*/
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.gui.JvOptionPane;
-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
{
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- static String TestFiles[][] = {
- { "Test example annotation import/export", "examples/uniref50.fa",
- "examples/testdata/example_annot_file.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",
+ { "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]));
}
}
- AlignmentI readAlignmentFile(File f)
+ protected AlignmentI readAlignmentFile(File f)
{
System.out.println("Reading file: " + f);
String ff = f.getPath();
{
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;
}
* - label for IO class used to write and read back in the data from
* f
*/
- 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);
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,
DataSourceType.FILE));
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<<EOF\n");
+ 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.",
+ 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, false);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+ false);
return;
} catch (Exception e)
{
e.printStackTrace();
}
- Assert.fail("Test "
- + testname
+ 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