X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fcontroller%2FAlignViewControllerTest.java;h=7990d21b9bb53dd854c87ff908ec1ca6658474a6;hb=9c8b674e5ab62309b0df090977c8bf8288deb98b;hp=55428b145de7393e09701edb5dc2c10d27d91130;hpb=528c0f1815bc67b54618ad5b16c2162946974caf;p=jalview.git diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java index 55428b1..7990d21 100644 --- a/test/jalview/controller/AlignViewControllerTest.java +++ b/test/jalview/controller/AlignViewControllerTest.java @@ -1,26 +1,69 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.controller; import static org.testng.AssertJUnit.assertEquals; 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; 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() { - 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 @@ -29,71 +72,173 @@ public class AlignViewControllerTest 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()); } + + /** + * shameless copy of test data from findFeature for testing mark columns from + * highlight + */ + @Test(groups = "Functional") + public void testSelectColumnsWithHighlight() + { + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n" + + "seq3 aaaaaaaaaaMMMMMaaaaa\n" + + "seq4 aaaaaaaaaaaaaaaaaaaa\n", DataSourceType.PASTE); + + SearchResultsI sr = new SearchResults(); + SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray(); + SequenceI seq1 = sqs[0]; + SequenceI seq2 = sqs[1]; + SequenceI seq3 = sqs[2]; + SequenceI seq4 = sqs[3]; + + /* + * features start/end are base 1 + */ + sr.addResult(seq1, 2, 4); + sr.addResult(seq2, 4, 10); + sr.addResult(seq3, 11, 15); + + /* + * test Match/Find works first + */ + 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()); + + /* + * now check simple mark columns from find operation + */ + af.getViewport().setSearchResults(sr); + 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 } })); + } }