JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/test/jalview/analysis/ParsePropertiesTest.java b/test/jalview/analysis/ParsePropertiesTest.java
index a679a46..5013b35 100644 (file)
--- a/test/jalview/analysis/ParsePropertiesTest.java
+++ b/test/jalview/analysis/ParsePropertiesTest.java
@@ -1,16 +1,38 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.analysis;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-
-import org.junit.Before;
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
 
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
+import java.util.List;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 public class ParsePropertiesTest
 {
 
@@ -21,11 +43,11 @@ public class ParsePropertiesTest
   /**
    * Construct an alignment with 4 sequences with varying description format
    */
-  @Before
+  @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
-    SequenceI[] seqs = new SequenceI[]
-    { new Sequence("sq1", "THISISAPLACEHOLDER"),
+    SequenceI[] seqs = new SequenceI[] {
+        new Sequence("sq1", "THISISAPLACEHOLDER"),
         new Sequence("sq2", "THISISAPLACEHOLDER"),
         new Sequence("sq3", "THISISAPLACEHOLDER"),
         new Sequence("sq4", "THISISAPLACEHOLDER") };
@@ -44,12 +66,9 @@ public class ParsePropertiesTest
    * more 'number characters' (0-9+.), i.e. greedily matches any trailing
    * numeric part of the string
    */
-  @Test
+  @Test(groups = { "Functional" })
   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);
@@ -83,7 +102,7 @@ public class ParsePropertiesTest
    * character, followed by at least one 'number character', then any trailing
    * characters.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testGetScoresFromDescription_twoScores()
   {
     String regex = ".*([-0-9.+]+).+([-0-9.+]+).*";
@@ -138,4 +157,57 @@ 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(groups = { "Functional" })
+  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);
+  }
 }