X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=821454f82fb56ccafb03df5769317c2f68dc277a;hb=252ddd218b716396b003b3fcbe0f8da499bde8c8;hp=fedfe3fc851015f42cdd6490d54fe29b151d809e;hpb=e16e9699b56f3db4e42dc694aaafad76dae66c4b;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index fedfe3f..821454f 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -20,28 +20,24 @@ */ package jalview.gui; -import static jalview.viewmodel.seqfeatures.FeatureRendererModel.COLOUR_COLUMN; -import static jalview.viewmodel.seqfeatures.FeatureRendererModel.FILTER_COLUMN; -import static jalview.viewmodel.seqfeatures.FeatureRendererModel.SHOW_COLUMN; -import static jalview.viewmodel.seqfeatures.FeatureRendererModel.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.Filter; import jalview.schemabinding.version2.JalviewUserColours; +import jalview.schemabinding.version2.MatcherSet; import jalview.schemes.FeatureColour; -import jalview.util.Format; import jalview.util.MessageManager; import jalview.util.Platform; -import jalview.util.QuickSort; -import jalview.util.matcher.KeyedMatcherSet; -import jalview.util.matcher.KeyedMatcherSetI; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; import jalview.ws.DasSequenceFeatureFetcher; import jalview.ws.dbsources.das.api.jalviewSourceI; @@ -70,6 +66,8 @@ 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; @@ -109,16 +107,26 @@ import javax.swing.table.TableColumn; 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"); + + /* + * 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; - private static final String COLON = ":"; + static final int SHOW_COLUMN = 3; + + private static final int COLUMN_COUNT = 4; private static final int MIN_WIDTH = 400; private static final int MIN_HEIGHT = 400; - private static final int MAX_TOOLTIP_LENGTH = 50; - DasSourceBrowser dassourceBrowser; DasSequenceFeatureFetcher dasFeatureFetcher; @@ -136,7 +144,7 @@ public class FeatureSettings extends JPanel private float originalTransparency; - private Map originalFilters; + private Map originalFilters; final JInternalFrame frame; @@ -188,7 +196,7 @@ 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 { @@ -213,7 +221,7 @@ public class FeatureSettings extends JPanel break; case FILTER_COLUMN: int row = table.rowAtPoint(e.getPoint()); - KeyedMatcherSet o = (KeyedMatcherSet) table.getValueAt(row, + FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row, column); tip = o.isEmpty() ? MessageManager.getString("label.filters_tooltip") @@ -234,8 +242,8 @@ public class FeatureSettings extends JPanel table.setDefaultEditor(FeatureColour.class, new ColorEditor(this)); table.setDefaultRenderer(FeatureColour.class, new ColorRenderer()); - table.setDefaultEditor(KeyedMatcherSet.class, new FilterEditor(this)); - table.setDefaultRenderer(KeyedMatcherSet.class, new FilterRenderer()); + table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor(this)); + table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer()); TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75, new ColorRenderer(), new ColorEditor(this)); @@ -651,8 +659,7 @@ 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()) @@ -677,9 +684,9 @@ public class FeatureSettings extends JPanel data[dataIndex][TYPE_COLUMN] = type; data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type); - KeyedMatcherSetI featureFilter = fr.getFeatureFilter(type); + FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type); data[dataIndex][FILTER_COLUMN] = featureFilter == null - ? new KeyedMatcherSet() + ? new FeatureMatcherSet() : featureFilter; data[dataIndex][SHOW_COLUMN] = new Boolean( af.getViewport().getFeaturesDisplayed().isVisible(type)); @@ -704,9 +711,9 @@ public class FeatureSettings extends JPanel fr.clearRenderOrder(); return; } - KeyedMatcherSetI featureFilter = fr.getFeatureFilter(type); + FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type); data[dataIndex][FILTER_COLUMN] = featureFilter == null - ? new KeyedMatcherSet() + ? new FeatureMatcherSet() : featureFilter; data[dataIndex][SHOW_COLUMN] = new Boolean(true); dataIndex++; @@ -715,11 +722,10 @@ 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 @@ -790,11 +796,12 @@ 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; @@ -848,10 +855,14 @@ 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")); @@ -862,88 +873,78 @@ 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); + JalviewUserColours jucs = JalviewUserColours.unmarshal(in); - 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)); + /* + * load feature colours + */ + for (int i = jucs.getColourCount() - 1; i >= 0; i--) + { + jalview.schemabinding.version2.Colour newcol = jucs.getColour(i); + FeatureColourI colour = Jalview2XML.unmarshalColour(newcol); + fr.setColour(newcol.getName(), colour); + fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount()); + } - } 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 filters; loaded filters will replace any that are + * currently defined, other defined filters are left unchanged + */ + for (int i = 0; i < jucs.getFilterCount(); i++) + { + jalview.schemabinding.version2.Filter filterModel = jucs + .getFilter(i); + String featureType = filterModel.getFeatureType(); + FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(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")); @@ -953,68 +954,87 @@ 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()); + } + } - 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()) + /** + * 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")); + + /* + * 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); + jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour( + featureType, fcol); + ucs.addColour(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(); + MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator, + filter.isAnded()); + Filter filterModel = new Filter(); + filterModel.setFeatureType(featureType); + filterModel.setMatcherSet(ms); + ucs.addFilter(filterModel); } - ucs.marshal(out); - out.close(); - } catch (Exception ex) - { - ex.printStackTrace(); } + + 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() @@ -1105,12 +1125,32 @@ public class FeatureSettings extends JPanel */ private void updateFeatureRenderer(Object[][] data, boolean visibleNew) { - if (fr.setFeaturePriority(data, visibleNew)) + FeatureSettingsBean[] rowData = getTableAsBeans(data); + + if (fr.setFeaturePriority(rowData, visibleNew)) { af.alignPanel.paintAlignment(true, true); } } + /** + * Converts table data into an array of data beans + */ + private FeatureSettingsBean[] getTableAsBeans(Object[][] data) + { + FeatureSettingsBean[] rowData = new FeatureSettingsBean[data.length]; + for (int i = 0; i < data.length; i++) + { + String type = (String) data[i][TYPE_COLUMN]; + FeatureColourI colour = (FeatureColourI) data[i][COLOUR_COLUMN]; + FeatureMatcherSetI theFilter = (FeatureMatcherSetI) data[i][FILTER_COLUMN]; + Boolean isShown = (Boolean) data[i][SHOW_COLUMN]; + rowData[i] = new FeatureSettingsBean(type, colour, theFilter, + isShown); + } + return rowData; + } + private void jbInit() throws Exception { this.setLayout(new BorderLayout()); @@ -1234,6 +1274,8 @@ 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 @@ -1246,6 +1288,8 @@ 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 @@ -1492,7 +1536,6 @@ public class FeatureSettings extends JPanel // /////////////////////////////////////////////////////////////////////// class FeatureTableModel extends AbstractTableModel { - private String[] columnNames = { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), @@ -1647,7 +1690,7 @@ public class FeatureSettings extends JPanel Object filter, boolean isSelected, boolean hasFocus, int row, int column) { - KeyedMatcherSetI theFilter = (KeyedMatcherSetI) filter; + FeatureMatcherSetI theFilter = (FeatureMatcherSetI) filter; setOpaque(true); String asText = theFilter.toString(); setBackground(tbl.getBackground()); @@ -1859,10 +1902,10 @@ public class FeatureSettings extends JPanel * update table data without triggering updateFeatureRenderer */ currentColor = fr.getFeatureColours().get(type); - KeyedMatcherSetI currentFilter = me.fr.getFeatureFilter(type); + FeatureMatcherSetI currentFilter = me.fr.getFeatureFilter(type); if (currentFilter == null) { - currentFilter = new KeyedMatcherSet(); + currentFilter = new FeatureMatcherSet(); } Object[] data = ((FeatureTableModel) table.getModel()) .getData()[rowSelected]; @@ -1921,7 +1964,7 @@ public class FeatureSettings extends JPanel { FeatureSettings me; - KeyedMatcherSetI currentFilter; + FeatureMatcherSetI currentFilter; Point lastLocation; @@ -1976,7 +2019,7 @@ public class FeatureSettings extends JPanel currentFilter = me.fr.getFeatureFilter(type); if (currentFilter == null) { - currentFilter = new KeyedMatcherSet(); + currentFilter = new FeatureMatcherSet(); } Object[] data = ((FeatureTableModel) table.getModel()) .getData()[rowSelected]; @@ -1997,7 +2040,7 @@ public class FeatureSettings extends JPanel public Component getTableCellEditorComponent(JTable theTable, Object value, boolean isSelected, int row, int column) { - currentFilter = (KeyedMatcherSetI) value; + currentFilter = (FeatureMatcherSetI) value; this.rowSelected = row; type = me.table.getValueAt(row, TYPE_COLUMN).toString(); button.setOpaque(true);