Parsing moved to (new) ScoreMatrixFile, drag and drop to alignment now

[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 7c62854..cbc834d 100644 (file)
--- a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
@@ -1,12 +1,6 @@
 package jalview.analysis.scoremodels;
 
 import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertFalse;
-import static org.testng.Assert.assertNotNull;
-import static org.testng.Assert.assertNull;
-import static org.testng.Assert.assertTrue;
-
-import java.io.ByteArrayInputStream;
 
 import org.testng.annotations.Test;
 
@@ -62,130 +56,4 @@ public class ScoreMatrixTest
       }
     }
   }
-
-  /**
-   * Test a successful parse of a (small) score matrix file
-   */
-  @Test(groups = "Functional")
-  public void testParse()
-  {
-    /*
-     * some messy but valid input data, with comma, space
-     * or tab (or combinations) as score value delimiters
-     * this example includes 'guide' symbols on score rows
-     */
-    String data = "ScoreMatrix MyTest\n" + "ATU tx-\n"
-            + "A,1.1,1.2,1.3,1.4, 1.5, 1.6, 1.7\n"
-            + "T,2.1 2.2 2.3 2.4 2.5 2.6 2.7\n"
-            + "U\t3.1\t3.2\t3.3\t3.4\t3.5\t3.6\t3.7\n"
-            + " 4.1 ,4.2,\t,4.3 ,\t4.4\t, \4.5,4.6 4.7\n"
-            + "t, 5.1,5.3,5.3,5.4,5.5, 5.6, 5.7\n"
-            + "x\t6.1, 6.2 6.3 6.4 6.5 6.6 6.7\n"
-            + "-, \t7.1\t7.2 7.3, 7.4, 7.5\t,7.6,7.7\n";
-    ScoreMatrix sm = ScoreMatrix.parse(new ByteArrayInputStream(data
-            .getBytes()));
-    assertNotNull(sm);
-    assertEquals(sm.getName(), "MyTest");
-    assertTrue(sm.isDNA());
-    assertFalse(sm.isProtein());
-    assertEquals(sm.getPairwiseScore('A', 'A'), 1.1f);
-    assertEquals(sm.getPairwiseScore('A', 'T'), 1.2f);
-    assertEquals(sm.getPairwiseScore('a', 'T'), 1.2f); // A/a equivalent
-    assertEquals(sm.getPairwiseScore('A', 't'), 1.5f); // T/t not equivalent
-    assertEquals(sm.getPairwiseScore('a', 't'), 1.5f);
-    assertEquals(sm.getPairwiseScore('T', ' '), 2.4f);
-    assertEquals(sm.getPairwiseScore('U', 'x'), 3.6f);
-    assertEquals(sm.getPairwiseScore('u', 'x'), 3.6f);
-    assertEquals(sm.getPairwiseScore('U', 'X'), 0f); // X (upper) unmapped
-    assertEquals(sm.getPairwiseScore('A', '.'), 0f); // . unmapped
-    assertEquals(sm.getPairwiseScore('-', '-'), 7.7f);
-    assertEquals(sm.getPairwiseScore('A', (char) 128), 0f); // out of range
-
-    /*
-     * without guide symbols on score rows
-     */
-    data = "ScoreMatrix MyTest\nXY\n1 2\n3 4\n";
-    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
-    assertNotNull(sm);
-    assertEquals(sm.getPairwiseScore('X', 'X'), 1f);
-    assertEquals(sm.getPairwiseScore('X', 'y'), 2f);
-    assertEquals(sm.getPairwiseScore('y', 'x'), 3f);
-    assertEquals(sm.getPairwiseScore('y', 'Y'), 4f);
-    assertEquals(sm.getPairwiseScore('D', 'R'), 0f);
-  }
-
-  @Test(groups = "Functional")
-  public void testParse_invalidInput()
-  {
-    /*
-     * valid first
-     */
-    String data = "ScoreMatrix MyTest\nXY\n1 2\n3 4\n";
-    ScoreMatrix sm = ScoreMatrix.parse(new ByteArrayInputStream(data
-            .getBytes()));
-    assertNotNull(sm);
-
-    /*
-     * Name missing
-     */
-    data = "ScoreMatrix\nXY\n1 2\n3 4\n";
-    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
-    assertNull(sm);
-
-    /*
-     * ScoreMatrix header missing
-     */
-    data = "XY\n1 2\n3 4\n";
-    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
-    assertNull(sm);
-
-    /*
-     * Not enough rows
-     */
-    data = "ScoreMatrix MyTest\nXY\n1 2\n";
-    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
-    assertNull(sm);
-
-    /*
-     * Not enough columns
-     */
-    data = "ScoreMatrix MyTest\nXY\n1 2\n3\n";
-    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
-    assertNull(sm);
-
-    /*
-     * Too many columns
-     */
-    data = "ScoreMatrix MyTest\nXY\n1 2\n3 4 5\n";
-    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
-    assertNull(sm);
-
-    /*
-     * Too many rows
-     */
-    data = "ScoreMatrix MyTest\nXY\n1 2\n3 4\n6 7";
-    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
-    assertNull(sm);
-
-    /*
-     * unsupported delimiter |
-     */
-    data = "ScoreMatrix MyTest\nXY\n1|2\n3|4\n";
-    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
-    assertNull(sm);
-
-    /*
-     * Bad float value
-     */
-    data = "ScoreMatrix MyTest\nXY\n1 2\n3 four\n";
-    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
-    assertNull(sm);
-
-    /*
-     * Bad guide character on scores row
-     */
-    data = "ScoreMatrix MyTest\nXY\nX 1 2\ny 3 4\n";
-    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
-    assertNull(sm);
-  }
 }