X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;h=09624520c7ffbfa810365006bfa7189800ff54c4;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=30f61d7572f83ab945b5c5b677a34723bcf168cb;hpb=f25b08ecec2855cc8b02806a849825408ecb334a;p=jalview.git diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java index 30f61d7..0962452 100644 --- a/test/jalview/io/AnnotationFileIOTest.java +++ b/test/jalview/io/AnnotationFileIOTest.java @@ -1,27 +1,63 @@ +/* + * 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.io; import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; +import jalview.io.AnnotationFile.ViewDef; import java.io.File; +import java.util.Hashtable; import org.junit.Test; public class AnnotationFileIOTest { - 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","examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva"}}; + 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", + "examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" }, + { + "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" } }; @Test public void exampleAnnotationFileIO() throws Exception { - for (String[] testPair:TestFiles) + 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])); } } @@ -35,11 +71,12 @@ public class AnnotationFileIOTest AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE, new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE)); - + // make sure dataset is initialised ? not sure about this for (int i = 0; i < al.getSequencesArray().length; ++i) { - al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i).createDatasetSequence()); + al.getSequenceAt(i).setDatasetSequence( + al.getSequenceAt(i).createDatasetSequence()); } assertNotNull("Couldn't read supplied alignment data.", al); return al; @@ -47,9 +84,10 @@ public class AnnotationFileIOTest { e.printStackTrace(); } - fail("Couln't read the alignment in file '"+f.toString()+"'"); + fail("Couln't read the alignment in file '" + f.toString() + "'"); return null; } + /** * test alignment data in given file can be imported, exported and reimported * with no dataloss @@ -60,25 +98,51 @@ public class AnnotationFileIOTest * - label for IO class used to write and read back in the data from * f */ - public static void testAnnotationFileIO(String testname, File f, File annotFile) + public static void testAnnotationFileIO(String testname, File f, + File annotFile) { - System.out.println("Test: "+testname+"\nReading annotation file '"+annotFile+"' onto : " + f); + System.out.println("Test: " + testname + "\nReading annotation file '" + + annotFile + "' onto : " + f); String af = annotFile.getPath(); try { AlignmentI al = readAlignmentFile(f); - - assertTrue("Test "+testname+"\nAlignment was not annotated - annotation file not imported.",new AnnotationFile().readAnnotationFile(al, af, FormatAdapter.FILE)); - - String anfileout = new AnnotationFile().printAnnotations(al.getAlignmentAnnotation(), al.getGroups(), al.getProperties()); - assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Null string",anfileout!=null); - assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Empty string",anfileout.length()>"JALVIEW_ANNOTATION".length()); + ColumnSelection cs = new ColumnSelection(); + assertTrue( + "Test " + + testname + + "\nAlignment was not annotated - annotation file not imported.", + new AnnotationFile().readAnnotationFile(al, cs, af, + FormatAdapter.FILE)); + + AnnotationFile aff = new AnnotationFile(); + 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", + anfileout != null); + 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<