/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
*
*/
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 static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+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 org.junit.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[][] =
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
{
- { "Test example annotation import/export", "examples/uniref50.fa",
- "examples/testdata/example_annot_file.jva" },
+ 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",
- "examples/uniref50.fa", "examples/testdata/test_grpannot.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
+ @Test(groups = { "Functional" })
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]));
}
}
- public static AlignmentI readAlignmentFile(File f)
+ protected AlignmentI readAlignmentFile(File f)
{
System.out.println("Reading file: " + f);
String ff = f.getPath();
{
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)
{
- al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i).createDatasetSequence());
+ 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()+"'");
+ Assert.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)
+ 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");
-
+ HiddenColumns cs = new HiddenColumns();
+ assertTrue("Test " + testname
+ + "\nAlignment was not annotated - annotation file not imported.",
+ new AnnotationFile().readAnnotationFile(al, cs, af,
+ 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",
+ 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,
+ DataSourceType.PASTE));
+
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+ false);
return;
} catch (Exception e)
{
e.printStackTrace();
}
- fail("Test "+testname+"\nCouldn't complete Annotation file roundtrip input/output/input test for '"+annotFile+"'.");
+ Assert.fail("Test " + testname
+ + "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
+ + annotFile + "'.");
+ }
+
+ @Test(groups = "Functional")
+ public void testAnnotateAlignmentView()
+ {
+ long t1 = System.currentTimeMillis();
+ /*
+ * JAL-3779 test multiple groups of the same name get annotated
+ */
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ ">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<SequenceGroup> 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());
}
}
git://source.jalview.org / jalview.git / blobdiff