X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FParsePropertiesTest.java;h=a01d255f7ee4436f0adf13b55517ccdf47d291ac;hb=ad251609d6d0d12aaa6d466b91d719dabf269d7b;hp=a679a469aa8fc8a9c36bac511f3dcb2eeaecfd40;hpb=d07fe6a0891b57a9d707e356f7769395ce94b0da;p=jalview.git

diff --git a/test/jalview/analysis/ParsePropertiesTest.java b/test/jalview/analysis/ParsePropertiesTest.java
index a679a46..a01d255 100644
--- a/test/jalview/analysis/ParsePropertiesTest.java
+++ b/test/jalview/analysis/ParsePropertiesTest.java
@@ -3,6 +3,8 @@ package jalview.analysis;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNull;
 
+import java.util.List;
+
 import org.junit.Before;
 import org.junit.Test;
 
@@ -47,9 +49,6 @@ public class ParsePropertiesTest
   @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);
@@ -138,4 +137,57 @@ public class ParsePropertiesTest
     assertEquals("my Score Description (column 1)", anns[1].description);
     assertEquals("my Score_1", anns[1].label);
   }
+
+  /**
+   * Test with a regex that looks for numbers separated by words - as currently
+   * used in Jalview (May 2015)
+   * 
+   * @see AlignFrame.extractScores_actionPerformed
+   */
+  @Test
+  public void testGetScoresFromDescription_wordBoundaries()
+  {
+    String regex = "\\W*([-+eE0-9.]+)";
+    List<SequenceI> seqs = al.getSequences();
+    seqs.get(0).setDescription("Ferredoxin");
+    seqs.get(1).setDescription(" Ferredoxin-1, chloroplast precursor");
+    seqs.get(2).setDescription("GH28E30p");
+    seqs.get(3).setDescription("At1g10960/T19D16_12");
+    final int count = pp.getScoresFromDescription("description column",
+            "score in description column ", regex, true);
+    assertEquals(3, count);
+
+    /*
+     * No score parsable from seq1 description
+     */
+    AlignmentAnnotation[] anns = al.getSequenceAt(0).getAnnotation();
+    assertNull(anns);
+
+    /*
+     * Seq2 description has a '1' in it
+     */
+    anns = al.getSequenceAt(1).getAnnotation();
+    assertEquals(1, anns.length);
+    assertEquals(1d, anns[0].getScore(), 0.001d);
+
+    /*
+     * Seq3 description has '28E30' in it
+     * 
+     * Note: 1.8E308 or larger would result in 'Infinity'
+     */
+    anns = al.getSequenceAt(2).getAnnotation();
+    assertEquals(1, anns.length);
+    assertEquals(2.8E31d, anns[0].getScore(), 0.001d);
+
+    /*
+     * Seq4 description has several numbers in it
+     */
+    anns = al.getSequenceAt(3).getAnnotation();
+    assertEquals(5, anns.length);
+    assertEquals(1d, anns[0].getScore(), 0.001d);
+    assertEquals(10960d, anns[1].getScore(), 0.001d);
+    assertEquals(19d, anns[2].getScore(), 0.001d);
+    assertEquals(16d, anns[3].getScore(), 0.001d);
+    assertEquals(12d, anns[4].getScore(), 0.001d);
+  }
 }