X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=955684c7cd175bfe919052d3e63ea2a8f7f4e8fc;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=eb744544ea74f33a4f33f8ed75037db17453a67f;hpb=22b9e04a8351aef1cb23a66d898502601499b673;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index eb74454..955684c 100755 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -18,318 +18,381 @@ */ package jalview.gui; -import jalview.datamodel.*; -import javax.swing.*; -import javax.swing.event.*; -import java.awt.*; +import java.io.*; import java.util.*; -import javax.swing.BorderFactory; + +import java.awt.*; import java.awt.event.*; +import javax.swing.*; +import javax.swing.event.*; import javax.swing.table.*; -import java.io.*; -import jalview.io.JalviewFileChooser; -public class FeatureSettings extends JPanel +import jalview.datamodel.*; +import jalview.io.*; + +public class FeatureSettings + extends JPanel { + DasSourceBrowser dassourceBrowser; + jalview.io.DasSequenceFeatureFetcher dasFeatureFetcher; + JPanel settingsPane = new JPanel(); + JPanel dasSettingsPane = new JPanel(); final FeatureRenderer fr; - final AlignmentPanel ap; - final AlignViewport av; - Object [][] originalData; + public final AlignFrame af; + Object[][] originalData; final JInternalFrame frame; JScrollPane scrollPane = new JScrollPane(); JTable table; JPanel groupPanel; + JSlider transparency = new JSlider(); + + JPanel transPanel = new JPanel(new FlowLayout()); - public FeatureSettings(AlignViewport av, final AlignmentPanel ap) + public FeatureSettings(AlignFrame af) { - this.ap = ap; - this.av = av; - fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); - av.alignment.getSequences(); - frame = new JInternalFrame(); - frame.setContentPane(this); - Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 300); + this.af = af; + fr = af.getFeatureRenderer(); - setTableData(); + transparency.setMaximum(100 - (int) (fr.transparency * 100)); - final JSlider transparency = new JSlider(0, 70, 0); - transparency.addChangeListener(new ChangeListener() + try { - public void stateChanged(ChangeEvent evt) - { - fr.setTransparency( (float) (100 - transparency.getValue()) / 100f); - ap.repaint(); - } - }); + jbInit(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } - JPanel transPanel = new JPanel(new FlowLayout()); - transPanel.add(new JLabel("Transparency")); - transPanel.add(transparency); + table = new JTable(); + table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12)); + table.setFont(new Font("Verdana", Font.PLAIN, 12)); + table.setDefaultRenderer(Color.class, + new ColorRenderer()); + + table.setDefaultEditor(Color.class, + new ColorEditor()); - ////////////////////////////////////////////// - //We're going to need those OK cancel buttons - JPanel buttonPanel = new JPanel(new FlowLayout()); - JButton button = new JButton("OK"); - button.addActionListener(new ActionListener() + table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); + + table.addMouseListener(new MouseAdapter() { - public void actionPerformed(ActionEvent evt) + public void mousePressed(MouseEvent evt) { - try - { - frame.setClosed(true); - } - catch (Exception exe) - {} + selectedRow = table.rowAtPoint(evt.getPoint()); } }); - buttonPanel.add(button); - button = new JButton("Cancel"); - button.addActionListener(new ActionListener() + + table.addMouseMotionListener(new MouseMotionAdapter() { - public void actionPerformed(ActionEvent evt) + public void mouseDragged(MouseEvent evt) { - try + int newRow = table.rowAtPoint(evt.getPoint()); + if (newRow != selectedRow + && selectedRow != -1 + && newRow != -1) { - updateFeatureRenderer(originalData); - frame.setClosed(true); + Object[] temp = new Object[3]; + temp[0] = table.getValueAt(selectedRow, 0); + temp[1] = table.getValueAt(selectedRow, 1); + temp[2] = table.getValueAt(selectedRow, 2); + + table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0); + table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1); + table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2); + + table.setValueAt(temp[0], newRow, 0); + table.setValueAt(temp[1], newRow, 1); + table.setValueAt(temp[2], newRow, 2); + + selectedRow = newRow; } - catch (Exception exe) - {} } }); - buttonPanel.add(button); - button = new JButton("Load Colours"); - button.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent evt) - { - load(); - } - }); - buttonPanel.add(button); - button = new JButton("Save Colours"); - button.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent evt) - { - save(); - } - }); - buttonPanel.add(button); + scrollPane.setViewportView(table); - this.setLayout(new BorderLayout()); - JPanel bigPanel = new JPanel(new BorderLayout()); - bigPanel.add(transPanel, BorderLayout.SOUTH); - bigPanel.add(scrollPane, BorderLayout.CENTER); - if(groupPanel!=null) - bigPanel.add(groupPanel, BorderLayout.NORTH); + dassourceBrowser = new DasSourceBrowser(); + dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER); - add(bigPanel, BorderLayout.CENTER); - add(buttonPanel, BorderLayout.SOUTH); + if (af.getViewport().featuresDisplayed == null || fr.renderOrder == null) + { + fr.findAllFeatures(); + } + setTableData(); + frame = new JInternalFrame(); + frame.setContentPane(this); + Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450); + frame.setLayer(JLayeredPane.PALETTE_LAYER); } - void setTableData() + synchronized public void setTableData() { if (fr.featureGroups == null) + { fr.featureGroups = new Hashtable(); - else - fr.featureGroups.clear(); + } Vector allFeatures = new Vector(); - Vector features; - Enumeration e; - SequenceFeature sf; + Vector allGroups = new Vector(); + SequenceFeature[] tmpfeatures; + String group; - for (int i = 0; i < av.alignment.getHeight(); i++) - { - features = av.alignment.getSequenceAt(i).getDatasetSequence(). - getSequenceFeatures(); - if (features == null) - continue; - - e = features.elements(); - while (e.hasMoreElements()) - { - sf = (SequenceFeature) e.nextElement(); - if(sf.getFeatureGroup()!=null - && !fr.featureGroups.containsKey(sf.getFeatureGroup())) - { - fr.featureGroups.put(sf.getFeatureGroup(), new Boolean(true)); - if(groupPanel==null) - groupPanel = new JPanel(); - - final JCheckBox check = new JCheckBox(sf.getFeatureGroup(), true); - check.setFont(new Font("Serif", Font.BOLD, 12)); - check.addItemListener(new ItemListener() + for (int i = 0; i < af.getViewport().alignment.getHeight(); i++) + { + if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence(). + getSequenceFeatures() == null) + { + continue; + } + + tmpfeatures = af.getViewport().alignment.getSequenceAt(i). + getDatasetSequence().getSequenceFeatures(); + + int index = 0; + while (index < tmpfeatures.length) + { + if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0) + { + index++; + continue; + } + + if (tmpfeatures[index].getFeatureGroup() != null) + { + group = tmpfeatures[index].featureGroup; + if (!allGroups.contains(group)) + { + allGroups.addElement(group); + + boolean visible = true; + if (fr.featureGroups.containsKey(group)) + { + visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue(); + } + + if (groupPanel == null) + { + groupPanel = new JPanel(); + } + + boolean alreadyAdded = false; + for (int g = 0; g < groupPanel.getComponentCount(); g++) + { + if ( ( (JCheckBox) groupPanel.getComponent(g)) + .getText().equals(group)) { - public void itemStateChanged(ItemEvent evt) - { - if (fr.featureGroups.containsKey(check.getText())) - { - fr.featureGroups.put(check.getText(), - new Boolean(check.isSelected())); - ap.seqPanel.seqCanvas.repaint(); - if (ap.overviewPanel != null) - ap.overviewPanel.updateOverviewImage(); - } + alreadyAdded = true; + break; + } + } + if (alreadyAdded) + { + continue; + } + + fr.featureGroups.put(group, new Boolean(visible)); + + final JCheckBox check = new JCheckBox(group, visible); + check.setFont(new Font("Serif", Font.BOLD, 12)); + check.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent evt) + { + fr.featureGroups.put(check.getText(), + new Boolean(check.isSelected())); + af.alignPanel.seqPanel.seqCanvas.repaint(); + if (af.alignPanel.overviewPanel != null) + { + af.alignPanel.overviewPanel.updateOverviewImage(); } - }); - groupPanel.add(check); - } - if (!allFeatures.contains(sf.getType())) - { - allFeatures.addElement(sf.getType()); + + resetTable(true); + } + }); + groupPanel.add(check); + } + } + + if (!allFeatures.contains(tmpfeatures[index].getType())) + { + allFeatures.addElement(tmpfeatures[index].getType()); + } + index++; } } + + resetTable(false); + + validate(); } - if(allFeatures.size()<1) - { - try - { frame.setClosed(true); } - catch (Exception ex){} - JOptionPane.showInternalMessageDialog( - Desktop.desktop, "No features have been added to this alignment!", - "No Sequence Features", JOptionPane.WARNING_MESSAGE); + void resetTable(boolean groupsChanged) + { + SequenceFeature[] tmpfeatures; + String group = null, type; + Vector visibleChecks = new Vector(); - return; - } + //Find out which features should be visible depending on which groups + //are selected / deselected + for (int i = 0; i < af.getViewport().alignment.getHeight(); i++) + { - int fSize = allFeatures.size(); + tmpfeatures = af.getViewport().alignment.getSequenceAt(i). + getDatasetSequence().getSequenceFeatures(); + if (tmpfeatures == null) + { + continue; + } - String type; - boolean originalExists = false; - if(originalData!=null) - originalExists = true; - else - originalData = new Object[fSize][3]; + int index = 0; + while (index < tmpfeatures.length) + { + group = tmpfeatures[index].featureGroup; - Object [][] data = new Object[fSize][3]; - for(int i=0; i -1; ro--) { - originalData[i][0] = type; - originalData[i][1] = col; - if (fr.featuresDisplayed != null) - originalData[i][2] = new Boolean(fr.featuresDisplayed.contains(type)); - else - originalData[i][2] = new Boolean(true); + type = fr.renderOrder[ro]; + + if (!visibleChecks.contains(type)) + { + continue; + } + + data[dataIndex][0] = type; + data[dataIndex][1] = fr.getColour(type); + data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed. + containsKey(type)); + dataIndex++; + visibleChecks.removeElement(type); } } - //////////////////////////////////// - //Now build the table - table = new JTable(new FeatureTableModel(data)); - scrollPane.setViewportView(table); - table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12)); - table.setFont(new Font("Verdana", Font.PLAIN, 12)); - table.setDefaultRenderer(Color.class, - new ColorRenderer()); - table.setDefaultEditor(Color.class, - new ColorEditor()); + fSize = visibleChecks.size(); + for (int i = 0; i < fSize; i++) + { + //These must be extra features belonging to the group + //which was just selected + type = visibleChecks.elementAt(i).toString(); + data[dataIndex][0] = type; - table.getColumnModel().getColumn(0).setPreferredWidth(200); + data[dataIndex][1] = fr.getColour(type); + if (data[dataIndex][1] == null) + { + //"Colour has been updated in another view!!" + fr.renderOrder = null; + return; + } - table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); + data[dataIndex][2] = new Boolean(true); + dataIndex++; + } - table.addMouseListener(new MouseAdapter() - { - public void mousePressed(MouseEvent evt) - { - selectedRow = table.rowAtPoint(evt.getPoint()); - } - }); + if (originalData == null) + { + originalData = new Object[data.length][3]; + System.arraycopy(data, 0, originalData, 0, data.length); + } - table.addMouseMotionListener(new MouseMotionAdapter() - { - public void mouseDragged(MouseEvent evt) - { - int newRow = table.rowAtPoint(evt.getPoint()); - if(newRow!=selectedRow - && selectedRow!=-1 - && newRow!=-1) - { - Object[] temp = new Object[3]; - temp[0] = table.getValueAt(selectedRow, 0); - temp[1] = table.getValueAt(selectedRow, 1); - temp[2] = table.getValueAt(selectedRow, 2); + table.setModel(new FeatureTableModel(data)); + table.getColumnModel().getColumn(0).setPreferredWidth(200); - table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0); - table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1); - table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2); + if (groupPanel != null) + { + groupPanel.setLayout( + new GridLayout(fr.featureGroups.size() / 4 + 1, 4)); - table.setValueAt(temp[0], newRow, 0); - table.setValueAt(temp[1], newRow, 1); - table.setValueAt(temp[2], newRow, 2); + groupPanel.validate(); + bigPanel.add(groupPanel, BorderLayout.NORTH); + } - selectedRow = newRow; - } - } - }); + updateFeatureRenderer(data); } void load() { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty( - "LAST_DIRECTORY"), new String[] { "fc" }, - new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours"); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Load Feature Colours"); - chooser.setToolTipText("Load"); - - int value = chooser.showOpenDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - File file = chooser.getSelectedFile(); - - try - { - InputStreamReader in = new InputStreamReader(new FileInputStream( - file), "UTF-8"); - - jalview.binding.JalviewUserColours jucs = new jalview.binding. - JalviewUserColours(); - jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in); - - - for (int i = 0; i < jucs.getColourCount(); i++) - { - fr.setColour( jucs.getColour(i).getName(), - new Color(Integer.parseInt( jucs.getColour(i).getRGB(), 16))); - } - - setTableData(); - ap.repaint(); - } - catch (Exception ex) - { - System.out.println("Error loading User ColourFile\n" + ex); - } - } + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. + getProperty( + "LAST_DIRECTORY"), new String[] + {"fc"}, + new String[] + {"Sequence Feature Colours"}, "Sequence Feature Colours"); + chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setDialogTitle("Load Feature Colours"); + chooser.setToolTipText("Load"); + + int value = chooser.showOpenDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + File file = chooser.getSelectedFile(); + + try + { + InputStreamReader in = new InputStreamReader(new FileInputStream( + file), "UTF-8"); + + jalview.binding.JalviewUserColours jucs = new jalview.binding. + JalviewUserColours(); + jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in); + + for (int i = 0; i < jucs.getColourCount(); i++) + { + fr.setColour(jucs.getColour(i).getName(), + new Color(Integer.parseInt(jucs.getColour(i).getRGB(), + 16))); + } + + setTableData(); + af.alignPanel.repaint(); + } + catch (Exception ex) + { + System.out.println("Error loading User Colour File\n" + ex); + } + } } void save() { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty( - "LAST_DIRECTORY"), new String[] { "fc" }, - new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours"); + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. + getProperty( + "LAST_DIRECTORY"), new String[] + {"fc"}, + new String[] + {"Sequence Feature Colours"}, "Sequence Feature Colours"); chooser.setFileView(new jalview.io.JalviewFileView()); chooser.setDialogTitle("Save Feature Colour Scheme"); chooser.setToolTipText("Save"); @@ -338,48 +401,252 @@ public class FeatureSettings extends JPanel if (value == JalviewFileChooser.APPROVE_OPTION) { - String choice = chooser.getSelectedFile().getPath(); - jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours(); - ucs.setSchemeName("Sequence Features"); - try + String choice = chooser.getSelectedFile().getPath(); + jalview.binding.JalviewUserColours ucs = new jalview.binding. + JalviewUserColours(); + ucs.setSchemeName("Sequence Features"); + try + { + PrintWriter out = new PrintWriter(new OutputStreamWriter( + new FileOutputStream(choice), "UTF-8")); + + Enumeration e = fr.featureColours.keys(); + while (e.hasMoreElements()) { - PrintWriter out = new PrintWriter(new OutputStreamWriter( - new FileOutputStream(choice), "UTF-8")); + jalview.binding.Colour col = new jalview.binding.Colour(); + col.setName(e.nextElement().toString()); + col.setRGB(jalview.util.Format.getHexString( + fr.getColour(col.getName()))); + ucs.addColour(col); + } + + ucs.marshal(out); + out.close(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + } - Enumeration e = fr.featureColours.keys(); - while(e.hasMoreElements()) - { + public void invertSelection() + { + for (int i = 0; i < table.getRowCount(); i++) + { + Boolean value = (Boolean) table.getValueAt(i, 2); + table.setValueAt( + new Boolean(!value.booleanValue()), + i, 2); + } + } - jalview.binding.Colour col = new jalview.binding.Colour(); - col.setName(e.nextElement().toString()); - col.setRGB(jalview.util.Format.getHexString( - fr.getColour(col.getName()))); - ucs.addColour(col); - } + public void close() + { + try + { + frame.setClosed(true); + } + catch (Exception exe) + {} - ucs.marshal(out); - out.close(); - } - catch (Exception ex) - { - ex.printStackTrace(); - } + } + + public void updateFeatureRenderer(Object[][] data) + { + fr.setFeaturePriority(data); + af.alignPanel.repaint(); + + if (af.alignPanel.overviewPanel != null) + { + af.alignPanel.overviewPanel.updateOverviewImage(); } + } + int selectedRow = -1; + JTabbedPane tabbedPane = new JTabbedPane(); + BorderLayout borderLayout1 = new BorderLayout(); + BorderLayout borderLayout2 = new BorderLayout(); + BorderLayout borderLayout3 = new BorderLayout(); + JPanel bigPanel = new JPanel(); + BorderLayout borderLayout4 = new BorderLayout(); + JButton invert = new JButton(); + JPanel buttonPanel = new JPanel(); + JButton cancel = new JButton(); + JButton ok = new JButton(); + JButton loadColours = new JButton(); + JButton saveColours = new JButton(); + JPanel dasButtonPanel = new JPanel(); + JButton fetchDAS = new JButton(); + JButton saveDAS = new JButton(); + JButton cancelDAS = new JButton(); + private void jbInit() + throws Exception + { + this.setLayout(borderLayout1); + settingsPane.setLayout(borderLayout2); + dasSettingsPane.setLayout(borderLayout3); + bigPanel.setLayout(borderLayout4); + invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + invert.setText("Invert Selection"); + invert.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + invertSelection(); + } + }); + cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + cancel.setText("Cancel"); + cancel.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + updateFeatureRenderer(originalData); + close(); + } + }); + ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + ok.setText("OK"); + ok.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + close(); + } + }); + loadColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + loadColours.setText("Load Colours"); + loadColours.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + load(); + } + }); + saveColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + saveColours.setText("Save Colours"); + saveColours.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + save(); + } + }); + transparency.addChangeListener(new ChangeListener() + { + public void stateChanged(ChangeEvent evt) + { + fr.setTransparency( (float) (100 - transparency.getValue()) / 100f); + af.alignPanel.repaint(); + } + }); + + transparency.setMaximum(70); + fetchDAS.setText("Fetch DAS Features"); + fetchDAS.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + fetchDAS_actionPerformed(e); + } + }); + saveDAS.setText("Save as default"); + saveDAS.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + saveDAS_actionPerformed(e); + } + }); + dasButtonPanel.setBorder(BorderFactory.createEtchedBorder()); + dasSettingsPane.setBorder(null); + cancelDAS.setEnabled(false); + cancelDAS.setText("Cancel Fetch"); + cancelDAS.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + cancelDAS_actionPerformed(e); + } + }); + this.add(tabbedPane, java.awt.BorderLayout.CENTER); + tabbedPane.addTab("Feature Settings", settingsPane); + tabbedPane.addTab("DAS Settings", dasSettingsPane); + bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH); + transPanel.add(transparency); + transPanel.add(invert); + buttonPanel.add(ok); + buttonPanel.add(cancel); + buttonPanel.add(loadColours); + buttonPanel.add(saveColours); + bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER); + dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH); + dasButtonPanel.add(fetchDAS); + dasButtonPanel.add(cancelDAS); + dasButtonPanel.add(saveDAS); + settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER); + settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH); } - public void updateFeatureRenderer(Object [][] data) + public void fetchDAS_actionPerformed(ActionEvent e) { - fr.setFeaturePriority( data ); - ap.repaint(); + fetchDAS.setEnabled(false); + cancelDAS.setEnabled(true); + Vector selectedSources = dassourceBrowser.getSelectedSources(); + + SequenceI[] dataset, seqs; + int iSize; - if(ap.overviewPanel!=null) - ap.overviewPanel.updateOverviewImage(); + if (af.getViewport().getSelectionGroup() != null + && af.getViewport().getSelectionGroup().getSize() > 0) + { + iSize = af.getViewport().getSelectionGroup().getSize(); + dataset = new SequenceI[iSize]; + seqs = af.getViewport().getSelectionGroup(). + getSequencesInOrder( + af.getViewport().getAlignment()); + } + else + { + iSize = af.getViewport().getAlignment().getHeight(); + seqs = af.getViewport().getAlignment().getSequencesArray(); + } + + dataset = new SequenceI[iSize]; + for (int i = 0; i < iSize; i++) + { + dataset[i] = seqs[i].getDatasetSequence(); + } + + dasFeatureFetcher = + new jalview.io.DasSequenceFeatureFetcher( + dataset, + this, + selectedSources); + + af.getViewport().setShowSequenceFeatures(true); + af.showSeqFeatures.setSelected(true); } - int selectedRow =-1; + public void saveDAS_actionPerformed(ActionEvent e) + { + dassourceBrowser.saveProperties(jalview.bin.Cache.applicationProperties); + } + public void complete() + { + fetchDAS.setEnabled(true); + cancelDAS.setEnabled(false); + } + + public void cancelDAS_actionPerformed(ActionEvent e) + { + dasFeatureFetcher.cancel(); + fetchDAS.setEnabled(true); + cancelDAS.setEnabled(false); + } ///////////////////////////////////////////////////////////////////////// // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html @@ -392,148 +659,179 @@ public class FeatureSettings extends JPanel this.data = data; } - private String[] columnNames = {"Feature Type", "Colour","Display"}; - private Object[][] data; + private String[] columnNames = + { + "Feature Type", "Colour", "Display"}; + private Object[][] data; - public Object[][] getData() - { - return data; - } + public Object[][] getData() + { + return data; + } - public int getColumnCount() { - return columnNames.length; - } + public void setData(Object[][] data) + { + this.data = data; + } - public Object[] getRow(int row) - { - return data[row]; - } + public int getColumnCount() + { + return columnNames.length; + } - public int getRowCount() { - return data.length; - } + public Object[] getRow(int row) + { + return data[row]; + } - public String getColumnName(int col) { - return columnNames[col]; - } + public int getRowCount() + { + return data.length; + } - public Object getValueAt(int row, int col) { - return data[row][col]; - } + public String getColumnName(int col) + { + return columnNames[col]; + } - public Class getColumnClass(int c) { - return getValueAt(0, c).getClass(); - } + public Object getValueAt(int row, int col) + { + return data[row][col]; + } - public boolean isCellEditable(int row, int col) { - return col==0 ? false:true; - } + public Class getColumnClass(int c) + { + return getValueAt(0, c).getClass(); + } - public void setValueAt(Object value, int row, int col) { - data[row][col] = value; - fireTableCellUpdated(row, col); - updateFeatureRenderer(data); - } + public boolean isCellEditable(int row, int col) + { + return col == 0 ? false : true; + } + + public void setValueAt(Object value, int row, int col) + { + data[row][col] = value; + fireTableCellUpdated(row, col); + updateFeatureRenderer(data); + } + } + + class ColorRenderer + extends JLabel implements TableCellRenderer + { + javax.swing.border.Border unselectedBorder = null; + javax.swing.border.Border selectedBorder = null; + + public ColorRenderer() + { + setOpaque(true); //MUST do this for background to show up. + } + + public Component getTableCellRendererComponent( + JTable table, Object color, + boolean isSelected, boolean hasFocus, + int row, int column) + { + Color newColor = (Color) color; + setBackground(newColor); + if (isSelected) + { + if (selectedBorder == null) + { + selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, + table.getSelectionBackground()); + } + setBorder(selectedBorder); + } + else + { + if (unselectedBorder == null) + { + unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, + table.getBackground()); + } + setBorder(unselectedBorder); + } + + setToolTipText("RGB value: " + newColor.getRed() + ", " + + newColor.getGreen() + ", " + + newColor.getBlue()); + return this; } - class ColorRenderer extends JLabel - implements TableCellRenderer { - javax.swing.border.Border unselectedBorder = null; - javax.swing.border.Border selectedBorder = null; - - public ColorRenderer() { - setOpaque(true); //MUST do this for background to show up. - } - - public Component getTableCellRendererComponent( - JTable table, Object color, - boolean isSelected, boolean hasFocus, - int row, int column) { - Color newColor = (Color)color; - setBackground(newColor); - if (isSelected) { - if (selectedBorder == null) { - selectedBorder = BorderFactory.createMatteBorder(2,5,2,5, - table.getSelectionBackground()); - } - setBorder(selectedBorder); - } else { - if (unselectedBorder == null) { - unselectedBorder = BorderFactory.createMatteBorder(2,5,2,5, - table.getBackground()); - } - setBorder(unselectedBorder); - } - - setToolTipText("RGB value: " + newColor.getRed() + ", " - + newColor.getGreen() + ", " - + newColor.getBlue()); - return this; - } - } + } } - class ColorEditor extends AbstractCellEditor - implements TableCellEditor, - ActionListener { - Color currentColor; - JButton button; - JColorChooser colorChooser; - JDialog dialog; - protected static final String EDIT = "edit"; - - public ColorEditor() { - //Set up the editor (from the table's point of view), - //which is a button. - //This button brings up the color chooser dialog, - //which is the editor from the user's point of view. - button = new JButton(); - button.setActionCommand(EDIT); - button.addActionListener(this); - button.setBorderPainted(false); - //Set up the dialog that the button brings up. - colorChooser = new JColorChooser(); - dialog = JColorChooser.createDialog(button, - "Select new Colour", - true, //modal - colorChooser, - this, //OK button handler - null); //no CANCEL button handler - } - - /** - * Handles events from the editor button and from - * the dialog's OK button. - */ - public void actionPerformed(ActionEvent e) { - - if (EDIT.equals(e.getActionCommand())) { - //The user has clicked the cell, so - //bring up the dialog. - button.setBackground(currentColor); - colorChooser.setColor(currentColor); - dialog.setVisible(true); - - //Make the renderer reappear. - fireEditingStopped(); - - } else { //User pressed dialog's "OK" button. - currentColor = colorChooser.getColor(); - } - } - - //Implement the one CellEditor method that AbstractCellEditor doesn't. - public Object getCellEditorValue() { - return currentColor; - } - - //Implement the one method defined by TableCellEditor. - public Component getTableCellEditorComponent(JTable table, - Object value, - boolean isSelected, - int row, - int column) { - currentColor = (Color)value; - return button; - } +class ColorEditor + extends AbstractCellEditor implements TableCellEditor, + ActionListener +{ + Color currentColor; + JButton button; + JColorChooser colorChooser; + JDialog dialog; + protected static final String EDIT = "edit"; + + public ColorEditor() + { + //Set up the editor (from the table's point of view), + //which is a button. + //This button brings up the color chooser dialog, + //which is the editor from the user's point of view. + button = new JButton(); + button.setActionCommand(EDIT); + button.addActionListener(this); + button.setBorderPainted(false); + //Set up the dialog that the button brings up. + colorChooser = new JColorChooser(); + dialog = JColorChooser.createDialog(button, + "Select new Colour", + true, //modal + colorChooser, + this, //OK button handler + null); //no CANCEL button handler + } + + /** + * Handles events from the editor button and from + * the dialog's OK button. + */ + public void actionPerformed(ActionEvent e) + { + + if (EDIT.equals(e.getActionCommand())) + { + //The user has clicked the cell, so + //bring up the dialog. + button.setBackground(currentColor); + colorChooser.setColor(currentColor); + dialog.setVisible(true); + + //Make the renderer reappear. + fireEditingStopped(); + + } + else + { //User pressed dialog's "OK" button. + currentColor = colorChooser.getColor(); + } + } + + //Implement the one CellEditor method that AbstractCellEditor doesn't. + public Object getCellEditorValue() + { + return currentColor; + } + + //Implement the one method defined by TableCellEditor. + public Component getTableCellEditorComponent(JTable table, + Object value, + boolean isSelected, + int row, + int column) + { + currentColor = (Color) value; + return button; + } }