[Obo-svn-commit] SF.net SVN: obo:[2200] phenex/trunk/src/org/phenoscape/view/ PhenotypeTableComponent.java

[<ba...@us...>]

Revision: 2200
          http://obo.svn.sourceforge.net/obo/?rev=2200&view=rev
Author:   balhoff
Date:     2008-11-04 15:13:14 +0000 (Tue, 04 Nov 2008)

Log Message:
-----------
Other phenotypes of the same state are now checked for a previously entered entity, before copying one from another state for that character.

Modified Paths:
--------------
    phenex/trunk/src/org/phenoscape/view/PhenotypeTableComponent.java

Modified: phenex/trunk/src/org/phenoscape/view/PhenotypeTableComponent.java
===================================================================
--- phenex/trunk/src/org/phenoscape/view/PhenotypeTableComponent.java	2008-11-04 02:39:46 UTC (rev 2199)
+++ phenex/trunk/src/org/phenoscape/view/PhenotypeTableComponent.java	2008-11-04 15:13:14 UTC (rev 2200)
@@ -42,286 +42,295 @@
 
 public class PhenotypeTableComponent extends PhenoscapeGUIComponent {
 
-  private JButton addPhenotypeButton;
-  private JButton deletePhenotypeButton;
-  private PopupListener tablePopup;
-  private PhenotypesTableFormat tableFormat;
-  private JTable phenotypesTable;
-  
-  public PhenotypeTableComponent(String id, PhenoscapeController controller) {
-    super(id, controller);
-  }
-  
-  @Override
-  public void init() {
-    super.init();
-    this.initializeInterface();
-  }
+    private JButton addPhenotypeButton;
+    private JButton deletePhenotypeButton;
+    private PopupListener tablePopup;
+    private PhenotypesTableFormat tableFormat;
+    private JTable phenotypesTable;
 
-  private void initializeInterface() {
-    this.setLayout(new BorderLayout());
-    this.tableFormat = new PhenotypesTableFormat();
-    final EventTableModel<Phenotype> phenotypesTableModel = new EventTableModel<Phenotype>(this.getController().getPhenotypesForCurrentStateSelection(), this.tableFormat);
-    this.phenotypesTable = new BugWorkaroundTable(phenotypesTableModel);
-    this.phenotypesTable.setSelectionModel(this.getController().getCurrentPhenotypesSelectionModel());
-    this.phenotypesTable.setDefaultRenderer(Object.class, new PlaceholderRenderer("None"));
-    this.phenotypesTable.setDefaultRenderer(OBOObject.class, new TermRenderer("None"));
-    for (int i = 0; i < this.phenotypesTable.getColumnCount(); i++) {
-      final TableCellEditor editor = this.tableFormat.getColumnEditor(i);
-      if (editor != null) { this.phenotypesTable.getColumnModel().getColumn(i).setCellEditor(editor); }
+    public PhenotypeTableComponent(String id, PhenoscapeController controller) {
+        super(id, controller);
     }
-    this.phenotypesTable.putClientProperty("Quaqua.Table.style", "striped");
-    new TableColumnPrefsSaver(this.phenotypesTable, this.getClass().getName());
-    this.tablePopup = new PopupListener(this.createTablePopupMenu());
-    this.phenotypesTable.addMouseListener(this.tablePopup);
-    final TableComparatorChooser<Phenotype> sortChooser = new TableComparatorChooser<Phenotype>(this.phenotypesTable, this.getController().getPhenotypesForCurrentStateSelection(), false);
-    sortChooser.addSortActionListener(new SortDisabler());
-    this.add(new JScrollPane(this.phenotypesTable), BorderLayout.CENTER);
-    this.add(this.createToolBar(), BorderLayout.NORTH);
-    this.getController().getCurrentStatesSelectionModel().addListSelectionListener(new StateSelectionListener());
-    this.getController().getCurrentPhenotypesSelectionModel().addListSelectionListener(new PhenotypeSelectionListener());
-  }
-  
-  private void addPhenotype() {
-    final State state = this.getSelectedState();
-    if (state != null) {
-      final Phenotype phenotype = state.newPhenotype();
-      phenotype.setEntity(this.getAutofillEntity());
+
+    @Override
+    public void init() {
+        super.init();
+        this.initializeInterface();
     }
-  }
-  
-  private OBOClass getAutofillEntity() {
-    for (State state : this.getController().getStatesForCurrentCharacterSelection()) {
-      for (Phenotype phenotype : state.getPhenotypes()) {
-        if (phenotype.getEntity() != null) {
-          return phenotype.getEntity();
+
+    private void initializeInterface() {
+        this.setLayout(new BorderLayout());
+        this.tableFormat = new PhenotypesTableFormat();
+        final EventTableModel<Phenotype> phenotypesTableModel = new EventTableModel<Phenotype>(this.getController().getPhenotypesForCurrentStateSelection(), this.tableFormat);
+        this.phenotypesTable = new BugWorkaroundTable(phenotypesTableModel);
+        this.phenotypesTable.setSelectionModel(this.getController().getCurrentPhenotypesSelectionModel());
+        this.phenotypesTable.setDefaultRenderer(Object.class, new PlaceholderRenderer("None"));
+        this.phenotypesTable.setDefaultRenderer(OBOObject.class, new TermRenderer("None"));
+        for (int i = 0; i < this.phenotypesTable.getColumnCount(); i++) {
+            final TableCellEditor editor = this.tableFormat.getColumnEditor(i);
+            if (editor != null) { this.phenotypesTable.getColumnModel().getColumn(i).setCellEditor(editor); }
         }
-      }
+        this.phenotypesTable.putClientProperty("Quaqua.Table.style", "striped");
+        new TableColumnPrefsSaver(this.phenotypesTable, this.getClass().getName());
+        this.tablePopup = new PopupListener(this.createTablePopupMenu());
+        this.phenotypesTable.addMouseListener(this.tablePopup);
+        final TableComparatorChooser<Phenotype> sortChooser = new TableComparatorChooser<Phenotype>(this.phenotypesTable, this.getController().getPhenotypesForCurrentStateSelection(), false);
+        sortChooser.addSortActionListener(new SortDisabler());
+        this.add(new JScrollPane(this.phenotypesTable), BorderLayout.CENTER);
+        this.add(this.createToolBar(), BorderLayout.NORTH);
+        this.getController().getCurrentStatesSelectionModel().addListSelectionListener(new StateSelectionListener());
+        this.getController().getCurrentPhenotypesSelectionModel().addListSelectionListener(new PhenotypeSelectionListener());
     }
-    return null;
-  }
-  
-  private void deleteSelectedPhenotype() {
-    final State state = this.getSelectedState();
-    if (state != null) {
-      final Phenotype phenotype = this.getSelectedPhenotype();
-      if (phenotype != null) { state.removePhenotype(phenotype); }
+
+    private void addPhenotype() {
+        final State state = this.getSelectedState();
+        if (state != null) {
+            final Phenotype phenotype = state.newPhenotype();
+            phenotype.setEntity(this.getAutofillEntity());
+        }
     }
-  }
-  
-  private State getSelectedState() {
-    final EventList<State> selected = this.getController().getCurrentStatesSelectionModel().getSelected();
-    if (selected.size() == 1) {
-      return selected.get(0);
-    } else {
-      return null;
+
+    private OBOClass getAutofillEntity() {
+        //check current state
+        for (State state : this.getController().getCurrentStatesSelectionModel().getSelected()) {
+            for (Phenotype phenotype : state.getPhenotypes()) {
+                if (phenotype.getEntity() != null) {
+                    return phenotype.getEntity();
+                }
+            }
+        }
+        //then check all states
+        for (State state : this.getController().getStatesForCurrentCharacterSelection()) {
+            for (Phenotype phenotype : state.getPhenotypes()) {
+                if (phenotype.getEntity() != null) {
+                    return phenotype.getEntity();
+                }
+            }
+        }
+        return null;
     }
-  }
-  
-  private Phenotype getSelectedPhenotype() {
-    final EventList<Phenotype> selected = this.getController().getCurrentPhenotypesSelectionModel().getSelected();
-    if (selected.size() == 1) {
-      return selected.get(0);
-    } else {
-      return null;
+
+    private void deleteSelectedPhenotype() {
+        final State state = this.getSelectedState();
+        if (state != null) {
+            final Phenotype phenotype = this.getSelectedPhenotype();
+            if (phenotype != null) { state.removePhenotype(phenotype); }
+        }
     }
-  }
-  
-  private void stateSelectionDidChange() {
-    final String unselectedTitle = "Phenotypes";
-    final String selectedPrefix = "Phenotypes for State: ";
-    final List<State> states = this.getController().getCurrentStatesSelectionModel().getSelected();
-    if (states.isEmpty()) {
-      this.updatePanelTitle(unselectedTitle);
-    } else {
-      this.updatePanelTitle(selectedPrefix + states.get(0));
+
+    private State getSelectedState() {
+        final EventList<State> selected = this.getController().getCurrentStatesSelectionModel().getSelected();
+        if (selected.size() == 1) {
+            return selected.get(0);
+        } else {
+            return null;
+        }
     }
-    this.updateButtonStates();
-  }
-  
-  private void phenotypeSelectionDidChange() {
-    this.updateButtonStates();
-  }
-  
-  private void updateButtonStates() {
-    this.addPhenotypeButton.setEnabled(this.getSelectedState() != null);
-    this.deletePhenotypeButton.setEnabled(this.getSelectedPhenotype() != null);
-  }
-  
-  private void runPostCompositionForTermAtPoint(Point p) {
-    final int column = this.phenotypesTable.getTableHeader().columnAtPoint(p);
-    final int row = this.phenotypesTable.rowAtPoint(p);
-    if (!this.tableFormat.getColumnClass(column).equals(OBOObject.class)) return;
-    final Phenotype phenotype = this.getController().getPhenotypesForCurrentStateSelection().get(row);
-    final OBOClass term = (OBOClass)(this.tableFormat.getColumnValue(phenotype, column));
-    final PostCompositionEditor pce = new PostCompositionEditor(this.getController(), this.tableFormat.getColumnTermSet(column));
-    pce.setTerm(term);
-    final int result = pce.runPostCompositionDialog();
-    if (result == JOptionPane.OK_OPTION) {
-      this.tableFormat.setColumnValue(phenotype, pce.getTerm(), column);
+
+    private Phenotype getSelectedPhenotype() {
+        final EventList<Phenotype> selected = this.getController().getCurrentPhenotypesSelectionModel().getSelected();
+        if (selected.size() == 1) {
+            return selected.get(0);
+        } else {
+            return null;
+        }
     }
-  }
 
-  private JToolBar createToolBar() {
-      final JToolBar toolBar = new JToolBar();
-      this.addPhenotypeButton = new JButton(new AbstractAction(null, new ImageIcon(this.getClass().getResource("/org/phenoscape/view/images/list-add.png"))) {
-          public void actionPerformed(ActionEvent e) {
-              addPhenotype();
-          }
-      });
-      this.addPhenotypeButton.setToolTipText("Add Phenotype");
-      toolBar.add(this.addPhenotypeButton);
-      this.deletePhenotypeButton = new JButton(new AbstractAction(null, new ImageIcon(this.getClass().getResource("/org/phenoscape/view/images/list-remove.png"))) {
-          public void actionPerformed(ActionEvent e) {
-              deleteSelectedPhenotype();
-          }
-      });
-      this.deletePhenotypeButton.setToolTipText("Delete Phenotype");
-      toolBar.add(this.deletePhenotypeButton);
-      toolBar.setFloatable(false);
-      return toolBar;
-  }
-  
-  private JPopupMenu createTablePopupMenu() {
-    final JPopupMenu menu = new JPopupMenu();
-    menu.add(new AbstractAction("Edit Post-composed Term") {
-      public void actionPerformed(ActionEvent e) {
-        runPostCompositionForTermAtPoint(tablePopup.getLocation());
-      }
-    });
-    return menu;
-  }
-  
-  private class PhenotypesTableFormat implements WritableTableFormat<Phenotype>, AdvancedTableFormat<Phenotype> {
-    
-    public boolean isEditable(Phenotype phenotype, int column) {
-      return true;
+    private void stateSelectionDidChange() {
+        final String unselectedTitle = "Phenotypes";
+        final String selectedPrefix = "Phenotypes for State: ";
+        final List<State> states = this.getController().getCurrentStatesSelectionModel().getSelected();
+        if (states.isEmpty()) {
+            this.updatePanelTitle(unselectedTitle);
+        } else {
+            this.updatePanelTitle(selectedPrefix + states.get(0));
+        }
+        this.updateButtonStates();
     }
 
-    public Phenotype setColumnValue(Phenotype phenotype, Object editedValue, int column) {
-      switch (column) {
-      case 0: phenotype.setEntity((OBOClass)editedValue); break;
-      case 1: phenotype.setQuality((OBOClass)editedValue); break;
-      case 2: phenotype.setRelatedEntity((OBOClass)editedValue); break;
-      case 3: phenotype.setCount((Integer)editedValue); break;
-      case 4: phenotype.setMeasurement((Float)editedValue); break;
-      case 5: phenotype.setUnit((OBOClass)editedValue); break;
-      case 6: phenotype.setComment(editedValue.toString()); break;
-      }
-      return phenotype;
+    private void phenotypeSelectionDidChange() {
+        this.updateButtonStates();
     }
 
-    public int getColumnCount() {
-      return 7;
+    private void updateButtonStates() {
+        this.addPhenotypeButton.setEnabled(this.getSelectedState() != null);
+        this.deletePhenotypeButton.setEnabled(this.getSelectedPhenotype() != null);
     }
 
-    public String getColumnName(int column) {
-      switch (column) {
-      case 0: return "Entity";
-      case 1: return "Quality";
-      case 2: return "Related Entity";
-      case 3: return "Count";
-      case 4: return "Measurement";
-      case 5: return "Unit";
-      case 6: return "Comment";
-      default: return null;
-      }
+    private void runPostCompositionForTermAtPoint(Point p) {
+        final int column = this.phenotypesTable.getTableHeader().columnAtPoint(p);
+        final int row = this.phenotypesTable.rowAtPoint(p);
+        if (!this.tableFormat.getColumnClass(column).equals(OBOObject.class)) return;
+        final Phenotype phenotype = this.getController().getPhenotypesForCurrentStateSelection().get(row);
+        final OBOClass term = (OBOClass)(this.tableFormat.getColumnValue(phenotype, column));
+        final PostCompositionEditor pce = new PostCompositionEditor(this.getController(), this.tableFormat.getColumnTermSet(column));
+        pce.setTerm(term);
+        final int result = pce.runPostCompositionDialog();
+        if (result == JOptionPane.OK_OPTION) {
+            this.tableFormat.setColumnValue(phenotype, pce.getTerm(), column);
+        }
     }
-    
-    public TermSet getColumnTermSet(int column) {
-      switch (column) {
-      case 0: return getController().getOntologyController().getEntityTermSet();
-      case 1: return getController().getOntologyController().getQualityTermSet();
-      case 2: return getController().getOntologyController().getRelatedEntityTermSet();
-      case 3: return null;
-      case 4: return null;
-      case 5: return getController().getOntologyController().getUnitTermSet();
-      case 6: return null;
-      default: return null;
-      }
+
+    private JToolBar createToolBar() {
+        final JToolBar toolBar = new JToolBar();
+        this.addPhenotypeButton = new JButton(new AbstractAction(null, new ImageIcon(this.getClass().getResource("/org/phenoscape/view/images/list-add.png"))) {
+            public void actionPerformed(ActionEvent e) {
+                addPhenotype();
+            }
+        });
+        this.addPhenotypeButton.setToolTipText("Add Phenotype");
+        toolBar.add(this.addPhenotypeButton);
+        this.deletePhenotypeButton = new JButton(new AbstractAction(null, new ImageIcon(this.getClass().getResource("/org/phenoscape/view/images/list-remove.png"))) {
+            public void actionPerformed(ActionEvent e) {
+                deleteSelectedPhenotype();
+            }
+        });
+        this.deletePhenotypeButton.setToolTipText("Delete Phenotype");
+        toolBar.add(this.deletePhenotypeButton);
+        toolBar.setFloatable(false);
+        return toolBar;
     }
-    
-    public TableCellEditor getColumnEditor(int column) {
-      switch (column) {
-      case 0: return createAutocompleteEditor(this.getColumnTermSet(column).getTerms());
-      case 1: return createAutocompleteEditor(this.getColumnTermSet(column).getTerms());
-      case 2: return createAutocompleteEditor(this.getColumnTermSet(column).getTerms());
-      case 3: return null;
-      case 4: return null;
-      case 5: return createAutocompleteEditor(this.getColumnTermSet(column).getTerms());
-      case 6: return null;
-      default: return null;
-      }
+
+    private JPopupMenu createTablePopupMenu() {
+        final JPopupMenu menu = new JPopupMenu();
+        menu.add(new AbstractAction("Edit Post-composed Term") {
+            public void actionPerformed(ActionEvent e) {
+                runPostCompositionForTermAtPoint(tablePopup.getLocation());
+            }
+        });
+        return menu;
     }
 
-    public Object getColumnValue(Phenotype phenotype, int column) {
-      switch (column) {
-      case 0: return phenotype.getEntity();
-      case 1: return phenotype.getQuality();
-      case 2: return phenotype.getRelatedEntity();
-      case 3: return phenotype.getCount();
-      case 4: return phenotype.getMeasurement();
-      case 5: return phenotype.getUnit();
-      case 6: return phenotype.getComment();
-      default: return null;
-      }
+    private class PhenotypesTableFormat implements WritableTableFormat<Phenotype>, AdvancedTableFormat<Phenotype> {
+
+        public boolean isEditable(Phenotype phenotype, int column) {
+            return true;
+        }
+
+        public Phenotype setColumnValue(Phenotype phenotype, Object editedValue, int column) {
+            switch (column) {
+            case 0: phenotype.setEntity((OBOClass)editedValue); break;
+            case 1: phenotype.setQuality((OBOClass)editedValue); break;
+            case 2: phenotype.setRelatedEntity((OBOClass)editedValue); break;
+            case 3: phenotype.setCount((Integer)editedValue); break;
+            case 4: phenotype.setMeasurement((Float)editedValue); break;
+            case 5: phenotype.setUnit((OBOClass)editedValue); break;
+            case 6: phenotype.setComment(editedValue.toString()); break;
+            }
+            return phenotype;
+        }
+
+        public int getColumnCount() {
+            return 7;
+        }
+
+        public String getColumnName(int column) {
+            switch (column) {
+            case 0: return "Entity";
+            case 1: return "Quality";
+            case 2: return "Related Entity";
+            case 3: return "Count";
+            case 4: return "Measurement";
+            case 5: return "Unit";
+            case 6: return "Comment";
+            default: return null;
+            }
+        }
+
+        public TermSet getColumnTermSet(int column) {
+            switch (column) {
+            case 0: return getController().getOntologyController().getEntityTermSet();
+            case 1: return getController().getOntologyController().getQualityTermSet();
+            case 2: return getController().getOntologyController().getRelatedEntityTermSet();
+            case 3: return null;
+            case 4: return null;
+            case 5: return getController().getOntologyController().getUnitTermSet();
+            case 6: return null;
+            default: return null;
+            }
+        }
+
+        public TableCellEditor getColumnEditor(int column) {
+            switch (column) {
+            case 0: return createAutocompleteEditor(this.getColumnTermSet(column).getTerms());
+            case 1: return createAutocompleteEditor(this.getColumnTermSet(column).getTerms());
+            case 2: return createAutocompleteEditor(this.getColumnTermSet(column).getTerms());
+            case 3: return null;
+            case 4: return null;
+            case 5: return createAutocompleteEditor(this.getColumnTermSet(column).getTerms());
+            case 6: return null;
+            default: return null;
+            }
+        }
+
+        public Object getColumnValue(Phenotype phenotype, int column) {
+            switch (column) {
+            case 0: return phenotype.getEntity();
+            case 1: return phenotype.getQuality();
+            case 2: return phenotype.getRelatedEntity();
+            case 3: return phenotype.getCount();
+            case 4: return phenotype.getMeasurement();
+            case 5: return phenotype.getUnit();
+            case 6: return phenotype.getComment();
+            default: return null;
+            }
+        }
+
+        public Class<?> getColumnClass(int column) {
+            switch (column) {
+            case 0: return OBOObject.class;
+            case 1: return OBOObject.class;
+            case 2: return OBOObject.class;
+            case 3: return Integer.class;
+            case 4: return Float.class;
+            case 5: return OBOObject.class;
+            case 6: return String.class;
+            default: return null;
+            }
+        }
+
+        public Comparator<?> getColumnComparator(int column) {
+            switch (column) {
+            case 0: return GlazedLists.comparableComparator();
+            case 1: return GlazedLists.comparableComparator();
+            case 2: return GlazedLists.comparableComparator();
+            case 3: return GlazedLists.comparableComparator();
+            case 4: return GlazedLists.comparableComparator();
+            case 5: return GlazedLists.comparableComparator();
+            case 6: return Strings.getNaturalComparator();
+            default: return null;
+            }
+        }
+
     }
 
-    public Class<?> getColumnClass(int column) {
-      switch (column) {
-      case 0: return OBOObject.class;
-      case 1: return OBOObject.class;
-      case 2: return OBOObject.class;
-      case 3: return Integer.class;
-      case 4: return Float.class;
-      case 5: return OBOObject.class;
-      case 6: return String.class;
-      default: return null;
-      }
+    private class StateSelectionListener implements ListSelectionListener {
+
+        public StateSelectionListener() {
+            stateSelectionDidChange();
+        }
+
+        public void valueChanged(ListSelectionEvent e) {
+            stateSelectionDidChange();      
+        }
+
     }
 
-    public Comparator<?> getColumnComparator(int column) {
-      switch (column) {
-      case 0: return GlazedLists.comparableComparator();
-      case 1: return GlazedLists.comparableComparator();
-      case 2: return GlazedLists.comparableComparator();
-      case 3: return GlazedLists.comparableComparator();
-      case 4: return GlazedLists.comparableComparator();
-      case 5: return GlazedLists.comparableComparator();
-      case 6: return Strings.getNaturalComparator();
-      default: return null;
-      }
+    private class PhenotypeSelectionListener implements ListSelectionListener {
+
+        public PhenotypeSelectionListener() {
+            phenotypeSelectionDidChange();
+        }
+
+        public void valueChanged(ListSelectionEvent e) {
+            phenotypeSelectionDidChange();      
+        }
+
     }
-    
-  }
-  
-  private class StateSelectionListener implements ListSelectionListener {
-    
-    public StateSelectionListener() {
-      stateSelectionDidChange();
-    }
 
-    public void valueChanged(ListSelectionEvent e) {
-      stateSelectionDidChange();      
+    @SuppressWarnings("unused")
+    private Logger log() {
+        return Logger.getLogger(this.getClass());
     }
-    
-  }
-  
-  private class PhenotypeSelectionListener implements ListSelectionListener {
-    
-    public PhenotypeSelectionListener() {
-      phenotypeSelectionDidChange();
-    }
 
-    public void valueChanged(ListSelectionEvent e) {
-      phenotypeSelectionDidChange();      
-    }
-    
-  }
-    
-  @SuppressWarnings("unused")
-private Logger log() {
-    return Logger.getLogger(this.getClass());
-  }
-  
 }


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