X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentAnnotationTests.java;h=e47e9d6804292f240d1986a8242ee4a20b6647cd;hb=0125cee3edfa0ba5584631bae3ad9c808ec0b30d;hp=6d639d0b2a8214236bb80cb6014185a9ada0fcd6;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java
index 6d639d0..e47e9d6 100644
--- a/test/jalview/datamodel/AlignmentAnnotationTests.java
+++ b/test/jalview/datamodel/AlignmentAnnotationTests.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -24,12 +24,24 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNull;
 
 import jalview.analysis.AlignSeq;
+import jalview.gui.JvOptionPane;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.FileFormat;
 
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class AlignmentAnnotationTests
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = { "Functional" })
   public void testCopyConstructor()
   {
@@ -119,7 +131,8 @@ public class AlignmentAnnotationTests
     alSeq2.setEnd(sqTo.getStart() + align.getSeq2End() - 1);
     alSeq2.setDatasetSequence(sqTo);
     System.out.println(new AppletFormatAdapter()
-            .formatSequences("STH", new Alignment(new SequenceI[] { sqFrom,
+.formatSequences(
+            FileFormat.Stockholm, new Alignment(new SequenceI[] { sqFrom,
                 alSeq1, sqTo, alSeq2 }), true));
 
     Mapping mp = align.getMappingFromS1(false);
@@ -143,7 +156,8 @@ public class AlignmentAnnotationTests
     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++)
@@ -280,4 +294,45 @@ public class AlignmentAnnotationTests
               ann.getDefaultRnaHelixSymbol(i));
     }
   }
-}
\ No newline at end of file
+
+  public static Annotation newAnnotation(String ann)
+  {
+    float val = 0f;
+    try
+    {
+      val = Float.parseFloat(ann);
+    } catch (NumberFormatException q)
+    {
+    }
+    ;
+    return new Annotation(ann, ann, '\0', val);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testIsQuantitative()
+  {
+    AlignmentAnnotation ann = null;
+
+    ann = new AlignmentAnnotation("an", "some an", null);
+    Assert.assertFalse(ann.isQuantitative(),
+            "Empty annotation set should not be quantitative.");
+
+    ann = new AlignmentAnnotation("an", "some an", new Annotation[] {
+        newAnnotation("4"), newAnnotation("1"), newAnnotation("1"),
+        newAnnotation("0.1"), newAnnotation("0.3") });
+    Assert.assertTrue(ann.isQuantitative(),
+            "All numbers annotation set should be quantitative.");
+
+    ann = new AlignmentAnnotation("an", "some an", new Annotation[] {
+        newAnnotation("E"), newAnnotation("E"), newAnnotation("E"),
+        newAnnotation("E"), newAnnotation("E") });
+    Assert.assertFalse(ann.isQuantitative(),
+            "All 'E' annotation set should not be quantitative.");
+
+    ann = new AlignmentAnnotation("an", "some an", new Annotation[] {
+        newAnnotation("E"), newAnnotation("1"), newAnnotation("2"),
+        newAnnotation("3"), newAnnotation("E") });
+    Assert.assertTrue(ann.isQuantitative(),
+            "Mixed 'E' annotation set should be quantitative.");
+  }
+}