import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
-import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.FeatureMatcher;
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.CompoundMatcher;
import jalview.schemabinding.version2.Filter;
import jalview.schemabinding.version2.JalviewUserColours;
-import jalview.schemabinding.version2.MatchCondition;
import jalview.schemabinding.version2.MatcherSet;
-import jalview.schemabinding.version2.types.ColourNoValueColourType;
-import jalview.schemabinding.version2.types.ColourThreshTypeType;
-import jalview.schemabinding.version2.types.FeatureMatcherByType;
import jalview.schemes.FeatureColour;
-import jalview.util.Format;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.util.matcher.Condition;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
import jalview.ws.DasSequenceFeatureFetcher;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.util.Arrays;
-import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
public class FeatureSettings extends JPanel
implements FeatureSettingsControllerI
{
+ private static final String SEQUENCE_FEATURE_COLOURS = MessageManager
+ .getString("label.sequence_feature_colours");
+
/*
* column indices of fields in Feature Settings table
*/
Map<String, float[]> typeWidth = null;
/**
- * Populates an XML model of the feature colour scheme for one feature type
- *
- * @param featureType
- * @param fcol
- * @return
- */
- protected static jalview.schemabinding.version2.Colour marshalColour(
- String featureType, FeatureColourI fcol)
- {
- jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
- 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() ? ColourThreshTypeType.ABOVE
- : (fcol.isBelowThreshold() ? ColourThreshTypeType.BELOW
- : ColourThreshTypeType.NONE));
- if (fcol.isColourByAttribute())
- {
- col.setAttributeName(fcol.getAttributeName());
- }
- Color noColour = fcol.getNoColour();
- if (noColour == null)
- {
- col.setNoValueColour(ColourNoValueColourType.NONE);
- }
- else if (noColour == fcol.getMaxColour())
- {
- col.setNoValueColour(ColourNoValueColourType.MAX);
- }
- else
- {
- col.setNoValueColour(ColourNoValueColourType.MIN);
- }
- }
- col.setName(featureType);
- return col;
- }
-
- /**
- * Populates an XML model of the feature filter(s) for one feature type
- *
- * @param firstMatcher
- * the first (or only) match condition)
- * @param filter
- * remaining match conditions (if any)
- * @param and
- * if true, conditions are and-ed, else or-ed
- */
- protected static MatcherSet marshalFilter(FeatureMatcherI firstMatcher,
- Iterator<FeatureMatcherI> filters, boolean and)
- {
- MatcherSet result = new MatcherSet();
-
- if (filters.hasNext())
- {
- /*
- * compound matcher
- */
- CompoundMatcher compound = new CompoundMatcher();
- compound.setAnd(and);
- MatcherSet matcher1 = marshalFilter(firstMatcher,
- Collections.emptyIterator(), and);
- compound.addMatcherSet(matcher1);
- FeatureMatcherI nextMatcher = filters.next();
- MatcherSet matcher2 = marshalFilter(nextMatcher, filters, and);
- compound.addMatcherSet(matcher2);
- result.setCompoundMatcher(compound);
- }
- else
- {
- /*
- * single condition matcher
- */
- MatchCondition matcherModel = new MatchCondition();
- matcherModel.setCondition(
- firstMatcher.getMatcher().getCondition().getStableName());
- matcherModel.setValue(firstMatcher.getMatcher().getPattern());
- if (firstMatcher.isByAttribute())
- {
- matcherModel.setBy(FeatureMatcherByType.BYATTRIBUTE);
- matcherModel.setAttributeName(firstMatcher.getAttribute());
- }
- else if (firstMatcher.isByLabel())
- {
- matcherModel.setBy(FeatureMatcherByType.BYLABEL);
- }
- else if (firstMatcher.isByScore())
- {
- matcherModel.setBy(FeatureMatcherByType.BYSCORE);
- }
- result.setMatchCondition(matcherModel);
- }
-
- return result;
- }
-
- /**
- * Loads one XML model of a feature filter to a Jalview object
- *
- * @param colourModel
- * @return
- */
- protected static FeatureMatcherSetI unmarshalFilter(Filter filterModel)
- {
- FeatureMatcherSetI result = new FeatureMatcherSet();
- MatcherSet matcherSetModel = filterModel.getMatcherSet();
- try
- {
- unmarshalFilterConditions(result, matcherSetModel, true);
- } catch (IllegalStateException e)
- {
- // mixing AND and OR conditions perhaps
- System.err.println(
- String.format("Error reading filter conditions for '%s': %s",
- filterModel.getFeatureType(), e.getMessage()));
- // return as much as was parsed up to the error
- }
-
- return result;
- }
-
- /**
- * Adds feature match conditions to matcherSet as unmarshalled from XML
- * (possibly recursively for compound conditions)
- *
- * @param matcherSet
- * @param matcherSetModel
- * @param and
- * if true, multiple conditions are AND-ed, else they are OR-ed
- * @throws IllegalStateException
- * if AND and OR conditions are mixed
- */
- protected static void unmarshalFilterConditions(
- FeatureMatcherSetI matcherSet, MatcherSet matcherSetModel,
- boolean and)
- {
- MatchCondition mc = matcherSetModel.getMatchCondition();
- if (mc != null)
- {
- /*
- * single condition
- */
- FeatureMatcherByType filterBy = mc.getBy();
- Condition cond = Condition.fromString(mc.getCondition());
- String pattern = mc.getValue();
- FeatureMatcherI matchCondition = null;
- if (filterBy == FeatureMatcherByType.BYLABEL)
- {
- matchCondition = FeatureMatcher.byLabel(cond, pattern);
- }
- else if (filterBy == FeatureMatcherByType.BYSCORE)
- {
- matchCondition = FeatureMatcher.byScore(cond, pattern);
-
- }
- else if (filterBy == FeatureMatcherByType.BYATTRIBUTE)
- {
- String[] attNames = mc.getAttributeName();
- matchCondition = FeatureMatcher.byAttribute(cond, pattern,
- attNames);
- }
-
- /*
- * note this throws IllegalStateException if AND-ing to a
- * previously OR-ed compound condition, or vice versa
- */
- if (and)
- {
- matcherSet.and(matchCondition);
- }
- else
- {
- matcherSet.or(matchCondition);
- }
- }
- else
- {
- /*
- * compound condition
- */
- MatcherSet[] matchers = matcherSetModel.getCompoundMatcher()
- .getMatcherSet();
- boolean anded = matcherSetModel.getCompoundMatcher().getAnd();
- if (matchers.length == 2)
- {
- unmarshalFilterConditions(matcherSet, matchers[0], anded);
- unmarshalFilterConditions(matcherSet, matchers[1], anded);
- }
- else
- {
- System.err.println("Malformed compound filter condition");
- }
- }
- }
-
- /**
- * Loads one XML model of a feature colour to a Jalview object
- *
- * @param colourModel
- * @return
- */
- protected static FeatureColourI unmarshalColour(
- jalview.schemabinding.version2.Colour colourModel)
- {
- FeatureColourI colour = null;
-
- if (colourModel.hasMax())
- {
- Color mincol = null;
- Color maxcol = null;
- Color noValueColour = null;
-
- try
- {
- mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
- maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
- } catch (Exception e)
- {
- Cache.log.warn("Couldn't parse out graduated feature color.", e);
- }
-
- ColourNoValueColourType noCol = colourModel.getNoValueColour();
- if (noCol == ColourNoValueColourType.MIN)
- {
- noValueColour = mincol;
- }
- else if (noCol == ColourNoValueColourType.MAX)
- {
- noValueColour = maxcol;
- }
-
- colour = new FeatureColour(mincol, maxcol, noValueColour,
- colourModel.getMin(),
- colourModel.getMax());
- String[] attributes = colourModel.getAttributeName();
- if (attributes != null && attributes.length > 0)
- {
- colour.setAttributeName(attributes);
- }
- if (colourModel.hasAutoScale())
- {
- colour.setAutoScaled(colourModel.getAutoScale());
- }
- if (colourModel.hasColourByLabel())
- {
- colour.setColourByLabel(colourModel.getColourByLabel());
- }
- if (colourModel.hasThreshold())
- {
- colour.setThreshold(colourModel.getThreshold());
- }
- ColourThreshTypeType ttyp = colourModel.getThreshType();
- if (ttyp != null)
- {
- if (ttyp == ColourThreshTypeType.ABOVE)
- {
- colour.setAboveThreshold(true);
- }
- else if (ttyp == ColourThreshTypeType.BELOW)
- {
- colour.setBelowThreshold(true);
- }
- }
- }
- else
- {
- Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
- colour = new FeatureColour(color);
- }
-
- return colour;
- }
-
- /**
* Constructor
*
* @param af
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"));
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);
- /*
- * load feature colours
- */
- for (int i = jucs.getColourCount() - 1; i >= 0; i--)
- {
- jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
- FeatureColourI colour = unmarshalColour(newcol);
- fr.setColour(newcol.getName(), colour);
- fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount());
- }
+ /*
+ * 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());
+ }
- /*
- * 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++)
+ /*
+ * 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())
{
- jalview.schemabinding.version2.Filter filterModel = jucs
- .getFilter(i);
- FeatureMatcherSetI filter = unmarshalFilter(filterModel);
- if (!filter.isEmpty())
- {
- fr.setFeatureFilter(filterModel.getFeatureType(), filter);
- }
+ fr.setFeatureFilter(featureType, filter);
}
+ }
- /*
- * update feature settings table
- */
- if (table != null)
- {
- resetTable(null);
- Object[][] data = ((FeatureTableModel) table.getModel())
- .getData();
- ensureOrder(data);
- updateFeatureRenderer(data, false);
- table.repaint();
- }
- } 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);
}
}
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"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- String choice = chooser.getSelectedFile().getPath();
- JalviewUserColours ucs = new JalviewUserColours();
- ucs.setSchemeName("Sequence Features");
- try
- {
- PrintWriter out = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(choice), "UTF-8"));
+ save(chooser.getSelectedFile());
+ }
+ }
- /*
- * sort feature types by colour order, from 0 (highest)
- * to 1 (lowest)
- */
- Set<String> fr_colours = fr.getAllFeatureColours();
- String[] sortedTypes = fr_colours
- .toArray(new String[fr_colours.size()]);
- Arrays.sort(sortedTypes, new Comparator<String>()
- {
- @Override
- public int compare(String type1, String type2)
- {
- return Float.compare(fr.getOrder(type1), fr.getOrder(type2));
- }
- });
+ /**
+ * 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"));
- /*
- * save feature colours
- */
- for (String featureType : sortedTypes)
+ /*
+ * sort feature types by colour order, from 0 (highest)
+ * to 1 (lowest)
+ */
+ Set<String> fr_colours = fr.getAllFeatureColours();
+ String[] sortedTypes = fr_colours
+ .toArray(new String[fr_colours.size()]);
+ Arrays.sort(sortedTypes, new Comparator<String>()
+ {
+ @Override
+ public int compare(String type1, String type2)
{
- FeatureColourI fcol = fr.getFeatureStyle(featureType);
- jalview.schemabinding.version2.Colour col = marshalColour(
- featureType, fcol);
- ucs.addColour(col);
+ return Float.compare(fr.getOrder(type1), fr.getOrder(type2));
}
+ });
- /*
- * save any feature filters
- */
- for (String featureType : sortedTypes)
- {
- FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
- if (filter != null && !filter.isEmpty())
- {
- Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
- FeatureMatcherI firstMatcher = iterator.next();
- MatcherSet ms = marshalFilter(firstMatcher, iterator,
- filter.isAnded());
- Filter filterModel = new Filter();
- filterModel.setFeatureType(featureType);
- filterModel.setMatcherSet(ms);
- ucs.addFilter(filterModel);
- }
- }
+ /*
+ * save feature colours
+ */
+ for (String featureType : sortedTypes)
+ {
+ FeatureColourI fcol = fr.getFeatureStyle(featureType);
+ jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour(
+ featureType, fcol);
+ ucs.addColour(col);
+ }
- ucs.marshal(out);
- out.close();
- } catch (Exception ex)
+ /*
+ * save any feature filters
+ */
+ for (String featureType : sortedTypes)
{
- ex.printStackTrace();
+ FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
+ if (filter != null && !filter.isEmpty())
+ {
+ Iterator<FeatureMatcherI> 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();
}
}
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()
}
}
});
- help.setFont(JvSwingUtils.getLabelFont());
- help.setText(MessageManager.getString("action.help"));
- help.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- try
- {
- Help.showHelpWindow(HelpId.SequenceFeatureSettings);
- } catch (HelpSetException e1)
- {
- e1.printStackTrace();
- }
- }
- });
JButton cancel = new JButton(MessageManager.getString("action.cancel"));
cancel.setFont(JvSwingUtils.getLabelFont());
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
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
git://source.jalview.org / jalview.git / blobdiff