Merge branch 'develop' into features/filetypeEnum

[jalview.git] / test / jalview / datamodel / AlignmentAnnotationTests.java

diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java
index d32105d..fb02166 100644 (file)
--- a/test/jalview/datamodel/AlignmentAnnotationTests.java
+++ b/test/jalview/datamodel/AlignmentAnnotationTests.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.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -5,12 +25,13 @@ import static org.testng.AssertJUnit.assertNull;
 
 import jalview.analysis.AlignSeq;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.FileFormat;
 
 import org.testng.annotations.Test;
 
 public class AlignmentAnnotationTests
 {
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testCopyConstructor()
   {
     SequenceI sq = new Sequence("Foo", "ARAARARARAWEAWEAWRAWEAWE");
@@ -23,6 +44,7 @@ public class AlignmentAnnotationTests
               alc.getProperty(key));
     }
   }
+
   /**
    * create some dummy annotation derived from the sequence
    * 
@@ -74,7 +96,7 @@ public class AlignmentAnnotationTests
    * different dataset frames (annotation transferred by mapping between
    * sequences)
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testLiftOver()
   {
     SequenceI sqFrom = new Sequence("fromLong", "QQQCDEWGH");
@@ -97,9 +119,10 @@ public class AlignmentAnnotationTests
     alSeq2.setStart(sqTo.getStart() + align.getSeq2Start() - 1);
     alSeq2.setEnd(sqTo.getStart() + align.getSeq2End() - 1);
     alSeq2.setDatasetSequence(sqTo);
-    System.out.println(new AppletFormatAdapter().formatSequences("STH",
-            new Alignment(new SequenceI[]
-            { sqFrom, alSeq1, sqTo, alSeq2 }), true));
+    System.out.println(new AppletFormatAdapter()
+.formatSequences(
+            FileFormat.Stockholm, new Alignment(new SequenceI[] { sqFrom,
+                alSeq1, sqTo, alSeq2 }), true));
 
     Mapping mp = align.getMappingFromS1(false);
 
@@ -119,11 +142,11 @@ public class AlignmentAnnotationTests
     almap2.setSequenceRef(alSeq2);
     almap2.adjustForAlignment();
 
-    AlignmentI all = new Alignment(new SequenceI[]
-    { alSeq1, alSeq2 });
+    AlignmentI all = new Alignment(new SequenceI[] { alSeq1, alSeq2 });
     all.addAnnotation(almap1);
     all.addAnnotation(almap2);
-    System.out.println(new AppletFormatAdapter().formatSequences("STH",
+    System.out.println(new AppletFormatAdapter().formatSequences(
+            FileFormat.Stockholm,
             all, true));
 
     for (int p = 0; p < alSeq1.getLength(); p++)
@@ -157,7 +180,7 @@ public class AlignmentAnnotationTests
     }
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testAdjustForAlignment()
   {
     SequenceI seq = new Sequence("TestSeq", "ABCDEFG");
@@ -166,8 +189,8 @@ public class AlignmentAnnotationTests
     /*
      * Annotate positions 3/4/5 (CDE) with values 1/2/3
      */
-    Annotation[] anns = new Annotation[]
-    { null, null, new Annotation(1), new Annotation(2), new Annotation(3) };
+    Annotation[] anns = new Annotation[] { null, null, new Annotation(1),
+        new Annotation(2), new Annotation(3) };
     AlignmentAnnotation ann = new AlignmentAnnotation("SS",
             "secondary structure", anns);
     seq.addAlignmentAnnotation(ann);
@@ -199,4 +222,65 @@ public class AlignmentAnnotationTests
     assertEquals(1, ann.annotations[1].value, 0.001);
     assertEquals(2, ann.annotations[2].value, 0.001);
   }
+
+  /**
+   * Test the method that defaults rna symbol to the one matching the preceding
+   * unmatched opening bracket (if any)
+   */
+  @Test(groups = { "Functional" })
+  public void testGetDefaultRnaHelixSymbol()
+  {
+    AlignmentAnnotation ann = new AlignmentAnnotation("SS",
+            "secondary structure", null);
+    assertEquals("(", ann.getDefaultRnaHelixSymbol(4));
+
+    Annotation[] anns = new Annotation[20];
+    ann.annotations = anns;
+    assertEquals("(", ann.getDefaultRnaHelixSymbol(4));
+
+    anns[1] = new Annotation("(", "S", '(', 0f);
+    assertEquals("(", ann.getDefaultRnaHelixSymbol(0));
+    assertEquals("(", ann.getDefaultRnaHelixSymbol(1));
+    assertEquals(")", ann.getDefaultRnaHelixSymbol(2));
+    assertEquals(")", ann.getDefaultRnaHelixSymbol(3));
+
+    /*
+     * .(.[.{.<.}.>.).].
+     */
+    anns[1] = new Annotation("(", "S", '(', 0f);
+    anns[3] = new Annotation("[", "S", '[', 0f);
+    anns[5] = new Annotation("{", "S", '{', 0f);
+    anns[7] = new Annotation("<", "S", '<', 0f);
+    anns[9] = new Annotation("}", "S", '}', 0f);
+    anns[11] = new Annotation(">", "S", '>', 0f);
+    anns[13] = new Annotation(")", "S", ')', 0f);
+    anns[15] = new Annotation("]", "S", ']', 0f);
+
+    String expected = "(())]]}}>>>>]]]](";
+    for (int i = 0; i < expected.length(); i++)
+    {
+      assertEquals("column " + i, String.valueOf(expected.charAt(i)),
+              ann.getDefaultRnaHelixSymbol(i));
+    }
+
+    /*
+     * .(.[.(.).{.}.<.].D.
+     */
+    anns[1] = new Annotation("(", "S", '(', 0f);
+    anns[3] = new Annotation("[", "S", '[', 0f);
+    anns[5] = new Annotation("(", "S", '(', 0f);
+    anns[7] = new Annotation(")", "S", ')', 0f);
+    anns[9] = new Annotation("{", "S", '{', 0f);
+    anns[11] = new Annotation("}", "S", '}', 0f);
+    anns[13] = new Annotation("<", "S", '>', 0f);
+    anns[15] = new Annotation("]", "S", ']', 0f);
+    anns[17] = new Annotation("D", "S", 'D', 0f);
+
+    expected = "(())]]))]]}}]]>>>>dd";
+    for (int i = 0; i < expected.length(); i++)
+    {
+      assertEquals("column " + i, String.valueOf(expected.charAt(i)),
+              ann.getDefaultRnaHelixSymbol(i));
+    }
+  }
 }