assertEquals(sm.getPairwiseScore('A', 'D'), 0f);
assertEquals(sm.getMatrixIndex('c'), 2);
assertEquals(sm.getMatrixIndex(' '), -1);
+
+ assertEquals(sm.getGapIndex(), -1); // no gap symbol
}
@Test(
@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
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
/*
@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);
}
@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();
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);
+ }
}