X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=90d7c35401f28b8251cb6848c1d442ca35f75d90;hb=0c805692348a8a45c279ee5f4702c7bd5a393c5e;hp=0c4cd56cb2966d18e66ce9daf73992c586018752;hpb=ef14d83cfe8ca0bb2271d50d638516cdc90c2b8b;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 0c4cd56..90d7c35 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -20,31 +20,24 @@ */ package jalview.gui; -import static jalview.gui.FeatureSettings.FeatureTableModel.COLOUR_COLUMN; -import static jalview.gui.FeatureSettings.FeatureTableModel.FILTER_COLUMN; -import static jalview.gui.FeatureSettings.FeatureTableModel.SHOW_COLUMN; -import static jalview.gui.FeatureSettings.FeatureTableModel.TYPE_COLUMN; - import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsControllerI; -import jalview.bin.Cache; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; +import jalview.datamodel.features.FeatureMatcherI; import jalview.datamodel.features.FeatureMatcherSet; import jalview.datamodel.features.FeatureMatcherSetI; import jalview.gui.Help.HelpId; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; -import jalview.schemabinding.version2.JalviewUserColours; import jalview.schemes.FeatureColour; -import jalview.util.Format; import jalview.util.MessageManager; import jalview.util.Platform; -import jalview.util.QuickSort; -import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; -import jalview.ws.DasSequenceFeatureFetcher; -import jalview.ws.dbsources.das.api.jalviewSourceI; +import jalview.xml.binding.jalview.JalviewUserColours; +import jalview.xml.binding.jalview.JalviewUserColours.Colour; +import jalview.xml.binding.jalview.JalviewUserColours.Filter; +import jalview.xml.binding.jalview.ObjectFactory; import java.awt.BorderLayout; import java.awt.Color; @@ -71,13 +64,14 @@ import java.io.InputStreamReader; import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.util.Arrays; +import java.util.Comparator; +import java.util.HashMap; import java.util.HashSet; import java.util.Hashtable; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; -import java.util.Vector; import javax.help.HelpSetException; import javax.swing.AbstractCellEditor; @@ -99,28 +93,40 @@ import javax.swing.JSlider; import javax.swing.JTable; import javax.swing.ListSelectionModel; import javax.swing.SwingConstants; -import javax.swing.SwingUtilities; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import javax.swing.table.AbstractTableModel; import javax.swing.table.TableCellEditor; import javax.swing.table.TableCellRenderer; import javax.swing.table.TableColumn; +import javax.xml.bind.JAXBContext; +import javax.xml.bind.JAXBElement; +import javax.xml.bind.Marshaller; +import javax.xml.stream.XMLInputFactory; +import javax.xml.stream.XMLStreamReader; public class FeatureSettings extends JPanel implements FeatureSettingsControllerI { - private static final int COLUMN_COUNT = 4; + private static final String SEQUENCE_FEATURE_COLOURS = MessageManager + .getString("label.sequence_feature_colours"); - private static final int MIN_WIDTH = 400; + /* + * column indices of fields in Feature Settings table + */ + static final int TYPE_COLUMN = 0; - private static final int MIN_HEIGHT = 400; + static final int COLOUR_COLUMN = 1; - DasSourceBrowser dassourceBrowser; + static final int FILTER_COLUMN = 2; - DasSequenceFeatureFetcher dasFeatureFetcher; + static final int SHOW_COLUMN = 3; - JPanel dasSettingsPane = new JPanel(); + private static final int COLUMN_COUNT = 4; + + private static final int MIN_WIDTH = 400; + + private static final int MIN_HEIGHT = 400; final FeatureRenderer fr; @@ -185,7 +191,7 @@ public class FeatureSettings extends JPanel int originalTransparencyAsPercent = (int) (originalTransparency * 100); transparency.setMaximum(100 - originalTransparencyAsPercent); - originalFilters = fr.getFeatureFilters(); + originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy try { @@ -314,9 +320,6 @@ public class FeatureSettings extends JPanel // MessageManager.getString("label.feature_settings_click_drag"))); scrollPane.setViewportView(table); - dassourceBrowser = new DasSourceBrowser(this); - dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER); - if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder()) { fr.findAllFeatures(true); // display everything! @@ -365,7 +368,6 @@ public class FeatureSettings extends JPanel javax.swing.event.InternalFrameEvent evt) { fr.removePropertyChangeListener(change); - dassourceBrowser.fs = null; }; }); frame.setLayer(JLayeredPane.PALETTE_LAYER); @@ -648,8 +650,7 @@ public class FeatureSettings extends JPanel } } - int columnCount = COLUMN_COUNT; - Object[][] data = new Object[displayableTypes.size()][columnCount]; + Object[][] data = new Object[displayableTypes.size()][COLUMN_COUNT]; int dataIndex = 0; if (fr.hasRenderOrder()) @@ -712,11 +713,10 @@ public class FeatureSettings extends JPanel if (originalData == null) { - int size = data[0].length; - originalData = new Object[data.length][size]; + originalData = new Object[data.length][COLUMN_COUNT]; for (int i = 0; i < data.length; i++) { - System.arraycopy(data[i], 0, originalData[i], 0, size); + System.arraycopy(data[i], 0, originalData[i], 0, COLUMN_COUNT); } } else @@ -787,11 +787,12 @@ public class FeatureSettings extends JPanel /* * new feature detected - add to original data (on top) */ - int size = currentData[0].length; - Object[][] newData = new Object[originalData.length + 1][size]; + Object[][] newData = new Object[originalData.length + + 1][COLUMN_COUNT]; for (int i = 0; i < originalData.length; i++) { - System.arraycopy(originalData[i], 0, newData[i + 1], 0, size); + System.arraycopy(originalData[i], 0, newData[i + 1], 0, + COLUMN_COUNT); } newData[0] = row; originalData = newData; @@ -845,10 +846,14 @@ public class FeatureSettings extends JPanel } } + /** + * Offers a file chooser dialog, and then loads the feature colours and + * filters from file in XML format and unmarshals to Jalview feature settings + */ void load() { JalviewFileChooser chooser = new JalviewFileChooser("fc", - "Sequence Feature Colours"); + SEQUENCE_FEATURE_COLOURS); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.load_feature_colours")); @@ -859,88 +864,87 @@ public class FeatureSettings extends JPanel if (value == JalviewFileChooser.APPROVE_OPTION) { File file = chooser.getSelectedFile(); + load(file); + } + } - try - { - InputStreamReader in = new InputStreamReader( - new FileInputStream(file), "UTF-8"); + /** + * Loads feature colours and filters from XML stored in the given file + * + * @param file + */ + void load(File file) + { + try + { + InputStreamReader in = new InputStreamReader( + new FileInputStream(file), "UTF-8"); - JalviewUserColours jucs = JalviewUserColours.unmarshal(in); + JAXBContext jc = JAXBContext + .newInstance("jalview.xml.binding.jalview"); + javax.xml.bind.Unmarshaller um = jc.createUnmarshaller(); + XMLStreamReader streamReader = XMLInputFactory.newInstance() + .createXMLStreamReader(in); + JAXBElement jbe = um.unmarshal(streamReader, + JalviewUserColours.class); + JalviewUserColours jucs = jbe.getValue(); - for (int i = jucs.getColourCount() - 1; i >= 0; i--) - { - String name; - jalview.schemabinding.version2.Colour newcol = jucs.getColour(i); - if (newcol.hasMax()) - { - Color mincol = null, maxcol = null; - try - { - mincol = new Color(Integer.parseInt(newcol.getMinRGB(), 16)); - maxcol = new Color(Integer.parseInt(newcol.getRGB(), 16)); + // JalviewUserColours jucs = JalviewUserColours.unmarshal(in); - } catch (Exception e) - { - Cache.log.warn("Couldn't parse out graduated feature color.", - e); - } - FeatureColourI gcol = new FeatureColour(mincol, maxcol, - newcol.getMin(), newcol.getMax()); - if (newcol.hasAutoScale()) - { - gcol.setAutoScaled(newcol.getAutoScale()); - } - if (newcol.hasColourByLabel()) - { - gcol.setColourByLabel(newcol.getColourByLabel()); - } - if (newcol.hasThreshold()) - { - gcol.setThreshold(newcol.getThreshold()); - } - if (newcol.getThreshType().length() > 0) - { - String ttyp = newcol.getThreshType(); - if (ttyp.equalsIgnoreCase("ABOVE")) - { - gcol.setAboveThreshold(true); - } - if (ttyp.equalsIgnoreCase("BELOW")) - { - gcol.setBelowThreshold(true); - } - } - fr.setColour(name = newcol.getName(), gcol); - } - else - { - Color color = new Color( - Integer.parseInt(jucs.getColour(i).getRGB(), 16)); - fr.setColour(name = jucs.getColour(i).getName(), - new FeatureColour(color)); - } - fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount()); - } - if (table != null) + /* + * load feature colours + */ + for (int i = jucs.getColour().size() - 1; i >= 0; i--) + { + Colour newcol = jucs.getColour().get(i); + FeatureColourI colour = jalview.project.Jalview2XML + .parseColour(newcol); + fr.setColour(newcol.getName(), colour); + fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size()); + } + + /* + * load feature filters; loaded filters will replace any that are + * currently defined, other defined filters are left unchanged + */ + for (int i = 0; i < jucs.getFilter().size(); i++) + { + Filter filterModel = jucs.getFilter().get(i); + String featureType = filterModel.getFeatureType(); + FeatureMatcherSetI filter = jalview.project.Jalview2XML + .parseFilter(featureType, filterModel.getMatcherSet()); + if (!filter.isEmpty()) { - resetTable(null); - Object[][] data = ((FeatureTableModel) table.getModel()) - .getData(); - ensureOrder(data); - updateFeatureRenderer(data, false); - table.repaint(); + fr.setFeatureFilter(featureType, filter); } - } catch (Exception ex) + } + + /* + * update feature settings table + */ + if (table != null) { - System.out.println("Error loading User Colour File\n" + ex); + resetTable(null); + Object[][] data = ((FeatureTableModel) table.getModel()) + .getData(); + ensureOrder(data); + updateFeatureRenderer(data, false); + table.repaint(); } + } catch (Exception ex) + { + System.out.println("Error loading User Colour File\n" + ex); } } + /** + * Offers a file chooser dialog, and then saves the current feature colours + * and any filters to the selected file in XML format + */ void save() { JalviewFileChooser chooser = new JalviewFileChooser("fc", - "Sequence Feature Colours"); + SEQUENCE_FEATURE_COLOURS); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.save_feature_colours")); @@ -950,68 +954,97 @@ public class FeatureSettings extends JPanel if (value == JalviewFileChooser.APPROVE_OPTION) { - String choice = chooser.getSelectedFile().getPath(); - jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours(); - ucs.setSchemeName("Sequence Features"); - try - { - PrintWriter out = new PrintWriter(new OutputStreamWriter( - new FileOutputStream(choice), "UTF-8")); + save(chooser.getSelectedFile()); + } + } + + /** + * Saves feature colours and filters to the given file + * + * @param file + */ + void save(File file) + { + JalviewUserColours ucs = new JalviewUserColours(); + ucs.setSchemeName("Sequence Features"); + try + { + PrintWriter out = new PrintWriter(new OutputStreamWriter( + new FileOutputStream(file), "UTF-8")); - Set fr_colours = fr.getAllFeatureColours(); - Iterator e = fr_colours.iterator(); - float[] sortOrder = new float[fr_colours.size()]; - String[] sortTypes = new String[fr_colours.size()]; - int i = 0; - while (e.hasNext()) + /* + * sort feature types by colour order, from 0 (highest) + * to 1 (lowest) + */ + Set fr_colours = fr.getAllFeatureColours(); + String[] sortedTypes = fr_colours + .toArray(new String[fr_colours.size()]); + Arrays.sort(sortedTypes, new Comparator() + { + @Override + public int compare(String type1, String type2) { - sortTypes[i] = e.next(); - sortOrder[i] = fr.getOrder(sortTypes[i]); - i++; + return Float.compare(fr.getOrder(type1), fr.getOrder(type2)); } - QuickSort.sort(sortOrder, sortTypes); - sortOrder = null; - for (i = 0; i < sortTypes.length; i++) + }); + + /* + * save feature colours + */ + for (String featureType : sortedTypes) + { + FeatureColourI fcol = fr.getFeatureStyle(featureType); + Colour col = jalview.project.Jalview2XML.marshalColour(featureType, + fcol); + ucs.getColour().add(col); + } + + /* + * save any feature filters + */ + for (String featureType : sortedTypes) + { + FeatureMatcherSetI filter = fr.getFeatureFilter(featureType); + if (filter != null && !filter.isEmpty()) { - jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); - col.setName(sortTypes[i]); - FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]); - if (fcol.isSimpleColour()) - { - col.setRGB(Format.getHexString(fcol.getColour())); - } - else - { - col.setRGB(Format.getHexString(fcol.getMaxColour())); - col.setMin(fcol.getMin()); - col.setMax(fcol.getMax()); - col.setMinRGB( - jalview.util.Format.getHexString(fcol.getMinColour())); - col.setAutoScale(fcol.isAutoScaled()); - col.setThreshold(fcol.getThreshold()); - col.setColourByLabel(fcol.isColourByLabel()); - col.setThreshType(fcol.isAboveThreshold() ? "ABOVE" - : (fcol.isBelowThreshold() ? "BELOW" : "NONE")); - } - ucs.addColour(col); + Iterator iterator = filter.getMatchers().iterator(); + FeatureMatcherI firstMatcher = iterator.next(); + jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML + .marshalFilter(firstMatcher, iterator, + filter.isAnded()); + Filter filterModel = new Filter(); + filterModel.setFeatureType(featureType); + filterModel.setMatcherSet(ms); + ucs.getFilter().add(filterModel); } - ucs.marshal(out); - out.close(); - } catch (Exception ex) - { - ex.printStackTrace(); } + JAXBContext jaxbContext = JAXBContext + .newInstance(JalviewUserColours.class); + Marshaller jaxbMarshaller = jaxbContext.createMarshaller(); + jaxbMarshaller.marshal( + new ObjectFactory().createJalviewUserColours(ucs), out); + + // jaxbMarshaller.marshal(object, pout); + // marshaller.marshal(object); + out.flush(); + + // ucs.marshal(out); + out.close(); + } catch (Exception ex) + { + ex.printStackTrace(); } } public void invertSelection() { - for (int i = 0; i < table.getRowCount(); i++) + Object[][] data = ((FeatureTableModel) table.getModel()).getData(); + for (int i = 0; i < data.length; i++) { - Boolean value = (Boolean) table.getValueAt(i, SHOW_COLUMN); - - table.setValueAt(new Boolean(!value.booleanValue()), i, SHOW_COLUMN); + data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN]; } + updateFeatureRenderer(data, true); + table.repaint(); } public void orderByAvWidth() @@ -1135,8 +1168,6 @@ public class FeatureSettings extends JPanel JPanel settingsPane = new JPanel(); settingsPane.setLayout(new BorderLayout()); - dasSettingsPane.setLayout(new BorderLayout()); - JPanel bigPanel = new JPanel(); bigPanel.setLayout(new BorderLayout()); @@ -1251,6 +1282,8 @@ public class FeatureSettings extends JPanel JButton loadColours = new JButton( MessageManager.getString("label.load_colours")); loadColours.setFont(JvSwingUtils.getLabelFont()); + loadColours.setToolTipText( + MessageManager.getString("label.load_colours_tooltip")); loadColours.addActionListener(new ActionListener() { @Override @@ -1263,6 +1296,8 @@ public class FeatureSettings extends JPanel JButton saveColours = new JButton( MessageManager.getString("label.save_colours")); saveColours.setFont(JvSwingUtils.getLabelFont()); + saveColours.setToolTipText( + MessageManager.getString("label.save_colours_tooltip")); saveColours.addActionListener(new ActionListener() { @Override @@ -1287,38 +1322,6 @@ public class FeatureSettings extends JPanel transparency.setMaximum(70); transparency.setToolTipText( MessageManager.getString("label.transparency_tip")); - fetchDAS.setText(MessageManager.getString("label.fetch_das_features")); - fetchDAS.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - fetchDAS_actionPerformed(e); - } - }); - saveDAS.setText(MessageManager.getString("action.save_as_default")); - saveDAS.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - saveDAS_actionPerformed(e); - } - }); - - JPanel dasButtonPanel = new JPanel(); - dasButtonPanel.setBorder(BorderFactory.createEtchedBorder()); - dasSettingsPane.setBorder(null); - cancelDAS.setEnabled(false); - cancelDAS.setText(MessageManager.getString("action.cancel_fetch")); - cancelDAS.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - cancelDAS_actionPerformed(e); - } - }); JPanel transPanel = new JPanel(new GridLayout(1, 2)); bigPanel.add(transPanel, BorderLayout.SOUTH); @@ -1338,188 +1341,16 @@ public class FeatureSettings extends JPanel buttonPanel.add(loadColours); buttonPanel.add(saveColours); bigPanel.add(scrollPane, BorderLayout.CENTER); - dasSettingsPane.add(dasButtonPanel, BorderLayout.SOUTH); - dasButtonPanel.add(fetchDAS); - dasButtonPanel.add(cancelDAS); - dasButtonPanel.add(saveDAS); settingsPane.add(bigPanel, BorderLayout.CENTER); settingsPane.add(buttonPanel, BorderLayout.SOUTH); this.add(settingsPane); } - public void fetchDAS_actionPerformed(ActionEvent e) - { - fetchDAS.setEnabled(false); - cancelDAS.setEnabled(true); - dassourceBrowser.setGuiEnabled(false); - Vector selectedSources = dassourceBrowser - .getSelectedSources(); - doDasFeatureFetch(selectedSources, true, true); - } - - /** - * get the features from selectedSources for all or the current selection - * - * @param selectedSources - * @param checkDbRefs - * @param promptFetchDbRefs - */ - private void doDasFeatureFetch(List selectedSources, - boolean checkDbRefs, boolean promptFetchDbRefs) - { - SequenceI[] dataset, seqs; - int iSize; - AlignmentViewport vp = af.getViewport(); - if (vp.getSelectionGroup() != null - && vp.getSelectionGroup().getSize() > 0) - { - iSize = vp.getSelectionGroup().getSize(); - dataset = new SequenceI[iSize]; - seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment()); - } - else - { - iSize = vp.getAlignment().getHeight(); - seqs = vp.getAlignment().getSequencesArray(); - } - - dataset = new SequenceI[iSize]; - for (int i = 0; i < iSize; i++) - { - dataset[i] = seqs[i].getDatasetSequence(); - } - - cancelDAS.setEnabled(true); - dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset, - this, selectedSources, checkDbRefs, promptFetchDbRefs); - af.getViewport().setShowSequenceFeatures(true); - af.showSeqFeatures.setSelected(true); - } - - /** - * blocking call to initialise the das source browser - */ - public void initDasSources() - { - dassourceBrowser.initDasSources(); - } - - /** - * examine the current list of das sources and return any matching the given - * nicknames in sources - * - * @param sources - * Vector of Strings to resolve to DAS source nicknames. - * @return sources that are present in source list. - */ - public List resolveSourceNicknames(Vector sources) - { - return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources); - } - - /** - * get currently selected das sources. ensure you have called initDasSources - * before calling this. - * - * @return vector of selected das source nicknames - */ - public Vector getSelectedSources() - { - return dassourceBrowser.getSelectedSources(); - } - - /** - * properly initialise DAS fetcher and then initiate a new thread to fetch - * features from the named sources (rather than any turned on by default) - * - * @param sources - * @param block - * if true then runs in same thread, otherwise passes to the Swing - * executor - */ - public void fetchDasFeatures(Vector sources, boolean block) - { - initDasSources(); - List resolved = dassourceBrowser.sourceRegistry - .resolveSourceNicknames(sources); - if (resolved.size() == 0) - { - resolved = dassourceBrowser.getSelectedSources(); - } - if (resolved.size() > 0) - { - final List dassources = resolved; - fetchDAS.setEnabled(false); - // cancelDAS.setEnabled(true); doDasFetch does this. - Runnable fetcher = new Runnable() - { - - @Override - public void run() - { - doDasFeatureFetch(dassources, true, false); - - } - }; - if (block) - { - fetcher.run(); - } - else - { - SwingUtilities.invokeLater(fetcher); - } - } - } - - public void saveDAS_actionPerformed(ActionEvent e) - { - dassourceBrowser - .saveProperties(jalview.bin.Cache.applicationProperties); - } - - public void complete() - { - fetchDAS.setEnabled(true); - cancelDAS.setEnabled(false); - dassourceBrowser.setGuiEnabled(true); - - } - - public void cancelDAS_actionPerformed(ActionEvent e) - { - if (dasFeatureFetcher != null) - { - dasFeatureFetcher.cancel(); - } - complete(); - } - - public void noDasSourceActive() - { - complete(); - JvOptionPane.showInternalConfirmDialog(Desktop.desktop, - MessageManager.getString("label.no_das_sources_selected_warn"), - MessageManager.getString("label.no_das_sources_selected_title"), - JvOptionPane.DEFAULT_OPTION, JvOptionPane.INFORMATION_MESSAGE); - } - // /////////////////////////////////////////////////////////////////////// // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html // /////////////////////////////////////////////////////////////////////// class FeatureTableModel extends AbstractTableModel { - /* - * column indices of fields in Feature Settings table - */ - static final int TYPE_COLUMN = 0; - - static final int COLOUR_COLUMN = 1; - - static final int FILTER_COLUMN = 2; - - static final int SHOW_COLUMN = 3; - private String[] columnNames = { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"),