JAL-1270 main methods converted to JUnit

[jalview.git] / test / jalview / analysis / ParsePropertiesTest.java

diff --git a/test/jalview/analysis/ParsePropertiesTest.java b/test/jalview/analysis/ParsePropertiesTest.java
new file mode 100644 (file)
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--- /dev/null
+++ b/test/jalview/analysis/ParsePropertiesTest.java
@@ -0,0 +1,141 @@
+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);
+  }
+}