2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
25 import java.awt.event.*;
26 import java.beans.PropertyChangeEvent;
27 import java.beans.PropertyChangeListener;
30 import javax.swing.event.*;
31 import javax.swing.table.*;
33 import jalview.datamodel.*;
36 public class FeatureSettings
39 DasSourceBrowser dassourceBrowser;
40 jalview.io.DasSequenceFeatureFetcher dasFeatureFetcher;
41 JPanel settingsPane = new JPanel();
42 JPanel dasSettingsPane = new JPanel();
44 final FeatureRenderer fr;
45 public final AlignFrame af;
46 Object[][] originalData;
47 final JInternalFrame frame;
48 JScrollPane scrollPane = new JScrollPane();
51 JSlider transparency = new JSlider();
53 JPanel transPanel = new JPanel(new FlowLayout());
55 public FeatureSettings(AlignFrame af)
58 fr = af.getFeatureRenderer();
60 transparency.setMaximum(100 - (int) (fr.transparency * 100));
72 table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
73 table.setFont(new Font("Verdana", Font.PLAIN, 12));
74 table.setDefaultRenderer(Color.class,
77 table.setDefaultEditor(Color.class,
80 table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
82 table.addMouseListener(new MouseAdapter()
84 public void mousePressed(MouseEvent evt)
86 selectedRow = table.rowAtPoint(evt.getPoint());
90 table.addMouseMotionListener(new MouseMotionAdapter()
92 public void mouseDragged(MouseEvent evt)
94 int newRow = table.rowAtPoint(evt.getPoint());
95 if (newRow != selectedRow
99 Object[] temp = new Object[3];
100 temp[0] = table.getValueAt(selectedRow, 0);
101 temp[1] = table.getValueAt(selectedRow, 1);
102 temp[2] = table.getValueAt(selectedRow, 2);
104 table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);
105 table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);
106 table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);
108 table.setValueAt(temp[0], newRow, 0);
109 table.setValueAt(temp[1], newRow, 1);
110 table.setValueAt(temp[2], newRow, 2);
112 selectedRow = newRow;
117 scrollPane.setViewportView(table);
119 dassourceBrowser = new DasSourceBrowser();
120 dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
122 if (af.getViewport().featuresDisplayed == null || fr.renderOrder == null)
124 fr.findAllFeatures(true); // display everything!
128 final PropertyChangeListener change;
129 final FeatureSettings fs=this;
130 fr.addPropertyChangeListener(change=new PropertyChangeListener() {
131 public void propertyChange(PropertyChangeEvent evt)
133 if (!fs.resettingTable && !fs.handlingUpdate) {
134 fs.handlingUpdate=true;
135 fs.resetTable(new String[] {}); // groups may be added
136 fs.handlingUpdate=false;
142 frame = new JInternalFrame();
143 frame.setContentPane(this);
144 Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
145 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
147 public void internalFrameClosed(
148 javax.swing.event.InternalFrameEvent evt)
150 fr.removePropertyChangeListener(change);
154 frame.setLayer(JLayeredPane.PALETTE_LAYER);
157 * true when Feature Settings are updating from feature renderer
159 private boolean handlingUpdate=false;
162 * contains a float[3] for each feature type string. created by setTableData
164 Hashtable typeWidth=null;
165 synchronized public void setTableData()
167 if (fr.featureGroups == null)
169 fr.featureGroups = new Hashtable();
171 Vector allFeatures = new Vector();
172 Vector allGroups = new Vector();
173 SequenceFeature[] tmpfeatures;
175 for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
177 if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().
178 getSequenceFeatures() == null)
183 tmpfeatures = af.getViewport().alignment.getSequenceAt(i).
184 getDatasetSequence().getSequenceFeatures();
187 while (index < tmpfeatures.length)
189 if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
195 if (tmpfeatures[index].getFeatureGroup() != null)
197 group = tmpfeatures[index].featureGroup;
198 if (!allGroups.contains(group))
200 allGroups.addElement(group);
203 if (fr.featureGroups.containsKey(group))
205 visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
207 visible=true; //initGroups || fr.av.featuresDisplayed.containsKey(tmpfeatures[index].getType());
210 if (groupPanel == null)
212 groupPanel = new JPanel();
215 boolean alreadyAdded = false;
216 for (int g = 0; g < groupPanel.getComponentCount(); g++)
218 if ( ( (JCheckBox) groupPanel.getComponent(g))
219 .getText().equals(group))
232 fr.featureGroups.put(group, new Boolean(visible));
233 final String grp = group;
234 final JCheckBox check = new JCheckBox(group, visible);
235 check.setFont(new Font("Serif", Font.BOLD, 12));
236 check.addItemListener(new ItemListener()
238 public void itemStateChanged(ItemEvent evt)
240 fr.featureGroups.put(check.getText(),
241 new Boolean(check.isSelected()));
242 af.alignPanel.seqPanel.seqCanvas.repaint();
243 if (af.alignPanel.overviewPanel != null)
245 af.alignPanel.overviewPanel.updateOverviewImage();
248 resetTable(new String[] { grp } );
251 groupPanel.add(check);
255 if (!allFeatures.contains(tmpfeatures[index].getType()))
257 allFeatures.addElement(tmpfeatures[index].getType());
267 boolean resettingTable=false;
268 void resetTable(String[] groupChanged)
271 typeWidth=new Hashtable();
272 Vector groupchanged = new Vector();
273 // TODO: change avWidth calculation to 'per-sequence' average and use long rather than float
274 float[] avWidth=null;
275 SequenceFeature[] tmpfeatures;
276 String group = null, type;
277 Vector visibleChecks = new Vector();
279 //Find out which features should be visible depending on which groups
280 //are selected / deselected
281 //and recompute average width ordering
282 for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
285 tmpfeatures = af.getViewport().alignment.getSequenceAt(i).
286 getDatasetSequence().getSequenceFeatures();
287 if (tmpfeatures == null)
293 while (index < tmpfeatures.length)
295 group = tmpfeatures[index].featureGroup;
297 if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
303 if (group == null || fr.featureGroups.get(group) == null ||
304 ( (Boolean) fr.featureGroups.get(group)).booleanValue())
306 type = tmpfeatures[index].getType();
307 if (!visibleChecks.contains(type))
309 visibleChecks.addElement(type);
312 if (!typeWidth.containsKey(tmpfeatures[index].getType())) {
313 typeWidth.put(tmpfeatures[index].getType(), avWidth=new float[3]);
315 avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType());
318 if (tmpfeatures[index].getBegin()>tmpfeatures[index].getEnd())
320 avWidth[1]+=1+tmpfeatures[index].getBegin()-tmpfeatures[index].getEnd();
322 avWidth[1]+=1+tmpfeatures[index].getEnd()-tmpfeatures[index].getBegin();
328 int fSize = visibleChecks.size();
329 Object[][] data = new Object[fSize][3];
332 if (fr.renderOrder != null)
335 fr.findAllFeatures(groupChanged!=null); // prod to update colourschemes. but don't affect display
336 //First add the checks in the previous render order,
337 //in case the window has been closed and reopened
338 for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)
340 type = fr.renderOrder[ro];
342 if (!visibleChecks.contains(type))
347 data[dataIndex][0] = type;
348 data[dataIndex][1] = fr.getColour(type);
349 data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.containsKey(type));
351 visibleChecks.removeElement(type);
355 fSize = visibleChecks.size();
356 for (int i = 0; i < fSize; i++)
358 //These must be extra features belonging to the group
359 //which was just selected
360 type = visibleChecks.elementAt(i).toString();
361 data[dataIndex][0] = type;
363 data[dataIndex][1] = fr.getColour(type);
364 if (data[dataIndex][1] == null)
366 //"Colour has been updated in another view!!"
367 fr.renderOrder = null;
371 data[dataIndex][2] = new Boolean(true);
375 if (originalData == null)
377 originalData = new Object[data.length][3];
378 System.arraycopy(data, 0, originalData, 0, data.length);
381 table.setModel(new FeatureTableModel(data));
382 table.getColumnModel().getColumn(0).setPreferredWidth(200);
384 if (groupPanel != null)
386 groupPanel.setLayout(
387 new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
389 groupPanel.validate();
390 bigPanel.add(groupPanel, BorderLayout.NORTH);
393 updateFeatureRenderer(data, groupChanged!=null);
394 resettingTable=false;
397 * reorder data based on the featureRenderers global priority list.
400 private void ensureOrder(Object[][] data)
403 float[] order = new float[data.length];
404 for (int i=0;i<order.length; i++)
406 order[i] = fr.getOrder(data[i][0].toString());
408 order[i] = fr.setOrder(data[i][0].toString(), i/order.length);
410 sort = sort || order[i-1]>order[i];
413 jalview.util.QuickSort.sort(order, data);
418 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
420 "LAST_DIRECTORY"), new String[]
423 {"Sequence Feature Colours"}, "Sequence Feature Colours");
424 chooser.setFileView(new jalview.io.JalviewFileView());
425 chooser.setDialogTitle("Load Feature Colours");
426 chooser.setToolTipText("Load");
428 int value = chooser.showOpenDialog(this);
430 if (value == JalviewFileChooser.APPROVE_OPTION)
432 File file = chooser.getSelectedFile();
436 InputStreamReader in = new InputStreamReader(new FileInputStream(
439 jalview.binding.JalviewUserColours jucs = new jalview.binding.
440 JalviewUserColours();
441 jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
443 for (int i = jucs.getColourCount()-1; i >=0; i--)
446 fr.setColour(name=jucs.getColour(i).getName(),
447 new Color(Integer.parseInt(jucs.getColour(i).getRGB(),
449 fr.setOrder(name,(i==0) ? 0 : i/jucs.getColourCount());
453 Object[][] data=((FeatureTableModel) table.getModel()).getData();
455 updateFeatureRenderer(data,false);
461 System.out.println("Error loading User Colour File\n" + ex);
468 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
470 "LAST_DIRECTORY"), new String[]
473 {"Sequence Feature Colours"}, "Sequence Feature Colours");
474 chooser.setFileView(new jalview.io.JalviewFileView());
475 chooser.setDialogTitle("Save Feature Colour Scheme");
476 chooser.setToolTipText("Save");
478 int value = chooser.showSaveDialog(this);
480 if (value == JalviewFileChooser.APPROVE_OPTION)
482 String choice = chooser.getSelectedFile().getPath();
483 jalview.binding.JalviewUserColours ucs = new jalview.binding.
484 JalviewUserColours();
485 ucs.setSchemeName("Sequence Features");
488 PrintWriter out = new PrintWriter(new OutputStreamWriter(
489 new FileOutputStream(choice), "UTF-8"));
491 Enumeration e = fr.featureColours.keys();
492 float[] sortOrder = new float[fr.featureColours.size()];
493 String[] sortTypes = new String[fr.featureColours.size()];
495 while (e.hasMoreElements())
497 sortTypes[i] = e.nextElement().toString();
498 sortOrder[i] = fr.getOrder(sortTypes[i]);
501 jalview.util.QuickSort.sort(sortOrder, sortTypes);
503 for (i=0; i<sortTypes.length; i++) {
504 jalview.binding.Colour col = new jalview.binding.Colour();
505 col.setName(sortTypes[i]);
506 col.setRGB(jalview.util.Format.getHexString(
507 fr.getColour(col.getName())));
515 ex.printStackTrace();
520 public void invertSelection()
522 for (int i = 0; i < table.getRowCount(); i++)
524 Boolean value = (Boolean) table.getValueAt(i, 2);
527 new Boolean(!value.booleanValue()),
531 public void orderByAvWidth() {
532 if (table==null || table.getModel()==null)
534 Object[][] data = ((FeatureTableModel) table.getModel()).getData();
535 float[] width = new float[data.length];
539 for (int i=0;i<data.length;i++) {
540 awidth = (float[]) typeWidth.get(data[i][0]);
542 width[i] = awidth[1]/awidth[0];// *awidth[0]*awidth[2]; - better weight - but have to make per sequence, too (awidth[2])
543 //if (width[i]==1) // hack to distinguish single width sequences.
552 for (int i=0;i<width.length; i++) {
553 //awidth = (float[]) typeWidth.get(data[i][0]);
556 width[i] = fr.getOrder(data[i][0].toString());
559 width[i] = fr.setOrder(data[i][0].toString(), i/data.length);
562 width[i] /=max; // normalize
563 fr.setOrder(data[i][0].toString(), width[i]); // store for later
566 sort = sort || width[i-1]>width[i];
569 jalview.util.QuickSort.sort(width, data);
570 // update global priority order
572 updateFeatureRenderer(data,false);
579 frame.setClosed(true);
581 catch (Exception exe)
586 public void updateFeatureRenderer(Object[][] data)
588 updateFeatureRenderer(data, true);
590 private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
592 fr.setFeaturePriority(data, visibleNew);
593 af.alignPanel.paintAlignment(true);
595 if (af.alignPanel.overviewPanel != null)
597 af.alignPanel.overviewPanel.updateOverviewImage();
601 int selectedRow = -1;
602 JTabbedPane tabbedPane = new JTabbedPane();
603 BorderLayout borderLayout1 = new BorderLayout();
604 BorderLayout borderLayout2 = new BorderLayout();
605 BorderLayout borderLayout3 = new BorderLayout();
606 JPanel bigPanel = new JPanel();
607 BorderLayout borderLayout4 = new BorderLayout();
608 JButton invert = new JButton();
609 JPanel buttonPanel = new JPanel();
610 JButton cancel = new JButton();
611 JButton ok = new JButton();
612 JButton loadColours = new JButton();
613 JButton saveColours = new JButton();
614 JPanel dasButtonPanel = new JPanel();
615 JButton fetchDAS = new JButton();
616 JButton saveDAS = new JButton();
617 JButton cancelDAS = new JButton();
618 JButton optimizeOrder = new JButton();
619 JPanel transbuttons = new JPanel(new BorderLayout());
620 private void jbInit()
623 this.setLayout(borderLayout1);
624 settingsPane.setLayout(borderLayout2);
625 dasSettingsPane.setLayout(borderLayout3);
626 bigPanel.setLayout(borderLayout4);
627 invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
628 invert.setText("Invert Selection");
629 invert.addActionListener(new ActionListener()
631 public void actionPerformed(ActionEvent e)
636 optimizeOrder.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
637 optimizeOrder.setText("Optimise Order");
638 optimizeOrder.addActionListener(new ActionListener() {
639 public void actionPerformed(ActionEvent e) {
643 cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
644 cancel.setText("Cancel");
645 cancel.addActionListener(new ActionListener()
647 public void actionPerformed(ActionEvent e)
649 updateFeatureRenderer(originalData);
653 ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
655 ok.addActionListener(new ActionListener()
657 public void actionPerformed(ActionEvent e)
662 loadColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
663 loadColours.setText("Load Colours");
664 loadColours.addActionListener(new ActionListener()
666 public void actionPerformed(ActionEvent e)
671 saveColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
672 saveColours.setText("Save Colours");
673 saveColours.addActionListener(new ActionListener()
675 public void actionPerformed(ActionEvent e)
680 transparency.addChangeListener(new ChangeListener()
682 public void stateChanged(ChangeEvent evt)
684 fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);
685 af.alignPanel.paintAlignment(true);
689 transparency.setMaximum(70);
690 fetchDAS.setText("Fetch DAS Features");
691 fetchDAS.addActionListener(new ActionListener()
693 public void actionPerformed(ActionEvent e)
695 fetchDAS_actionPerformed(e);
698 saveDAS.setText("Save as default");
699 saveDAS.addActionListener(new ActionListener()
701 public void actionPerformed(ActionEvent e)
703 saveDAS_actionPerformed(e);
706 dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
707 dasSettingsPane.setBorder(null);
708 cancelDAS.setEnabled(false);
709 cancelDAS.setText("Cancel Fetch");
710 cancelDAS.addActionListener(new ActionListener()
712 public void actionPerformed(ActionEvent e)
714 cancelDAS_actionPerformed(e);
717 this.add(tabbedPane, java.awt.BorderLayout.CENTER);
718 tabbedPane.addTab("Feature Settings", settingsPane);
719 tabbedPane.addTab("DAS Settings", dasSettingsPane);
720 bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
721 transPanel.add(transparency);
722 transbuttons.add(invert, java.awt.BorderLayout.NORTH);
723 transbuttons.add(optimizeOrder,java.awt.BorderLayout.SOUTH);
724 transPanel.add(transbuttons);
726 buttonPanel.add(cancel);
727 buttonPanel.add(loadColours);
728 buttonPanel.add(saveColours);
729 bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER);
730 dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH);
731 dasButtonPanel.add(fetchDAS);
732 dasButtonPanel.add(cancelDAS);
733 dasButtonPanel.add(saveDAS);
734 settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER);
735 settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH);
738 public void fetchDAS_actionPerformed(ActionEvent e)
740 fetchDAS.setEnabled(false);
741 cancelDAS.setEnabled(true);
742 Vector selectedSources = dassourceBrowser.getSelectedSources();
744 SequenceI[] dataset, seqs;
747 if (af.getViewport().getSelectionGroup() != null
748 && af.getViewport().getSelectionGroup().getSize() > 0)
750 iSize = af.getViewport().getSelectionGroup().getSize();
751 dataset = new SequenceI[iSize];
752 seqs = af.getViewport().getSelectionGroup().
754 af.getViewport().getAlignment());
758 iSize = af.getViewport().getAlignment().getHeight();
759 seqs = af.getViewport().getAlignment().getSequencesArray();
762 dataset = new SequenceI[iSize];
763 for (int i = 0; i < iSize; i++)
765 dataset[i] = seqs[i].getDatasetSequence();
769 new jalview.io.DasSequenceFeatureFetcher(
773 cancelDAS.setEnabled(true);
774 af.getViewport().setShowSequenceFeatures(true);
775 af.showSeqFeatures.setSelected(true);
778 public void saveDAS_actionPerformed(ActionEvent e)
780 dassourceBrowser.saveProperties(jalview.bin.Cache.applicationProperties);
783 public void complete()
785 fetchDAS.setEnabled(true);
786 cancelDAS.setEnabled(false);
789 public void cancelDAS_actionPerformed(ActionEvent e)
791 dasFeatureFetcher.cancel();
792 fetchDAS.setEnabled(true);
793 cancelDAS.setEnabled(false);
796 /////////////////////////////////////////////////////////////////////////
797 // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
798 /////////////////////////////////////////////////////////////////////////
799 class FeatureTableModel
800 extends AbstractTableModel
802 FeatureTableModel(Object[][] data)
807 private String[] columnNames =
809 "Feature Type", "Colour", "Display"};
810 private Object[][] data;
812 public Object[][] getData()
817 public void setData(Object[][] data)
822 public int getColumnCount()
824 return columnNames.length;
827 public Object[] getRow(int row)
832 public int getRowCount()
837 public String getColumnName(int col)
839 return columnNames[col];
842 public Object getValueAt(int row, int col)
844 return data[row][col];
847 public Class getColumnClass(int c)
849 return getValueAt(0, c).getClass();
852 public boolean isCellEditable(int row, int col)
854 return col == 0 ? false : true;
857 public void setValueAt(Object value, int row, int col)
859 data[row][col] = value;
860 fireTableCellUpdated(row, col);
861 updateFeatureRenderer(data);
867 extends JLabel implements TableCellRenderer
869 javax.swing.border.Border unselectedBorder = null;
870 javax.swing.border.Border selectedBorder = null;
872 public ColorRenderer()
874 setOpaque(true); //MUST do this for background to show up.
877 public Component getTableCellRendererComponent(
878 JTable table, Object color,
879 boolean isSelected, boolean hasFocus,
882 Color newColor = (Color) color;
883 setBackground(newColor);
886 if (selectedBorder == null)
888 selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
889 table.getSelectionBackground());
891 setBorder(selectedBorder);
895 if (unselectedBorder == null)
897 unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
898 table.getBackground());
900 setBorder(unselectedBorder);
903 setToolTipText("RGB value: " + newColor.getRed() + ", "
904 + newColor.getGreen() + ", "
905 + newColor.getBlue());
912 extends AbstractCellEditor implements TableCellEditor,
917 JColorChooser colorChooser;
919 protected static final String EDIT = "edit";
923 //Set up the editor (from the table's point of view),
925 //This button brings up the color chooser dialog,
926 //which is the editor from the user's point of view.
927 button = new JButton();
928 button.setActionCommand(EDIT);
929 button.addActionListener(this);
930 button.setBorderPainted(false);
931 //Set up the dialog that the button brings up.
932 colorChooser = new JColorChooser();
933 dialog = JColorChooser.createDialog(button,
937 this, //OK button handler
938 null); //no CANCEL button handler
942 * Handles events from the editor button and from
943 * the dialog's OK button.
945 public void actionPerformed(ActionEvent e)
948 if (EDIT.equals(e.getActionCommand()))
950 //The user has clicked the cell, so
951 //bring up the dialog.
952 button.setBackground(currentColor);
953 colorChooser.setColor(currentColor);
954 dialog.setVisible(true);
956 //Make the renderer reappear.
957 fireEditingStopped();
961 { //User pressed dialog's "OK" button.
962 currentColor = colorChooser.getColor();
966 //Implement the one CellEditor method that AbstractCellEditor doesn't.
967 public Object getCellEditorValue()
972 //Implement the one method defined by TableCellEditor.
973 public Component getTableCellEditorComponent(JTable table,
979 currentColor = (Color) value;