JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/test/jalview/analysis/AnnotationSorterTest.java b/test/jalview/analysis/AnnotationSorterTest.java
index 37bfca4..9dd2972 100644 (file)
--- a/test/jalview/analysis/AnnotationSorterTest.java
+++ b/test/jalview/analysis/AnnotationSorterTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.testng.AssertJUnit.assertEquals;
@@ -30,7 +50,7 @@ public class AnnotationSorterTest
   /*
    * Set up 6 sequences and 7 annotations.
    */
-  @BeforeMethod
+  @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
     al = buildAlignment(NUM_SEQS);
@@ -84,15 +104,15 @@ public class AnnotationSorterTest
    * sequence ref</li>
    * </ul>
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testSortBySequenceAndType_autocalcLast()
   {
     // @formatter:off
     anns[0].sequenceRef = al.getSequenceAt(1); anns[0].label = "label0";
     anns[1].sequenceRef = al.getSequenceAt(3); anns[1].label = "structure";
     anns[2].sequenceRef = al.getSequenceAt(3); anns[2].label = "iron";
-    anns[3].sequenceRef = null;                anns[3].label = "Quality";
-    anns[4].sequenceRef = null;                anns[4].label = "Consensus";
+    anns[3].autoCalculated = true;             anns[3].label = "Quality";
+    anns[4].autoCalculated = true;             anns[4].label = "Consensus";
     anns[5].sequenceRef = al.getSequenceAt(0); anns[5].label = "label5";
     anns[6].sequenceRef = al.getSequenceAt(3); anns[6].label = "IRP";
     // @formatter:on
@@ -104,29 +124,29 @@ public class AnnotationSorterTest
     assertEquals("iron", anns[2].label); // sequence 3 /iron
     assertEquals("IRP", anns[3].label); // sequence 3/IRP
     assertEquals("structure", anns[4].label); // sequence 3/structure
-    assertEquals("Quality", anns[5].label); // non-sequence annotations
+    assertEquals("Quality", anns[5].label); // autocalc annotations
     assertEquals("Consensus", anns[6].label); // retain ordering
   }
 
   /**
    * Variant with autocalculated annotations sorting to front
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testSortBySequenceAndType_autocalcFirst()
   {
     // @formatter:off
     anns[0].sequenceRef = al.getSequenceAt(1); anns[0].label = "label0";
     anns[1].sequenceRef = al.getSequenceAt(3); anns[1].label = "structure";
     anns[2].sequenceRef = al.getSequenceAt(3); anns[2].label = "iron";
-    anns[3].sequenceRef = null;                anns[3].label = "Quality";
-    anns[4].sequenceRef = null;                anns[4].label = "Consensus";
+    anns[3].autoCalculated = true;             anns[3].label = "Quality";
+    anns[4].autoCalculated = true;             anns[4].label = "Consensus";
     anns[5].sequenceRef = al.getSequenceAt(0); anns[5].label = "label5";
     anns[6].sequenceRef = al.getSequenceAt(3); anns[6].label = "IRP";
     // @formatter:on
 
     AnnotationSorter testee = new AnnotationSorter(al, true);
     testee.sort(anns, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
-    assertEquals("Quality", anns[0].label); // non-sequence annotations
+    assertEquals("Quality", anns[0].label); // autocalc annotations
     assertEquals("Consensus", anns[1].label); // retain ordering
     assertEquals("label5", anns[2].label); // for sequence 0
     assertEquals("label0", anns[3].label); // for sequence 1
@@ -147,15 +167,15 @@ public class AnnotationSorterTest
    * sequence ref</li>
    * </ul>
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testSortByTypeAndSequence_autocalcLast()
   {
     // @formatter:off
     anns[0].sequenceRef = al.getSequenceAt(1); anns[0].label = "label0";
     anns[1].sequenceRef = al.getSequenceAt(3); anns[1].label = "structure";
     anns[2].sequenceRef = al.getSequenceAt(3); anns[2].label = "iron";
-    anns[3].sequenceRef = null;                anns[3].label = "Quality";
-    anns[4].sequenceRef = null;                anns[4].label = "Consensus";
+    anns[3].autoCalculated = true;             anns[3].label = "Quality";
+    anns[4].autoCalculated = true;             anns[4].label = "Consensus";
     anns[5].sequenceRef = al.getSequenceAt(0); anns[5].label = "IRON";
     anns[6].sequenceRef = al.getSequenceAt(2); anns[6].label = "Structure";
     // @formatter:on
@@ -167,29 +187,29 @@ public class AnnotationSorterTest
     assertEquals("label0", anns[2].label); // label0 / sequence 1
     assertEquals("Structure", anns[3].label); // Structure / sequence 2
     assertEquals("structure", anns[4].label); // structure / sequence 3
-    assertEquals("Quality", anns[5].label); // non-sequence annotations
+    assertEquals("Quality", anns[5].label); // autocalc annotations
     assertEquals("Consensus", anns[6].label); // retain ordering
   }
 
   /**
    * Variant of test with autocalculated annotations sorted to front
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testSortByTypeAndSequence_autocalcFirst()
   {
     // @formatter:off
     anns[0].sequenceRef = al.getSequenceAt(1); anns[0].label = "label0";
     anns[1].sequenceRef = al.getSequenceAt(3); anns[1].label = "structure";
     anns[2].sequenceRef = al.getSequenceAt(3); anns[2].label = "iron";
-    anns[3].sequenceRef = null;                anns[3].label = "Quality";
-    anns[4].sequenceRef = null;                anns[4].label = "Consensus";
+    anns[3].autoCalculated = true;             anns[3].label = "Quality";
+    anns[4].autoCalculated = true;             anns[4].label = "Consensus";
     anns[5].sequenceRef = al.getSequenceAt(0); anns[5].label = "IRON";
     anns[6].sequenceRef = al.getSequenceAt(2); anns[6].label = "Structure";
     // @formatter:on
 
     AnnotationSorter testee = new AnnotationSorter(al, true);
     testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
-    assertEquals("Quality", anns[0].label); // non-sequence annotations
+    assertEquals("Quality", anns[0].label); // autocalc annotations
     assertEquals("Consensus", anns[1].label); // retain ordering
     assertEquals("IRON", anns[2].label); // IRON / sequence 0
     assertEquals("iron", anns[3].label); // iron / sequence 3
@@ -202,22 +222,22 @@ public class AnnotationSorterTest
    * Variant of test with autocalculated annotations sorted to front but
    * otherwise no change.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testNoSort_autocalcFirst()
   {
     // @formatter:off
     anns[0].sequenceRef = al.getSequenceAt(1); anns[0].label = "label0";
     anns[1].sequenceRef = al.getSequenceAt(3); anns[1].label = "structure";
     anns[2].sequenceRef = al.getSequenceAt(3); anns[2].label = "iron";
-    anns[3].sequenceRef = null;                anns[3].label = "Quality";
-    anns[4].sequenceRef = null;                anns[4].label = "Consensus";
+    anns[3].autoCalculated = true;             anns[3].label = "Quality";
+    anns[4].autoCalculated = true;             anns[4].label = "Consensus";
     anns[5].sequenceRef = al.getSequenceAt(0); anns[5].label = "IRON";
     anns[6].sequenceRef = al.getSequenceAt(2); anns[6].label = "Structure";
     // @formatter:on
 
     AnnotationSorter testee = new AnnotationSorter(al, true);
     testee.sort(anns, SequenceAnnotationOrder.NONE);
-    assertEquals("Quality", anns[0].label); // non-sequence annotations
+    assertEquals("Quality", anns[0].label); // autocalc annotations
     assertEquals("Consensus", anns[1].label); // retain ordering
     assertEquals("label0", anns[2].label);
     assertEquals("structure", anns[3].label);
@@ -226,7 +246,7 @@ public class AnnotationSorterTest
     assertEquals("Structure", anns[6].label);
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testSort_timingPresorted()
   {
     testTiming_presorted(50, 100);
@@ -262,14 +282,14 @@ public class AnnotationSorterTest
     long endTime = System.currentTimeMillis();
     final long elapsed = endTime - startTime;
     System.out.println("Timing test for presorted " + numSeqs
-            + " sequences and "
-            + numAnns + " annotations took " + elapsed + "ms");
+            + " sequences and " + numAnns + " annotations took " + elapsed
+            + "ms");
   }
 
   /**
    * Timing tests for sorting randomly sorted annotations for various sizes.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testSort_timingUnsorted()
   {
     testTiming_unsorted(50, 100);
@@ -306,14 +326,14 @@ public class AnnotationSorterTest
     long endTime = System.currentTimeMillis();
     final long elapsed = endTime - startTime;
     System.out.println("Timing test for unsorted " + numSeqs
-            + " sequences and "
-            + numAnns + " annotations took " + elapsed + "ms");
+            + " sequences and " + numAnns + " annotations took " + elapsed
+            + "ms");
   }
 
   /**
    * Timing test for sorting annotations with a limited range of types (labels).
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testSort_timingSemisorted()
   {
     testTiming_semiSorted(50, 100);
@@ -339,8 +359,8 @@ public class AnnotationSorterTest
     Alignment alignment = buildAlignment(numSeqs);
     AlignmentAnnotation[] annotations = buildAnnotations(numAnns);
 
-    String[] labels = new String[]
-    { "label1", "label2", "label3", "label4", "label5", "label6" };
+    String[] labels = new String[] { "label1", "label2", "label3",
+        "label4", "label5", "label6" };
 
     /*
      * Set the annotations in sequence order with randomly assigned labels.
@@ -359,8 +379,8 @@ public class AnnotationSorterTest
     long endTime = System.currentTimeMillis();
     long elapsed = endTime - startTime;
     System.out.println("Sort by label for semisorted " + numSeqs
-            + " sequences and "
-            + numAnns + " annotations took " + elapsed + "ms");
+            + " sequences and " + numAnns + " annotations took " + elapsed
+            + "ms");
 
     // now resort by sequence
     startTime = System.currentTimeMillis();