import jalview.analysis.Finder;
import jalview.api.AlignViewControllerI;
+import jalview.api.FeatureColourI;
+import jalview.api.FinderI;
+import jalview.datamodel.Alignment;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
+import jalview.schemes.FeatureColour;
+import java.awt.Color;
import java.util.Arrays;
import java.util.BitSet;
@Test(groups = "Functional")
public void testFindColumnsWithFeature()
{
- SequenceI seq1 = new Sequence("seq1", "aMMMaaaaaaaaaaaaaaaa");
- SequenceI seq2 = new Sequence("seq2", "aaaMMMMMMMaaaaaaaaaa");
- SequenceI seq3 = new Sequence("seq3", "aaaaaaaaaaMMMMMaaaaa");
- SequenceI seq4 = new Sequence("seq3", "aaaaaaaaaaaaaaaaaaaa");
+ SequenceI seq1 = new Sequence("seq1", "-a-MMMaaaaaaaaaaaaaaaa");
+ SequenceI seq2 = new Sequence("seq2", "aa--aMM-MMMMMaaaaaaaaaa");
+ SequenceI seq3 = new Sequence("seq3", "abcab-caD-aaMMMMMaaaaa");
+ SequenceI seq4 = new Sequence("seq4", "abc--abcaaaaaaaaaaaaaa");
/*
* features start/end are base 1
null));
seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
null));
- seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10, 0f,
+ seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10,
+ 10f,
null));
seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
- 0f, null));
+ 10f, null));
+ // disulfide bond is a 'contact feature' - only select its 'start' and 'end'
+ seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc",
+ 8, 12, 0f, null));
/*
- * select the first three columns --> Metal in seq1 2-3
+ * select the first five columns --> Metal in seq1 cols 4-5
*/
SequenceGroup sg = new SequenceGroup();
sg.setStartRes(0); // base 0
- sg.setEndRes(2);
+ sg.setEndRes(4);
sg.addSequence(seq1, false);
sg.addSequence(seq2, false);
sg.addSequence(seq3, false);
sg.addSequence(seq4, false);
+ /*
+ * set features visible on a viewport as only visible features are selected
+ */
+ AlignFrame af = new AlignFrame(new Alignment(new SequenceI[] { seq1,
+ seq2, seq3, seq4 }), 100, 100);
+ af.getFeatureRenderer().findAllFeatures(true);
+
+ AlignViewController avc = new AlignViewController(af, af.getViewport(),
+ af.alignPanel);
+
BitSet bs = new BitSet();
- int seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
- bs);
+ int seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
assertEquals(1, seqCount);
assertEquals(2, bs.cardinality());
- assertTrue(bs.get(1));
- assertTrue(bs.get(2));
+ assertTrue(bs.get(3)); // base 0
+ assertTrue(bs.get(4));
/*
- * select the first four columns: Metal in seq1 2:4, seq2 4:4
+ * select the first seven columns: Metal in seq1 cols 4-6, seq2 cols 6-7
*/
- sg.setEndRes(3);
+ sg.setEndRes(6);
bs.clear();
- seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+ seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
assertEquals(2, seqCount);
- assertEquals(3, bs.cardinality());
- assertTrue(bs.get(1));
- assertTrue(bs.get(2));
+ assertEquals(4, bs.cardinality());
assertTrue(bs.get(3));
+ assertTrue(bs.get(4));
+ assertTrue(bs.get(5));
+ assertTrue(bs.get(6));
/*
- * select column 11: Metal in seq3 only
+ * select column 14: Metal in seq3 only
*/
- sg.setStartRes(10);
- sg.setEndRes(10);
+ sg.setStartRes(13);
+ sg.setEndRes(13);
bs.clear();
- seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+ seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
assertEquals(1, seqCount);
assertEquals(1, bs.cardinality());
- assertTrue(bs.get(10));
+ assertTrue(bs.get(13));
/*
- * select columns 16-20: no Metal feature
+ * select columns 18-20: no Metal feature
*/
- sg.setStartRes(15);
+ sg.setStartRes(17);
sg.setEndRes(19);
bs.clear();
- seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+ seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
assertEquals(0, seqCount);
assertEquals(0, bs.cardinality());
/*
+ * threshold Metal to hide where score < 5
+ * seq1 feature in columns 4-6 is hidden
+ * seq2 feature in columns 6-7 is shown
+ */
+ FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
+ 0f, 10f);
+ fc.setAboveThreshold(true);
+ fc.setThreshold(5f);
+ af.getFeatureRenderer().setColour("Metal", fc);
+ sg.setStartRes(0);
+ sg.setEndRes(6);
+ bs.clear();
+ seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
+ assertEquals(1, seqCount);
+ assertEquals(2, bs.cardinality());
+ assertTrue(bs.get(5));
+ assertTrue(bs.get(6));
+
+ /*
+ * columns 11-13 should not match disulfide bond at 8/12
+ */
+ sg.setStartRes(10);
+ sg.setEndRes(12);
+ bs.clear();
+ seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
+ assertEquals(0, seqCount);
+ assertEquals(0, bs.cardinality());
+
+ /*
+ * columns 6-18 should match disulfide bond at columns 9, 14
+ */
+ sg.setStartRes(5);
+ sg.setEndRes(17);
+ bs.clear();
+ seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
+ assertEquals(1, seqCount);
+ assertEquals(2, bs.cardinality());
+ assertTrue(bs.get(8));
+ assertTrue(bs.get(13));
+
+ /*
* look for a feature that isn't there
*/
sg.setStartRes(0);
sg.setEndRes(19);
bs.clear();
- seqCount = AlignViewController.findColumnsWithFeature("Pfam", sg, bs);
+ seqCount = avc.findColumnsWithFeature("Pfam", sg, bs);
assertEquals(0, seqCount);
assertEquals(0, bs.cardinality());
}
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n"
+ "seq3 aaaaaaaaaaMMMMMaaaaa\n"
- + "seq4 aaaaaaaaaaaaaaaaaaaa\n", FormatAdapter.PASTE);
+ + "seq4 aaaaaaaaaaaaaaaaaaaa\n", DataSourceType.PASTE);
SearchResultsI sr = new SearchResults();
SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
/*
* test Match/Find works first
*/
- Finder f = new Finder(af.getViewport().getAlignment(), null);
- f.setFindAll(true);
- f.setCaseSensitive(true);
- f.find("M+");
+ FinderI f = new Finder(af.getViewport());
+ f.findAll("M+", true, false);
assertEquals(
"Finder found different set of results to manually created SearchResults",
sr, f.getSearchResults());
git://source.jalview.org / jalview.git / blobdiff