+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
import static org.junit.Assert.assertNotNull;
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
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]));
}
}
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;
{
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
* - 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());
- System.out.println("Output annotation file:\n"+anfileout+"\n<<EOF\n");
-
+ 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());
+
+ System.out.println("Output annotation file:\n" + anfileout
+ + "\n<<EOF\n");
+
AlignmentI al_new = readAlignmentFile(f);
- assertTrue("Test "+testname+"\nregenerated annotation file did not annotate alignment.",new AnnotationFile().readAnnotationFile(al_new, anfileout, FormatAdapter.PASTE));
-
+ assertTrue(
+ "Test "
+ + testname
+ + "\nregenerated annotation file did not annotate alignment.",
+ new AnnotationFile().readAnnotationFile(al_new, anfileout,
+ FormatAdapter.PASTE));
+
// test for consistency in io
StockholmFileTest.testAlignmentEquivalence(al, al_new);
return;
{
e.printStackTrace();
}
- fail("Test "+testname+"\nCouldn't complete Annotation file roundtrip input/output/input test for '"+annotFile+"'.");
+ fail("Test "
+ + testname
+ + "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
+ + annotFile + "'.");
}
}