/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.
*
import static org.testng.AssertJUnit.assertNull;
import jalview.analysis.AlignSeq;
+import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
+import jalview.io.FileFormat;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AlignmentAnnotationTests
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testCopyConstructor()
{
alSeq2.setEnd(sqTo.getStart() + align.getSeq2End() - 1);
alSeq2.setDatasetSequence(sqTo);
System.out.println(new AppletFormatAdapter()
- .formatSequences("STH", new Alignment(new SequenceI[] { sqFrom,
+.formatSequences(
+ FileFormat.Stockholm, new Alignment(new SequenceI[] { sqFrom,
alSeq1, sqTo, alSeq2 }), true));
Mapping mp = align.getMappingFromS1(false);
AlignmentI all = new Alignment(new SequenceI[] { alSeq1, alSeq2 });
all.addAnnotation(almap1);
all.addAnnotation(almap2);
- System.out.println(new AppletFormatAdapter().formatSequences("STH",
+ System.out.println(new AppletFormatAdapter().formatSequences(
+ FileFormat.Stockholm,
all, true));
for (int p = 0; p < alSeq1.getLength(); p++)
ann.getDefaultRnaHelixSymbol(i));
}
}
-}
\ No newline at end of file
+
+ public static Annotation newAnnotation(String ann)
+ {
+ float val = 0f;
+ try
+ {
+ val = Float.parseFloat(ann);
+ } catch (NumberFormatException q)
+ {
+ }
+ ;
+ return new Annotation(ann, ann, '\0', val);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testIsQuantitative()
+ {
+ AlignmentAnnotation ann = null;
+
+ ann = new AlignmentAnnotation("an", "some an", null);
+ Assert.assertFalse(ann.isQuantitative(),
+ "Empty annotation set should not be quantitative.");
+
+ ann = new AlignmentAnnotation("an", "some an", new Annotation[] {
+ newAnnotation("4"), newAnnotation("1"), newAnnotation("1"),
+ newAnnotation("0.1"), newAnnotation("0.3") });
+ Assert.assertTrue(ann.isQuantitative(),
+ "All numbers annotation set should be quantitative.");
+
+ ann = new AlignmentAnnotation("an", "some an", new Annotation[] {
+ newAnnotation("E"), newAnnotation("E"), newAnnotation("E"),
+ newAnnotation("E"), newAnnotation("E") });
+ Assert.assertFalse(ann.isQuantitative(),
+ "All 'E' annotation set should not be quantitative.");
+
+ ann = new AlignmentAnnotation("an", "some an", new Annotation[] {
+ newAnnotation("E"), newAnnotation("1"), newAnnotation("2"),
+ newAnnotation("3"), newAnnotation("E") });
+ Assert.assertTrue(ann.isQuantitative(),
+ "Mixed 'E' annotation set should be quantitative.");
+ }
+}