(int j=0; j<groups.size(); j++)\r
  92       {\r
  93         SequenceGroup sg = (SequenceGroup)groups.elementAt(j);\r
  94         for(int k=0; k<sg.getSize(); k++)\r
  95         {\r
  96           if(sg.getSequenceAt(k).getDisplayId().equals( align.getSequenceAt(i).getDisplayId() ) )\r
  97           {\r
  98             assigned = true; break;\r
  99           }\r
 100         }\r
 101 \r
 102         if(assigned)\r
 103           break;\r
 104       }\r
 105 \r
 106       if(!assigned)\r
 107           unassignedVector.add(align.getSequenceAt(i).getDisplayId());\r
 108 \r
 109     }\r
 110 \r
 111     unassignedList.setListData(unassignedVector);\r
 112   }\r
 113 \r
 114 \r
 115   void showGroup()\r
 116   {\r
 117     if(groups.size()<1)\r
 118        return;\r
 119 \r
 120     assignedVector = new Vector();\r
 121     if(selectedGroupIndex!=-1)\r
 122     {\r
 123       SequenceGroup sg = (SequenceGroup) groups.elementAt(selectedGroupIndex);\r
 124       for (int j = 0; j < sg.getSize(); j++)\r
 125       {\r
 126         Sequence s = (Sequence) sg.getSequenceAt(j);\r
 127         assignedVector.addElement(s.getDisplayId());\r
 128       }\r
 129       int num = ColourProperties.indexOfClass(sg.cs);\r
 130       colourCombo.setSelectedIndex(num);\r
 131 \r
 132       boxesCheck.setSelected(sg.getDisplayBoxes());\r
 133       textCheck.setSelected(sg.getDisplayText());\r
 134       colourTextCheck.setSelected(sg.getColourText());\r
 135     }\r
 136 \r
 137 \r
 138     assignedList.setListData( assignedVector );\r
 139   }\r
 140 \r
 141 \r
 142   protected void groupsCombo_actionPerformed(ActionEvent e)\r
 143   {\r
 144     if( !updating )\r
 145     {\r
 146       selectedGroupIndex = groupsCombo.getSelectedIndex();\r
 147       showGroup();\r
 148     }\r
 149   }\r
 150 \r
 151   protected void groupName_actionPerformed(ActionEvent e)\r
 152   {\r
 153     String reply = JOptionPane.showInternalInputDialog(this, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);\r
 154     if(reply==null)\r
 155       return;\r
 156 \r
 157     SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);\r
 158     sg.setName(reply);\r
 159     updateGroupcombo();\r
 160   }\r
 161 \r
 162   protected void colourCombo_actionPerformed(ActionEvent e)\r
 163   {\r
 164      if(groups.size()<1)\r
 165        return;\r
 166 \r
 167      SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);\r
 168 \r
 169      sg.cs = ColourSchemeFactory.get( (String)colourCombo.getSelectedItem() );\r
 170      //ColourProperties.getColourScheme( colourCombo.getSelectedIndex() );\r
 171      ap.RefreshPanels();\r
 172   }\r
 173 \r
 174   protected void boxesCheck_actionPerformed(ActionEvent e)\r
 175   {\r
 176     SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);\r
 177     sg.setDisplayBoxes( boxesCheck.isSelected());\r
 178         ap.RefreshPanels();\r
 179   }\r
 180 \r
 181   protected void textCheck_actionPerformed(ActionEvent e)\r
 182   {\r
 183     SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);\r
 184     sg.setDisplayText( textCheck.isSelected() );\r
 185         ap.RefreshPanels();\r
 186   }\r
 187 \r
 188   protected void colourTextCheck_actionPerformed(ActionEvent e)\r
 189   {\r
 190     SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);\r
 191     sg.setColourText( colourTextCheck.isSelected());\r
 192         ap.RefreshPanels();\r
 193   }\r
 194 \r
 195   protected void addSelectedIds_actionPerformed(ActionEvent e)\r
 196   {\r
 197     if(selectedGroupIndex==-1)\r
 198       return;\r
 199 \r
 200     SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);\r
 201 \r
 202     for(int i=0; i<av.getSelectionGroup().getSize(); i++)\r
 203     {\r
 204       int index = unassignedVector.indexOf( av.getSelectionGroup().getSequenceAt(i).getDisplayId() );\r
 205       if(index!=-1)\r
 206       {\r
 207         sg.addSequence( (SequenceI) sequenceHash.get( unassignedVector.elementAt(index) ));\r
 208         assignedVector.addElement( unassignedVector.elementAt(index));\r
 209         unassignedVector.removeElementAt( index );\r
 210       }\r
 211 \r
 212     }\r
 213     updateGui();\r
 214   }\r
 215 \r
 216   protected void add_actionPerformed(ActionEvent e)\r
 217   {\r
 218     if(selectedGroupIndex==-1)\r
 219       return;\r
 220 \r
 221     int [] indices  = unassignedList.getSelectedIndices();\r
 222     if(indices.length<1)\r
 223       return;\r
 224 \r
 225     SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);\r
 226 \r
 227     for(int i=0; i<indices.length; i++)\r
 228     {\r
 229       assignedVector.addElement(unassignedVector.elementAt(indices[i]-i));\r
 230       sg.addSequence( (SequenceI)sequenceHash.get( unassignedVector.elementAt(indices[i]-i) ));\r
 231       unassignedVector.removeElementAt(indices[i]-i);\r
 232     }\r
 233     updateGui();\r
 234   }\r
 235 \r
 236   protected void addAll_actionPerformed(ActionEvent e)\r
 237   {\r
 238     if(selectedGroupIndex==-1)\r
 239       return;\r
 240 \r
 241     SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);\r
 242     Enumeration enum = unassignedVector.elements();\r
 243     while(enum.hasMoreElements())\r
 244     {\r
 245       String id = (String)enum.nextElement();\r
 246       assignedVector.addElement( id );\r
 247       sg.addSequence( (SequenceI)sequenceHash.get( id ));\r
 248     }\r
 249 \r
 250     unassignedVector.clear();\r
 251     updateGui();\r
 252   }\r
 253 \r
 254   protected void remove_actionPerformed(ActionEvent e)\r
 255   {\r
 256     if(selectedGroupIndex==-1)\r
 257       return;\r
 258 \r
 259     SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);\r
 260 \r
 261     int [] indices = assignedList.getSelectedIndices();\r
 262     if(indices.length<1)\r
 263       return;\r
 264 \r
 265     for(int i=0; i<indices.length; i++)\r
 266     {\r
 267 \r
 268       unassignedVector.addElement(assignedVector.elementAt(indices[i]-i));\r
 269       SequenceI removeSequence = (SequenceI)sequenceHash.get( assignedVector.elementAt(indices[i]-i) );\r
 270       av.getSelectionGroup().deleteSequence( removeSequence );\r
 271       sg.deleteSequence( removeSequence );\r
 272       assignedVector.removeElementAt(indices[i]-i);\r
 273 \r
 274     }\r
 275 \r
 276     updateGui();\r
 277   }\r
 278 \r
 279   protected void removeAll_actionPerformed(ActionEvent e)\r
 280   {\r
 281     if(selectedGroupIndex==-1)\r
 282       return;\r
 283 \r
 284     SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);\r
 285     Enumeration enum = assignedVector.elements();\r
 286     while(enum.hasMoreElements())\r
 287     {\r
 288       String id = (String)enum.nextElement();\r
 289       unassignedVector.addElement( id );\r
 290       SequenceI removeSequence = (SequenceI)sequenceHash.get( id );\r
 291       av.getSelectionGroup().deleteSequence( removeSequence );\r
 292       sg.deleteSequence( removeSequence );\r
 293     }\r
 294 \r
 295     assignedVector.clear();\r
 296     updateGui();\r
 297   }\r
 298 \r
 299   protected void addGroup_actionPerformed(ActionEvent e)\r
 300   {\r
 301 \r
 302    ColourSchemeI cs = ColourSchemeFactory.get( (String)colourCombo.getSelectedItem() );\r
 303     //   ColourProperties.getColourScheme( colourCombo.getSelectedIndex() );\r
 304 \r
 305    groups.add(\r
 306       new SequenceGroup("Group "+(groups.size()+1),\r
 307                         cs,\r
 308                         boxesCheck.isSelected(),\r
 309                         textCheck.isSelected(),\r
 310                         colourTextCheck.isSelected(),\r
 311                         0, av.alignment.getWidth()\r
 312                         ) );\r
 313 \r
 314    updateGroupcombo();\r
 315    groupsCombo.setSelectedIndex( groupsCombo.getItemCount()-1 );\r
 316    showGroup();\r
 317   }\r
 318 \r
 319   protected void deleteGroup_actionPerformed(ActionEvent e)\r
 320   {\r
 321     removeAll_actionPerformed(null);\r
 322     groups.remove( selectedGroupIndex );\r
 323     selectedGroupIndex=-1;\r
 324     updateGroupcombo();\r
 325     groupsCombo.setSelectedIndex( groupsCombo.getItemCount()-1 );\r
 326     showGroup();\r
 327   }\r
 328 \r
 329 }\r