X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;h=de78aa1e871a7645425962d9ffd53187e2894265;hb=ca47f64efa144d68e7f6e01ad2c147a7832e97a7;hp=c9b5f4a1f3ea2eca45b57e24c2778a7ebfca9d01;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java index c9b5f4a..de78aa1 100644 --- a/test/jalview/io/AnnotationFileIOTest.java +++ b/test/jalview/io/AnnotationFileIOTest.java @@ -20,48 +20,60 @@ */ package jalview.io; +import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertTrue; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; -import jalview.io.AnnotationFile.ViewDef; - +import java.awt.Color; import java.io.File; import java.util.Hashtable; +import java.util.List; import org.testng.Assert; +import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SequenceGroup; +import jalview.gui.AlignFrame; +import jalview.gui.JvOptionPane; +import jalview.io.AnnotationFile.ViewDef; + public class AnnotationFileIOTest { - static String TestFiles[][] = { - { "Test example annotation import/export", "examples/uniref50.fa", - "examples/testdata/example_annot_file.jva" }, + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + + static String TestFiles[][] = { { "Test example annotation import/export", + "examples/uniref50.fa", "examples/testdata/example_annot_file.jva" }, { "Test multiple combine annotation statements import/export", "examples/uniref50.fa", "examples/testdata/test_combine_annot.jva" }, - { - "Test multiple combine annotation statements with sequence_ref import/export", + { "Test multiple combine annotation statements with sequence_ref import/export", "examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" }, - { - "Test group only annotation file parsing results in parser indicating annotation was parsed", + { "Test group only annotation file parsing results in parser indicating annotation was parsed", "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" }, { "Test hiding/showing of insertions on sequence_ref", - "examples/uniref50.fa", "examples/testdata/uniref50_seqref.jva" } }; + "examples/uniref50.fa", + "examples/testdata/uniref50_seqref.jva" } }; @Test(groups = { "Functional" }) public void exampleAnnotationFileIO() throws Exception { for (String[] testPair : TestFiles) { - testAnnotationFileIO(testPair[0], new File(testPair[1]), new File( - testPair[2])); + testAnnotationFileIO(testPair[0], new File(testPair[1]), + new File(testPair[2])); } } - public static AlignmentI readAlignmentFile(File f) + protected AlignmentI readAlignmentFile(File f) { System.out.println("Reading file: " + f); String ff = f.getPath(); @@ -69,8 +81,8 @@ public class AnnotationFileIOTest { FormatAdapter rf = new FormatAdapter(); - AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE, - new IdentifyFile().identify(ff, AppletFormatAdapter.FILE)); + AlignmentI al = rf.readFile(ff, DataSourceType.FILE, + new IdentifyFile().identify(ff, DataSourceType.FILE)); // make sure dataset is initialised ? not sure about this for (int i = 0; i < al.getSequencesArray().length; ++i) @@ -83,7 +95,8 @@ public class AnnotationFileIOTest { e.printStackTrace(); } - Assert.fail("Couln't read the alignment in file '" + f.toString() + "'"); + Assert.fail( + "Couln't read the alignment in file '" + f.toString() + "'"); return null; } @@ -97,10 +110,7 @@ public class AnnotationFileIOTest * - label for IO class used to write and read back in the data from * f */ - - // @Test(groups ={ "Functional" }) - public static void testAnnotationFileIO(String testname, File f, - File annotFile) + void testAnnotationFileIO(String testname, File f, File annotFile) { System.out.println("Test: " + testname + "\nReading annotation file '" + annotFile + "' onto : " + f); @@ -108,52 +118,87 @@ public class AnnotationFileIOTest try { AlignmentI al = readAlignmentFile(f); - ColumnSelection cs = new ColumnSelection(); - assertTrue( - "Test " - + testname - + "\nAlignment was not annotated - annotation file not imported.", + HiddenColumns cs = new HiddenColumns(); + assertTrue("Test " + testname + + "\nAlignment was not annotated - annotation file not imported.", new AnnotationFile().readAnnotationFile(al, cs, af, - FormatAdapter.FILE)); + DataSourceType.FILE)); AnnotationFile aff = new AnnotationFile(); + // ViewDef is not used by Jalview ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs, new Hashtable()); String anfileout = new AnnotationFile().printAnnotations( al.getAlignmentAnnotation(), al.getGroups(), al.getProperties(), null, al, v); - assertTrue( - "Test " - + testname - + "\nAlignment annotation file was not regenerated. Null string", + assertTrue("Test " + testname + + "\nAlignment annotation file was not regenerated. Null string", anfileout != null); - assertTrue( - "Test " - + testname - + "\nAlignment annotation file was not regenerated. Empty string", + assertTrue("Test " + testname + + "\nAlignment annotation file was not regenerated. Empty string", anfileout.length() > "JALVIEW_ANNOTATION".length()); - System.out.println("Output annotation file:\n" + anfileout - + "\n<Seq1\nQRSIL\n>Seq2\nFTHND\n>Seq3\nRPVSL\n", + DataSourceType.PASTE); + long t2 = System.currentTimeMillis(); + System.err.println("t0: " + (t2 - t1)); + // seq1 and seq3 are in distinct groups both named Group1 + String annotationFile = "JALVIEW_ANNOTATION\nSEQUENCE_GROUP\tGroup1\t*\t*\t1\n" + + "SEQUENCE_GROUP\tGroup2\t*\t*\t2\n" + + "SEQUENCE_GROUP\tGroup1\t*\t*\t3\n" + + "PROPERTIES\tGroup1\toutlineColour=blue\tidColour=red\n"; + new AnnotationFile().annotateAlignmentView(af.getViewport(), + annotationFile, DataSourceType.PASTE); + + AlignmentI al = af.getViewport().getAlignment(); + List groups = al.getGroups(); + assertEquals(3, groups.size()); + SequenceGroup sg = groups.get(0); + assertEquals("Group1", sg.getName()); + assertTrue(sg.contains(al.getSequenceAt(0))); + assertEquals(Color.BLUE, sg.getOutlineColour()); + assertEquals(Color.RED, sg.getIdColour()); + sg = groups.get(1); + assertEquals("Group2", sg.getName()); + assertTrue(sg.contains(al.getSequenceAt(1))); + + /* + * the bug fix: a second group of the same name is also given properties + */ + sg = groups.get(2); + assertEquals("Group1", sg.getName()); + assertTrue(sg.contains(al.getSequenceAt(2))); + assertEquals(Color.BLUE, sg.getOutlineColour()); + assertEquals(Color.RED, sg.getIdColour()); + } }