X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fcontroller%2FAlignViewControllerTest.java;h=ca3b55c07cd33784147d173e2e41cd5705bdfa18;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=f037599f7044a8d06bac6146a704169220509918;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java index f037599..ca3b55c 100644 --- a/test/jalview/controller/AlignViewControllerTest.java +++ b/test/jalview/controller/AlignViewControllerTest.java @@ -25,6 +25,9 @@ import static org.testng.AssertJUnit.assertTrue; 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; @@ -32,16 +35,28 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; +import jalview.gui.JvOptionPane; import jalview.io.DataSourceType; import jalview.io.FileLoader; +import jalview.schemes.FeatureColour; +import java.awt.Color; import java.util.Arrays; import java.util.BitSet; +import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; public class AlignViewControllerTest { + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + @Test(groups = "Functional") public void testFindColumnsWithFeature() { @@ -53,17 +68,17 @@ public class AlignViewControllerTest /* * features start/end are base 1 */ - seq1.addSequenceFeature(new SequenceFeature("Metal", "desc", 2, 4, 0f, - null)); - seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f, - null)); - seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10, 0f, - null)); - seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15, - 0f, null)); + seq1.addSequenceFeature( + new SequenceFeature("Metal", "desc", 2, 4, 0f, null)); + seq1.addSequenceFeature( + new SequenceFeature("Helix", "desc", 1, 15, 0f, null)); + seq2.addSequenceFeature( + new SequenceFeature("Metal", "desc", 4, 10, 10f, null)); + seq3.addSequenceFeature( + new SequenceFeature("Metal", "desc", 11, 15, 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)); + seq3.addSequenceFeature( + new SequenceFeature("disulfide bond", "desc", 8, 12, 0f, null)); /* * select the first five columns --> Metal in seq1 cols 4-5 @@ -76,9 +91,19 @@ public class AlignViewControllerTest 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(3)); // base 0 @@ -89,7 +114,7 @@ public class AlignViewControllerTest */ sg.setEndRes(6); bs.clear(); - seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs); + seqCount = avc.findColumnsWithFeature("Metal", sg, bs); assertEquals(2, seqCount); assertEquals(4, bs.cardinality()); assertTrue(bs.get(3)); @@ -103,7 +128,7 @@ public class AlignViewControllerTest 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(13)); @@ -114,18 +139,36 @@ public class AlignViewControllerTest 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 = AlignViewController.findColumnsWithFeature("disulfide bond", - sg, bs); + seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs); assertEquals(0, seqCount); assertEquals(0, bs.cardinality()); @@ -135,8 +178,7 @@ public class AlignViewControllerTest sg.setStartRes(5); sg.setEndRes(17); bs.clear(); - seqCount = AlignViewController.findColumnsWithFeature("disulfide bond", - sg, bs); + seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs); assertEquals(1, seqCount); assertEquals(2, bs.cardinality()); assertTrue(bs.get(8)); @@ -148,7 +190,7 @@ public class AlignViewControllerTest 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()); } @@ -163,7 +205,8 @@ public class AlignViewControllerTest AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n" + "seq3 aaaaaaaaaaMMMMMaaaaa\n" - + "seq4 aaaaaaaaaaaaaaaaaaaa\n", DataSourceType.PASTE); + + "seq4 aaaaaaaaaaaaaaaaaaaa\n", + DataSourceType.PASTE); SearchResultsI sr = new SearchResults(); SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray(); @@ -182,10 +225,8 @@ public class AlignViewControllerTest /* * 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, false); assertEquals( "Finder found different set of results to manually created SearchResults", sr, f.getSearchResults()); @@ -197,8 +238,9 @@ public class AlignViewControllerTest AlignViewControllerI avc = af.avc; avc.markHighlightedColumns(false, false, false); - assertTrue("Didn't select highlighted columns", Arrays.deepEquals(af - .getViewport().getColumnSelection().getSelectedRanges() - .toArray(), new int[][] { { 1, 14 } })); + assertTrue("Didn't select highlighted columns", + Arrays.deepEquals(af.getViewport().getColumnSelection() + .getSelectedRanges().toArray(), new int[][] + { { 1, 14 } })); } }