import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcher;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.gui.AlignFrame;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.schemes.FeatureColour;
import jalview.util.matcher.Condition;
-import jalview.util.matcher.KeyedMatcher;
-import jalview.util.matcher.KeyedMatcherSet;
-import jalview.util.matcher.KeyedMatcherSetI;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
seqs.get(2).addSequenceFeature(
new SequenceFeature("Pfam", "Desc", 14, 22, 2f, "RfamGroup"));
// bug in findAllFeatures - group not checked for a known feature type
- seqs.get(2).addSequenceFeature(
- new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN,
- "RfamGroup"));
+ seqs.get(2).addSequenceFeature(new SequenceFeature("Rfam", "Desc", 5, 9,
+ Float.NaN, "RfamGroup"));
// existing feature type with null group
seqs.get(3).addSequenceFeature(
new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN, null));
* change render order (todo: an easier way)
* nb here last comes first in the data array
*/
- Object[][] data = new Object[3][];
+ FeatureSettingsBean[] data = new FeatureSettingsBean[3];
FeatureColourI colour = new FeatureColour(Color.RED);
- data[0] = new Object[] { "Rfam", colour, true };
- data[1] = new Object[] { "Pfam", colour, false };
- data[2] = new Object[] { "Scop", colour, false };
+ data[0] = new FeatureSettingsBean("Rfam", colour, null, true);
+ data[1] = new FeatureSettingsBean("Pfam", colour, null, false);
+ data[2] = new FeatureSettingsBean("Scop", colour, null, false);
fr.setFeaturePriority(data);
- assertEquals(fr.getRenderOrder(), Arrays.asList("Scop", "Pfam", "Rfam"));
+ assertEquals(fr.getRenderOrder(),
+ Arrays.asList("Scop", "Pfam", "Rfam"));
assertEquals(fr.getDisplayedFeatureTypes(), Arrays.asList("Rfam"));
/*
/*
* make "Type2" not displayed
*/
- Object[][] data = new Object[4][];
FeatureColourI colour = new FeatureColour(Color.RED);
- data[0] = new Object[] { "Type1", colour, true };
- data[1] = new Object[] { "Type2", colour, false };
- data[2] = new Object[] { "Type3", colour, true };
- data[3] = new Object[] { "Disulphide Bond", colour, true };
+ FeatureSettingsBean[] data = new FeatureSettingsBean[4];
+ data[0] = new FeatureSettingsBean("Type1", colour, null, true);
+ data[1] = new FeatureSettingsBean("Type2", colour, null, false);
+ data[2] = new FeatureSettingsBean("Type3", colour, null, true);
+ data[3] = new FeatureSettingsBean("Disulphide Bond", colour, null,
+ true);
fr.setFeaturePriority(data);
features = fr.findFeaturesAtColumn(seq, 15);
features = fr.findFeaturesAtColumn(seq, 5);
assertEquals(features.size(), 1);
assertTrue(features.contains(sf8));
-
+
/*
* give "Type3" features a graduated colour scheme
* - first with no threshold
/*
* hide feature type, then unhide
+ * - feature type visibility should not affect the result
*/
- Object[][] data = new Object[1][];
- data[0] = new Object[] { "Cath", fc, false };
+ FeatureSettingsBean[] data = new FeatureSettingsBean[1];
+ data[0] = new FeatureSettingsBean("Cath", fc, null, false);
fr.setFeaturePriority(data);
- assertNull(fr.getColour(sf1));
- data[0] = new Object[] { "Cath", fc, true };
+ assertEquals(fr.getColour(sf1), Color.red);
+ data[0] = new FeatureSettingsBean("Cath", fc, null, true);
fr.setFeaturePriority(data);
assertEquals(fr.getColour(sf1), Color.red);
SequenceFeature sf2 = new SequenceFeature("Cath", "", 6, 8, 6f,
"group1");
// score 6 is half way from yellow(255, 255, 0) to red(255, 0, 0)
- assertEquals(fr.getColour(sf2), new Color(255, 128, 0));
-
+ Color expected = new Color(255, 128, 0);
+ assertEquals(fr.getColour(sf2), expected);
+
/*
* above threshold, score is above threshold - no change
*/
gc.setAboveThreshold(true);
gc.setThreshold(5f);
- assertEquals(fr.getColour(sf2), new Color(255, 128, 0));
+ assertEquals(fr.getColour(sf2), expected);
/*
* threshold is min-max; now score 6 is 1/6 of the way from 5 to 11
// with numeric attribute value
sf2.setValue("AF", "6");
- assertEquals(fr.getColour(sf2), new Color(255, 128, 0));
+ assertEquals(fr.getColour(sf2), expected);
// with numeric value outwith threshold
gc.setAboveThreshold(true);
// with filter on AF < 4
gc.setAboveThreshold(false);
- assertEquals(fr.getColour(sf2), new Color(255, 128, 0));
- KeyedMatcherSetI filter = new KeyedMatcherSet();
- filter.and(new KeyedMatcher(Condition.LT, 4f, "AF"));
+ assertEquals(fr.getColour(sf2), expected);
+ FeatureMatcherSetI filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byAttribute(Condition.LT, "4.0", "AF"));
fr.setFeatureFilter("Cath", filter);
assertNull(fr.getColour(sf2));
// with filter on 'Consequence contains missense'
- filter = new KeyedMatcherSet();
- filter.and(new KeyedMatcher(Condition.Contains, "missense",
+ filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byAttribute(Condition.Contains, "missense",
"Consequence"));
fr.setFeatureFilter("Cath", filter);
// if feature has no Consequence attribute, no colour
assertNull(fr.getColour(sf2));
// attribute matches filter
sf2.setValue("Consequence", "Missense variant");
- assertEquals(fr.getColour(sf2), new Color(255, 128, 0));
+ assertEquals(fr.getColour(sf2), expected);
+
+ // with filter on CSQ:Feature contains "ENST01234"
+ filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byAttribute(Condition.Matches, "ENST01234",
+ "CSQ", "Feature"));
+ fr.setFeatureFilter("Cath", filter);
+ // if feature has no CSQ data, no colour
+ assertNull(fr.getColour(sf2));
+ // if CSQ data does not include Feature, no colour
+ Map<String, String> csqData = new HashMap<>();
+ csqData.put("BIOTYPE", "Transcript");
+ sf2.setValue("CSQ", csqData);
+ assertNull(fr.getColour(sf2));
+ // if attribute does not match filter, no colour
+ csqData.put("Feature", "ENST9876");
+ assertNull(fr.getColour(sf2));
+ // attribute matches filter
+ csqData.put("Feature", "ENST01234");
+ assertEquals(fr.getColour(sf2), expected);
}
}