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;
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
for (int i = jucs.getColourCount() - 1; i >= 0; i--)
{
jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
- FeatureColourI colour = unmarshalColour(newcol);
+ FeatureColourI colour = Jalview2XML.unmarshalColour(newcol);
fr.setColour(newcol.getName(), colour);
fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount());
}
{
jalview.schemabinding.version2.Filter filterModel = jucs
.getFilter(i);
- FeatureMatcherSetI filter = unmarshalFilter(filterModel);
+ String featureType = filterModel.getFeatureType();
+ FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(featureType,
+ filterModel.getMatcherSet());
if (!filter.isEmpty())
{
- fr.setFeatureFilter(filterModel.getFeatureType(), filter);
+ fr.setFeatureFilter(featureType, filter);
}
}
for (String featureType : sortedTypes)
{
FeatureColourI fcol = fr.getFeatureStyle(featureType);
- jalview.schemabinding.version2.Colour col = marshalColour(
+ jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour(
featureType, fcol);
ucs.addColour(col);
}
{
Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
FeatureMatcherI firstMatcher = iterator.next();
- MatcherSet ms = marshalFilter(firstMatcher, iterator,
+ MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator,
filter.isAnded());
Filter filterModel = new Filter();
filterModel.setFeatureType(featureType);
git://source.jalview.org / jalview.git / blobdiff