+package jalview.analysis;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
+import org.junit.Before;
+import org.junit.Test;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+public class ParsePropertiesTest
+{
+
+ private Alignment al;
+
+ private ParseProperties pp;
+
+ /**
+ * Construct an alignment with 4 sequences with varying description format
+ */
+ @Before
+ public void setUp()
+ {
+ SequenceI[] seqs = new SequenceI[]
+ { new Sequence("sq1", "THISISAPLACEHOLDER"),
+ new Sequence("sq2", "THISISAPLACEHOLDER"),
+ new Sequence("sq3", "THISISAPLACEHOLDER"),
+ new Sequence("sq4", "THISISAPLACEHOLDER") };
+ seqs[0].setDescription("1 mydescription1");
+ seqs[1].setDescription("mydescription2");
+ seqs[2].setDescription("2. 0.1 mydescription+3");
+ seqs[3].setDescription("3 0.01 mydescription4");
+ al = new Alignment(seqs);
+
+ pp = new ParseProperties(al);
+
+ }
+
+ /**
+ * Test with a description pattern that matches any string ending in one or
+ * more 'number characters' (0-9+.), i.e. greedily matches any trailing
+ * numeric part of the string
+ */
+ @Test
+ public void testGetScoresFromDescription()
+ {
+ // TODO - test the regex actually used by Jalview?
+ // \\W*([-+eE0-9.]+)
+ // see AlignFrame.extractScores_actionPerformed
+ String regex = ".*([-0-9.+]+)";
+ final int count = pp.getScoresFromDescription("my Score",
+ "my Score Description", regex, true);
+ System.out.println("Matched " + count + " for " + regex);
+ assertEquals(4, count);
+
+ /*
+ * Verify values 1/2/3/4 have been parsed from sequence descriptions
+ */
+ AlignmentAnnotation[] anns = al.getSequenceAt(0).getAnnotation();
+ assertEquals(1, anns.length);
+ assertEquals(1d, anns[0].getScore(), 0.001d);
+ assertEquals("my Score Description", anns[0].description);
+ assertEquals("my Score", anns[0].label);
+ anns = al.getSequenceAt(1).getAnnotation();
+ assertEquals(1, anns.length);
+ assertEquals(2d, anns[0].getScore(), 0.001d);
+ assertEquals("my Score Description", anns[0].description);
+ assertEquals("my Score", anns[0].label);
+ anns = al.getSequenceAt(2).getAnnotation();
+ assertEquals(1, anns.length);
+ assertEquals(3d, anns[0].getScore(), 0.001d);
+ anns = al.getSequenceAt(3).getAnnotation();
+ assertEquals(1, anns.length);
+ assertEquals(4d, anns[0].getScore(), 0.001d);
+ }
+
+ /**
+ * Test with a description pattern that matches any string (or none), followed
+ * by a 'number character' (0-9+.), followed by at least one separator
+ * character, followed by at least one 'number character', then any trailing
+ * characters.
+ */
+ @Test
+ public void testGetScoresFromDescription_twoScores()
+ {
+ String regex = ".*([-0-9.+]+).+([-0-9.+]+).*";
+ final int count = pp.getScoresFromDescription("my Score",
+ "my Score Description", regex, true);
+ System.out.println("Matched " + count + " for " + regex);
+ assertEquals(3, count);
+
+ /*
+ * Seq1 has two score values parsed out
+ */
+ AlignmentAnnotation[] anns = al.getSequenceAt(0).getAnnotation();
+ assertEquals(2, anns.length);
+ assertEquals(1d, anns[0].getScore(), 0.001d);
+ assertEquals("my Score Description", anns[0].description);
+ assertEquals("my Score", anns[0].label);
+ assertEquals(1d, anns[1].getScore(), 0.001d);
+ assertEquals("my Score Description (column 1)", anns[1].description);
+ assertEquals("my Score_1", anns[1].label);
+
+ /*
+ * Seq2 has no score parsed out (is this right?)
+ */
+ assertNull(al.getSequenceAt(1).getAnnotation());
+
+ /*
+ * Seq3 has two score values parsed out
+ */
+ // TODO parsed values (1.0 and 3.0) look wrong v description
+ // would expect 2.0 and 0.1
+ // undesired 'greedy' behaviour of regex?
+ anns = al.getSequenceAt(2).getAnnotation();
+ assertEquals(2, anns.length);
+ assertEquals(1d, anns[0].getScore(), 0.001d);
+ assertEquals("my Score Description", anns[0].description);
+ assertEquals("my Score", anns[0].label);
+ assertEquals(3d, anns[1].getScore(), 0.001d);
+ assertEquals("my Score Description (column 1)", anns[1].description);
+ assertEquals("my Score_1", anns[1].label);
+
+ /*
+ * Seq3 has two score values parsed out
+ */
+ // TODO parsed values (1.0 and 4.0) look wrong v description
+ // would expect 3 and 0.01
+ anns = al.getSequenceAt(3).getAnnotation();
+ assertEquals(2, anns.length);
+ assertEquals(1d, anns[0].getScore(), 0.001d);
+ assertEquals("my Score Description", anns[0].description);
+ assertEquals("my Score", anns[0].label);
+ assertEquals(4d, anns[1].getScore(), 0.001d);
+ assertEquals("my Score Description (column 1)", anns[1].description);
+ assertEquals("my Score_1", anns[1].label);
+ }
+}