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