X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=7b8eae4d9df62ded24caf498c18c95d171b4b577;hb=1f61b56f403ba1b5810e31148d1d944db7958ddd;hp=1358c8f64784786eedb646fbe378b75998d3d55a;hpb=5b126eb259ecff2dce5c024066ced2528d87d39a;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 1358c8f..7b8eae4 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.api.AlignViewportI; import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsControllerI; import jalview.datamodel.AlignmentI; @@ -30,13 +31,14 @@ import jalview.datamodel.features.FeatureMatcherSetI; import jalview.gui.Help.HelpId; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; -import jalview.schemabinding.version2.Filter; -import jalview.schemabinding.version2.JalviewUserColours; -import jalview.schemabinding.version2.MatcherSet; import jalview.schemes.FeatureColour; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; +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; @@ -78,7 +80,6 @@ import javax.swing.BorderFactory; import javax.swing.Icon; import javax.swing.JButton; import javax.swing.JCheckBox; -import javax.swing.JCheckBoxMenuItem; import javax.swing.JColorChooser; import javax.swing.JDialog; import javax.swing.JInternalFrame; @@ -98,6 +99,11 @@ 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 @@ -145,6 +151,8 @@ public class FeatureSettings extends JPanel JSlider transparency = new JSlider(); + JCheckBox showComplement; + /* * when true, constructor is still executing - so ignore UI events */ @@ -213,7 +221,8 @@ public class FeatureSettings extends JPanel FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row, column); tip = o.isEmpty() - ? MessageManager.getString("label.filters_tooltip") + ? MessageManager + .getString("label.configure_feature_tooltip") : o.toString(); break; default: @@ -409,69 +418,6 @@ public class FeatureSettings extends JPanel }); men.add(dens); - /* - * variable colour options include colour by label, by score, - * by selected attribute text, or attribute value - */ - final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem( - MessageManager.getString("label.variable_colour")); - mxcol.setSelected(!featureColour.isSimpleColour()); - men.add(mxcol); - mxcol.addActionListener(new ActionListener() - { - JColorChooser colorChooser; - - @Override - public void actionPerformed(ActionEvent e) - { - if (e.getSource() == mxcol) - { - if (featureColour.isSimpleColour()) - { - FeatureTypeSettings fc = new FeatureTypeSettings(me.fr, type); - fc.addActionListener(this); - } - else - { - // bring up simple color chooser - colorChooser = new JColorChooser(); - String title = MessageManager - .getString("label.select_colour"); - JDialog dialog = JColorChooser.createDialog(me, - title, true, // modal - colorChooser, this, // OK button handler - null); // no CANCEL button handler - colorChooser.setColor(featureColour.getMaxColour()); - dialog.setVisible(true); - } - } - else - { - if (e.getSource() instanceof FeatureTypeSettings) - { - /* - * update after OK in feature colour dialog; the updated - * colour will have already been set in the FeatureRenderer - */ - FeatureColourI fci = fr.getFeatureColours().get(type); - table.setValueAt(fci, rowSelected, 1); - table.validate(); - } - else - { - // probably the color chooser! - table.setValueAt(new FeatureColour(colorChooser.getColor()), - rowSelected, 1); - table.validate(); - me.updateFeatureRenderer( - ((FeatureTableModel) table.getModel()).getData(), - false); - } - } - } - - }); - JMenuItem selCols = new JMenuItem( MessageManager.getString("label.select_columns_containing")); selCols.addActionListener(new ActionListener() @@ -575,7 +521,7 @@ public class FeatureSettings extends JPanel { fr.setGroupVisibility(check.getText(), check.isSelected()); resetTable(new String[] { grp }); - af.alignPanel.paintAlignment(true, true); + refreshDisplay(); } }); groupPanel.add(check); @@ -874,30 +820,39 @@ public class FeatureSettings extends JPanel 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(); + + // JalviewUserColours jucs = JalviewUserColours.unmarshal(in); /* * load feature colours */ - for (int i = jucs.getColourCount() - 1; i >= 0; i--) + for (int i = jucs.getColour().size() - 1; i >= 0; i--) { - jalview.schemabinding.version2.Colour newcol = jucs.getColour(i); - FeatureColourI colour = Jalview2XML.unmarshalColour(newcol); + 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.getColourCount()); + 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.getFilterCount(); i++) + for (int i = 0; i < jucs.getFilter().size(); i++) { - jalview.schemabinding.version2.Filter filterModel = jucs - .getFilter(i); + Filter filterModel = jucs.getFilter().get(i); String featureType = filterModel.getFeatureType(); - FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(featureType, - filterModel.getMatcherSet()); + FeatureMatcherSetI filter = jalview.project.Jalview2XML + .parseFilter(featureType, filterModel.getMatcherSet()); if (!filter.isEmpty()) { fr.setFeatureFilter(featureType, filter); @@ -979,9 +934,9 @@ public class FeatureSettings extends JPanel for (String featureType : sortedTypes) { FeatureColourI fcol = fr.getFeatureStyle(featureType); - jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour( - featureType, fcol); - ucs.addColour(col); + Colour col = jalview.project.Jalview2XML.marshalColour(featureType, + fcol); + ucs.getColour().add(col); } /* @@ -994,16 +949,26 @@ public class FeatureSettings extends JPanel { Iterator iterator = filter.getMatchers().iterator(); FeatureMatcherI firstMatcher = iterator.next(); - MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator, + 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.addFilter(filterModel); + ucs.getFilter().add(filterModel); } } + 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); + // ucs.marshal(out); out.close(); } catch (Exception ex) { @@ -1114,7 +1079,7 @@ public class FeatureSettings extends JPanel if (fr.setFeaturePriority(rowData, visibleNew)) { - af.alignPanel.paintAlignment(true, true); + refreshDisplay(); } } @@ -1289,7 +1254,7 @@ public class FeatureSettings extends JPanel if (!inConstruction) { fr.setTransparency((100 - transparency.getValue()) / 100f); - af.alignPanel.paintAlignment(true, true); + refreshDisplay(); } } }); @@ -1298,6 +1263,21 @@ public class FeatureSettings extends JPanel transparency.setToolTipText( MessageManager.getString("label.transparency_tip")); + boolean nucleotide = af.getViewport().getAlignment().isNucleotide(); + showComplement = new JCheckBox( + "Show " + (nucleotide ? "protein" : "CDS") + " features"); + showComplement.setSelected(af.getViewport().isShowComplementFeatures()); + showComplement.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + af.getViewport() + .setShowComplementFeatures(showComplement.isSelected()); + refreshDisplay(); + } + }); + JPanel transPanel = new JPanel(new GridLayout(1, 2)); bigPanel.add(transPanel, BorderLayout.SOUTH); @@ -1307,7 +1287,16 @@ public class FeatureSettings extends JPanel transbuttons.add(sortByScore); transbuttons.add(sortByDens); transbuttons.add(help); - transPanel.add(transparency); + + boolean hasComplement = af.getViewport().getCodingComplement() != null; + JPanel transPanelLeft = new JPanel( + new GridLayout(hasComplement ? 2 : 1, 1)); + transPanelLeft.add(transparency); + if (hasComplement) + { + transPanelLeft.add(showComplement); + } + transPanel.add(transPanelLeft); transPanel.add(transbuttons); JPanel buttonPanel = new JPanel(); @@ -1321,6 +1310,22 @@ public class FeatureSettings extends JPanel this.add(settingsPane); } + /** + * Repaints alignment, structure and overview (if shown). If there is a + * complementary view which is showing this view's features, then also + * repaints that. + */ + void refreshDisplay() + { + af.alignPanel.paintAlignment(true, true); + AlignViewportI complement = af.getViewport().getCodingComplement(); + if (complement != null && complement.isShowComplementFeatures()) + { + AlignFrame af2 = Desktop.getAlignFrameFor(complement); + af2.alignPanel.paintAlignment(true, true); + } + } + // /////////////////////////////////////////////////////////////////////// // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html // /////////////////////////////////////////////////////////////////////// @@ -1329,7 +1334,7 @@ public class FeatureSettings extends JPanel private String[] columnNames = { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), - MessageManager.getString("label.filter"), + MessageManager.getString("label.configuration"), MessageManager.getString("label.show") }; private Object[][] data; @@ -1379,13 +1384,22 @@ public class FeatureSettings extends JPanel } /** - * Answers the class of the object in column c of the first row of the table + * Answers the class of column c of the table */ @Override public Class getColumnClass(int c) { - Object v = getValueAt(0, c); - return v == null ? null : v.getClass(); + switch (c) + { + case TYPE_COLUMN: + return String.class; + case COLOUR_COLUMN: + return FeatureColour.class; + case FILTER_COLUMN: + return FeatureMatcherSet.class; + default: + return Boolean.class; + } } @Override