X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentAnnotationTests.java;h=19a725ecfb1fd3ddc09edc3e627b085dea18ad0a;hb=5c1e80ada930876d477059fd92c68c898659efbf;hp=4981db6fa49e70f50f7dbd04d2207557a9428d1c;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java index 4981db6..19a725e 100644 --- a/test/jalview/datamodel/AlignmentAnnotationTests.java +++ b/test/jalview/datamodel/AlignmentAnnotationTests.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,16 +20,28 @@ */ package jalview.datamodel; +import static org.testng.Assert.assertNull; import static org.testng.AssertJUnit.assertEquals; -import static org.testng.AssertJUnit.assertNull; import jalview.analysis.AlignSeq; +import jalview.gui.JvOptionPane; import jalview.io.AppletFormatAdapter; +import jalview.io.FileFormat; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; public class AlignmentAnnotationTests { + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + @Test(groups = { "Functional" }) public void testCopyConstructor() { @@ -119,7 +131,8 @@ public class AlignmentAnnotationTests alSeq2.setEnd(sqTo.getStart() + align.getSeq2End() - 1); alSeq2.setDatasetSequence(sqTo); System.out.println(new AppletFormatAdapter() - .formatSequences("STH", new Alignment(new SequenceI[] { sqFrom, +.formatSequences( + FileFormat.Stockholm, new Alignment(new SequenceI[] { sqFrom, alSeq1, sqTo, alSeq2 }), true)); Mapping mp = align.getMappingFromS1(false); @@ -143,7 +156,8 @@ public class AlignmentAnnotationTests AlignmentI all = new Alignment(new SequenceI[] { alSeq1, alSeq2 }); all.addAnnotation(almap1); all.addAnnotation(almap2); - System.out.println(new AppletFormatAdapter().formatSequences("STH", + System.out.println(new AppletFormatAdapter().formatSequences( + FileFormat.Stockholm, all, true)); for (int p = 0; p < alSeq1.getLength(); p++) @@ -219,4 +233,194 @@ public class AlignmentAnnotationTests assertEquals(1, ann.annotations[1].value, 0.001); assertEquals(2, ann.annotations[2].value, 0.001); } + + /** + * Test the method that defaults rna symbol to the one matching the preceding + * unmatched opening bracket (if any) + */ + @Test(groups = { "Functional" }) + public void testGetDefaultRnaHelixSymbol() + { + AlignmentAnnotation ann = new AlignmentAnnotation("SS", + "secondary structure", null); + assertEquals("(", ann.getDefaultRnaHelixSymbol(4)); + + Annotation[] anns = new Annotation[20]; + ann.annotations = anns; + assertEquals("(", ann.getDefaultRnaHelixSymbol(4)); + + anns[1] = new Annotation("(", "S", '(', 0f); + assertEquals("(", ann.getDefaultRnaHelixSymbol(0)); + assertEquals("(", ann.getDefaultRnaHelixSymbol(1)); + assertEquals(")", ann.getDefaultRnaHelixSymbol(2)); + assertEquals(")", ann.getDefaultRnaHelixSymbol(3)); + + /* + * .(.[.{.<.}.>.).]. + */ + anns[1] = new Annotation("(", "S", '(', 0f); + anns[3] = new Annotation("[", "S", '[', 0f); + anns[5] = new Annotation("{", "S", '{', 0f); + anns[7] = new Annotation("<", "S", '<', 0f); + anns[9] = new Annotation("}", "S", '}', 0f); + anns[11] = new Annotation(">", "S", '>', 0f); + anns[13] = new Annotation(")", "S", ')', 0f); + anns[15] = new Annotation("]", "S", ']', 0f); + + String expected = "(())]]}}>>>>]]]]("; + for (int i = 0; i < expected.length(); i++) + { + assertEquals("column " + i, String.valueOf(expected.charAt(i)), + ann.getDefaultRnaHelixSymbol(i)); + } + + /* + * .(.[.(.).{.}.<.].D. + */ + anns[1] = new Annotation("(", "S", '(', 0f); + anns[3] = new Annotation("[", "S", '[', 0f); + anns[5] = new Annotation("(", "S", '(', 0f); + anns[7] = new Annotation(")", "S", ')', 0f); + anns[9] = new Annotation("{", "S", '{', 0f); + anns[11] = new Annotation("}", "S", '}', 0f); + anns[13] = new Annotation("<", "S", '>', 0f); + anns[15] = new Annotation("]", "S", ']', 0f); + anns[17] = new Annotation("D", "S", 'D', 0f); + + expected = "(())]]))]]}}]]>>>>dd"; + for (int i = 0; i < expected.length(); i++) + { + assertEquals("column " + i, String.valueOf(expected.charAt(i)), + ann.getDefaultRnaHelixSymbol(i)); + } + } + + public static Annotation newAnnotation(String ann) + { + float val = 0f; + try + { + val = Float.parseFloat(ann); + } catch (NumberFormatException q) + { + } + ; + return new Annotation(ann, ann, '\0', val); + } + + @Test(groups = { "Functional" }) + public void testIsQuantitative() + { + AlignmentAnnotation ann = null; + + ann = new AlignmentAnnotation("an", "some an", null); + Assert.assertFalse(ann.isQuantitative(), + "Empty annotation set should not be quantitative."); + + ann = new AlignmentAnnotation("an", "some an", new Annotation[] { + newAnnotation("4"), newAnnotation("1"), newAnnotation("1"), + newAnnotation("0.1"), newAnnotation("0.3") }); + Assert.assertTrue(ann.isQuantitative(), + "All numbers annotation set should be quantitative."); + + ann = new AlignmentAnnotation("an", "some an", new Annotation[] { + newAnnotation("E"), newAnnotation("E"), newAnnotation("E"), + newAnnotation("E"), newAnnotation("E") }); + Assert.assertFalse(ann.isQuantitative(), + "All 'E' annotation set should not be quantitative."); + + ann = new AlignmentAnnotation("an", "some an", new Annotation[] { + newAnnotation("E"), newAnnotation("1"), newAnnotation("2"), + newAnnotation("3"), newAnnotation("E") }); + Assert.assertTrue(ann.isQuantitative(), + "Mixed 'E' annotation set should be quantitative."); + } + + @Test(groups = "Functional") + public void testMakeVisibleAnnotation() + { + HiddenColumns h = new HiddenColumns(); + Annotation[] anns = new Annotation[] { null, null, new Annotation(1), + new Annotation(2), new Annotation(3), null, null, new Annotation(4), + new Annotation(5), new Annotation(6), new Annotation(7), + new Annotation(8) }; + AlignmentAnnotation ann = new AlignmentAnnotation("an", "some an", + anns); + + // null annotations + AlignmentAnnotation emptyann = new AlignmentAnnotation("an", "some ann", + null); + emptyann.makeVisibleAnnotation(h); + assertNull(emptyann.annotations); + + emptyann.makeVisibleAnnotation(3, 4, h); + assertNull(emptyann.annotations); + + // without bounds, does everything + ann.makeVisibleAnnotation(h); + assertEquals(12, ann.annotations.length); + assertNull(ann.annotations[0]); + assertNull(ann.annotations[1]); + assertEquals(1.0f, ann.annotations[2].value); + assertEquals(2.0f, ann.annotations[3].value); + assertEquals(3.0f, ann.annotations[4].value); + assertNull(ann.annotations[5]); + assertNull(ann.annotations[6]); + assertEquals(4.0f, ann.annotations[7].value); + assertEquals(5.0f, ann.annotations[8].value); + assertEquals(6.0f, ann.annotations[9].value); + assertEquals(7.0f, ann.annotations[10].value); + assertEquals(8.0f, ann.annotations[11].value); + + // without hidden cols, just truncates + ann.makeVisibleAnnotation(3, 5, h); + assertEquals(3, ann.annotations.length); + assertEquals(2.0f, ann.annotations[0].value); + assertEquals(3.0f, ann.annotations[1].value); + assertNull(ann.annotations[2]); + + anns = new Annotation[] { null, null, new Annotation(1), + new Annotation(2), new Annotation(3), null, null, new Annotation(4), + new Annotation(5), new Annotation(6), new Annotation(7), + new Annotation(8) }; + ann = new AlignmentAnnotation("an", "some an", anns); + h.hideColumns(4, 7); + ann.makeVisibleAnnotation(1, 9, h); + assertEquals(5, ann.annotations.length); + assertNull(ann.annotations[0]); + assertEquals(1.0f, ann.annotations[1].value); + assertEquals(2.0f, ann.annotations[2].value); + assertEquals(5.0f, ann.annotations[3].value); + assertEquals(6.0f, ann.annotations[4].value); + + anns = new Annotation[] { null, null, new Annotation(1), + new Annotation(2), new Annotation(3), null, null, new Annotation(4), + new Annotation(5), new Annotation(6), new Annotation(7), + new Annotation(8) }; + ann = new AlignmentAnnotation("an", "some an", anns); + h.hideColumns(1, 2); + ann.makeVisibleAnnotation(1, 9, h); + assertEquals(3, ann.annotations.length); + assertEquals(2.0f, ann.annotations[0].value); + assertEquals(5.0f, ann.annotations[1].value); + assertEquals(6.0f, ann.annotations[2].value); + + anns = new Annotation[] { null, null, new Annotation(1), + new Annotation(2), new Annotation(3), null, null, new Annotation(4), + new Annotation(5), new Annotation(6), new Annotation(7), + new Annotation(8), new Annotation(9), new Annotation(10), + new Annotation(11), new Annotation(12), new Annotation(13), + new Annotation(14), new Annotation(15) }; + ann = new AlignmentAnnotation("an", "some an", anns); + h = new HiddenColumns(); + h.hideColumns(5, 18); + h.hideColumns(20, 21); + ann.makeVisibleAnnotation(1, 21, h); + assertEquals(5, ann.annotations.length); + assertEquals(1.0f, ann.annotations[1].value); + assertEquals(2.0f, ann.annotations[2].value); + assertEquals(3.0f, ann.annotations[3].value); + assertNull(ann.annotations[0]); + assertNull(ann.annotations[4]); + } }