JAL-2416 score matrix gap symbol (if any) dynamically determined

[jalview.git] / test / jalview / analysis / scoremodels / ScoreMatrixTest.java

diff --git a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
index 5c699d1..24db894 100644 (file)
--- a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
@@ -38,6 +38,8 @@ public class ScoreMatrixTest
     assertEquals(sm.getPairwiseScore('A', 'D'), 0f);
     assertEquals(sm.getMatrixIndex('c'), 2);
     assertEquals(sm.getMatrixIndex(' '), -1);
+
+    assertEquals(sm.getGapIndex(), -1); // no gap symbol
   }
 
   @Test(
@@ -76,7 +78,12 @@ public class ScoreMatrixTest
   @Test(groups = "Functional")
   public void testBuildSymbolIndex()
   {
-    short[] index = ScoreMatrix.buildSymbolIndex("AX-. yxYp".toCharArray());
+    float[][] scores = new float[2][];
+    scores[0] = new float[] { 1f, 2f };
+    scores[1] = new float[] { 3f, 4f };
+    ScoreMatrix sm = new ScoreMatrix("Test", new char[] { 'A', '.' },
+            scores);
+    short[] index = sm.buildSymbolIndex("AX-yxYp".toCharArray());
 
     assertEquals(index.length, 128); // ASCII character set size
 
@@ -84,12 +91,10 @@ public class ScoreMatrixTest
     assertEquals(index['a'], 0); // lower-case mapping added
     assertEquals(index['X'], 1);
     assertEquals(index['-'], 2);
-    assertEquals(index['.'], 3);
-    assertEquals(index[' '], 4);
-    assertEquals(index['y'], 5); // lower-case override
-    assertEquals(index['x'], 6); // lower-case override
-    assertEquals(index['Y'], 7);
-    assertEquals(index['p'], 8);
+    assertEquals(index['y'], 3); // lower-case override
+    assertEquals(index['x'], 4); // lower-case override
+    assertEquals(index['Y'], 5);
+    assertEquals(index['p'], 6);
     assertEquals(index['P'], -1); // lower-case doesn't map upper-case
 
     /*
@@ -110,8 +115,13 @@ public class ScoreMatrixTest
   @Test(groups = "Functional")
   public void testBuildSymbolIndex_nonAscii()
   {
+    float[][] scores = new float[2][];
+    scores[0] = new float[] { 1f, 2f };
+    scores[1] = new float[] { 3f, 4f };
+    ScoreMatrix sm = new ScoreMatrix("Test", new char[] { 'A', '.' },
+            scores);
     char[] weird = new char[] { 128, 245, 'P' };
-    short[] index = ScoreMatrix.buildSymbolIndex(weird);
+    short[] index = sm.buildSymbolIndex(weird);
     assertEquals(index.length, 128);
     assertEquals(index['P'], 2);
     assertEquals(index['p'], 2);
@@ -157,6 +167,13 @@ public class ScoreMatrixTest
   }
 
   @Test(groups = "Functional")
+  public void testGetGapIndex()
+  {
+    ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+    assertEquals(sm.getGapIndex(), 23);
+  }
+
+  @Test(groups = "Functional")
   public void testGetSize()
   {
     ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
@@ -477,4 +494,27 @@ public class ScoreMatrixTest
               String.format("%s->%s", res, c2));
     }
   }
+
+  @Test(groups = "Functional")
+  public void testConstructor_gapDash()
+  {
+    float[][] scores = new float[2][];
+    scores[0] = new float[] { 1f, 2f };
+    scores[1] = new float[] { 4f, 5f };
+    ScoreMatrix sm = new ScoreMatrix("Test", new char[] { 'A', '-' },
+            scores);
+    assertEquals(sm.getSize(), 2);
+    assertArrayEquals(scores, sm.getMatrix());
+    assertEquals(sm.getPairwiseScore('A', 'a'), 1f);
+    assertEquals(sm.getPairwiseScore('A', 'A'), 1f);
+    assertEquals(sm.getPairwiseScore('a', '-'), 2f);
+    assertEquals(sm.getPairwiseScore('-', 'A'), 4f);
+    assertEquals(sm.getMatrixIndex('a'), 0);
+    assertEquals(sm.getMatrixIndex('A'), 0);
+    assertEquals(sm.getMatrixIndex('-'), 1);
+    assertEquals(sm.getMatrixIndex(' '), -1);
+    assertEquals(sm.getMatrixIndex('.'), -1);
+  
+    assertEquals(sm.getGapIndex(), 1);
+  }
 }