X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;h=09624520c7ffbfa810365006bfa7189800ff54c4;hb=e309b8d9bd62fb304fdd612c7385e76027d2f2d7;hp=cfbc8849eec735296c9218a77008750be230ed37;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index cfbc884..0962452 100644
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 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.
*
* 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.
+ * 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 .
+ * 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;
@@ -22,24 +24,40 @@ 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]));
}
}
@@ -53,11 +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;
@@ -65,9 +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
@@ -78,25 +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<