X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=61828859ffacc21a41db5256255c0ada27c2e8e7;hp=811b3770159aff73ce055190acf3b1c70ba50bfb;hb=aa4e99f8937ce22963cf32f1e92f174ee52ad7ee;hpb=805fc960e7c2d92e1c5222a303c2d65817b04957 diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 811b377..6182885 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -22,29 +22,20 @@ package jalview.gui; 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; @@ -75,7 +66,6 @@ import java.io.InputStreamReader; 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; @@ -189,290 +179,6 @@ public class FeatureSettings extends JPanel Map 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 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 @@ -1178,7 +884,7 @@ public class FeatureSettings extends JPanel 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()); } @@ -1191,10 +897,12 @@ public class FeatureSettings extends JPanel { 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); } } @@ -1264,7 +972,7 @@ public class FeatureSettings extends JPanel 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); } @@ -1279,7 +987,7 @@ public class FeatureSettings extends JPanel { Iterator 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);