X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FResidueCountTest.java;fp=test%2Fjalview%2Fanalysis%2FResidueCountTest.java;h=0000000000000000000000000000000000000000;hb=0a5ce6145bb76fc7eb8a5cc2670e20453fbedd29;hp=4a71f8988977e77690cb0dc623eac298589cfa79;hpb=30ac662ca0b66f445e34e90127c05b3e26d90621;p=jalview.git

diff --git a/test/jalview/analysis/ResidueCountTest.java b/test/jalview/analysis/ResidueCountTest.java
deleted file mode 100644
index 4a71f89..0000000
--- a/test/jalview/analysis/ResidueCountTest.java
+++ /dev/null
@@ -1,404 +0,0 @@
-package jalview.analysis;
-
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertFalse;
-import static org.testng.Assert.assertTrue;
-
-import jalview.analysis.ResidueCount.SymbolCounts;
-
-import org.junit.Assert;
-import org.testng.annotations.Test;
-
-public class ResidueCountTest
-{
-  /**
-   * Test a mix of add and put for nucleotide counting
-   */
-  @Test(groups = "Functional")
-  public void test_countNucleotide()
-  {
-    ResidueCount rc = new ResidueCount(true);
-    assertEquals(rc.getCount('A'), 0);
-    assertEquals(rc.getGapCount(), 0);
-    // add then add
-    assertEquals(rc.add('A'), 1);
-    assertEquals(rc.add('a'), 2);
-    // put then add
-    rc.put('g', 3);
-    assertEquals(rc.add('G'), 4);
-    // add then put
-    assertEquals(rc.add('c'), 1);
-    rc.put('C', 4);
-    assertEquals(rc.add('N'), 1);
-
-    assertEquals(rc.getCount('a'), 2);
-    assertEquals(rc.getCount('A'), 2);
-    assertEquals(rc.getCount('G'), 4);
-    assertEquals(rc.getCount('c'), 4);
-    assertEquals(rc.getCount('T'), 0); // never seen
-    assertEquals(rc.getCount('N'), 1);
-    assertEquals(rc.getCount('?'), 0);
-    assertEquals(rc.getCount('-'), 0);
-
-    assertFalse(rc.isCountingInts());
-    assertFalse(rc.isUsingOtherData());
-  }
-
-  /**
-   * Test adding to gap count (either using addGap or add)
-   */
-  @Test(groups = "Functional")
-  public void testAddGap()
-  {
-    ResidueCount rc = new ResidueCount(true);
-    rc.addGap();
-    rc.add('-');
-    rc.add('.');
-    rc.add(' ');
-    
-    assertEquals(rc.getGapCount(), 4);
-    assertEquals(rc.getCount(' '), 4);
-    assertEquals(rc.getCount('-'), 4);
-    assertEquals(rc.getCount('.'), 4);
-    assertFalse(rc.isUsingOtherData());
-    assertFalse(rc.isCountingInts());
-  }
-
-  @Test(groups = "Functional")
-  public void testOverflow()
-  {
-    /*
-     * overflow from add
-     */
-    ResidueCount rc = new ResidueCount(true);
-    rc.addGap();
-    rc.put('A', Short.MAX_VALUE - 1);
-    assertFalse(rc.isCountingInts());
-    rc.add('A');
-    assertFalse(rc.isCountingInts());
-    rc.add('A');
-    assertTrue(rc.isCountingInts());
-    assertEquals(rc.getCount('a'), Short.MAX_VALUE + 1);
-    rc.add('A');
-    assertTrue(rc.isCountingInts());
-    assertEquals(rc.getCount('a'), Short.MAX_VALUE + 2);
-    assertEquals(rc.getGapCount(), 1);
-    rc.addGap();
-    assertEquals(rc.getGapCount(), 2);
-
-    /*
-     * overflow from put
-     */
-    rc = new ResidueCount(true);
-    rc.put('G', Short.MAX_VALUE + 1);
-    assertTrue(rc.isCountingInts());
-    assertEquals(rc.getCount('g'), Short.MAX_VALUE + 1);
-    rc.put('G', 1);
-    assertTrue(rc.isCountingInts());
-    assertEquals(rc.getCount('g'), 1);
-
-    /*
-     * underflow from put
-     */
-    rc = new ResidueCount(true);
-    rc.put('G', Short.MIN_VALUE - 1);
-    assertTrue(rc.isCountingInts());
-    assertEquals(rc.getCount('g'), Short.MIN_VALUE - 1);
-  }
-
-  /**
-   * Test a mix of add and put for peptide counting
-   */
-  @Test(groups = "Functional")
-  public void test_countPeptide()
-  {
-    ResidueCount rc = new ResidueCount(false);
-    rc.put('q', 4);
-    rc.add('Q');
-    rc.add('X');
-    rc.add('x');
-    rc.add('W');
-    rc.put('w', 7);
-    rc.put('m', 12);
-    rc.put('M', 13);
-
-    assertEquals(rc.getCount('q'), 5);
-    assertEquals(rc.getCount('X'), 2);
-    assertEquals(rc.getCount('W'), 7);
-    assertEquals(rc.getCount('m'), 13);
-    assertEquals(rc.getCount('G'), 0);
-    assertEquals(rc.getCount('-'), 0);
-
-    assertFalse(rc.isCountingInts());
-    assertFalse(rc.isUsingOtherData());
-  }
-
-  @Test(groups = "Functional")
-  public void test_unexpectedPeptide()
-  {
-    ResidueCount rc = new ResidueCount(false);
-    // expected characters (upper or lower case):
-    String aas = "ACDEFGHIKLMNPQRSTVWXY";
-    String lower = aas.toLowerCase();
-    for (int i = 0; i < aas.length(); i++)
-    {
-      rc.put(aas.charAt(i), i);
-      rc.add(lower.charAt(i));
-    }
-    for (int i = 0; i < aas.length(); i++)
-    {
-      assertEquals(rc.getCount(aas.charAt(i)), i + 1);
-    }
-    assertFalse(rc.isUsingOtherData());
-
-    rc.put('J', 4);
-    assertTrue(rc.isUsingOtherData());
-    assertEquals(rc.getCount('J'), 4);
-    rc.add('j');
-    assertEquals(rc.getCount('J'), 5);
-  }
-
-  @Test(groups = "Functional")
-  public void test_unexpectedNucleotide()
-  {
-    ResidueCount rc = new ResidueCount(true);
-    // expected characters (upper or lower case):
-    String nucs = "ACGTUN";
-    String lower = nucs.toLowerCase();
-    for (int i = 0; i < nucs.length(); i++)
-    {
-      rc.put(nucs.charAt(i), i);
-      rc.add(lower.charAt(i));
-    }
-    for (int i = 0; i < nucs.length(); i++)
-    {
-      assertEquals(rc.getCount(nucs.charAt(i)), i + 1);
-    }
-    assertFalse(rc.isUsingOtherData());
-
-    rc.add('J');
-    assertTrue(rc.isUsingOtherData());
-  }
-
-  @Test(groups = "Functional")
-  public void testGetModalCount()
-  {
-    ResidueCount rc = new ResidueCount(true);
-    rc.add('c');
-    rc.add('g');
-    rc.add('c');
-    assertEquals(rc.getModalCount(), 2);
-
-    // modal count is in the 'short overflow' counts
-    rc = new ResidueCount();
-    rc.add('c');
-    rc.put('g', Short.MAX_VALUE);
-    rc.add('G');
-    assertEquals(rc.getModalCount(), Short.MAX_VALUE + 1);
-
-    // modal count is in the 'other data' counts
-    rc = new ResidueCount(false);
-    rc.add('Q');
-    rc.add('{');
-    rc.add('{');
-    assertEquals(rc.getModalCount(), 2);
-
-    // verify modal count excludes gap
-    rc = new ResidueCount();
-    rc.add('Q');
-    rc.add('P');
-    rc.add('Q');
-    rc.addGap();
-    rc.addGap();
-    rc.addGap();
-    assertEquals(rc.getModalCount(), 2);
-  }
-
-  @Test(groups = "Functional")
-  public void testGetResiduesForCount()
-  {
-    ResidueCount rc = new ResidueCount(true);
-    rc.add('c');
-    rc.add('g');
-    rc.add('c');
-    assertEquals(rc.getResiduesForCount(2), "C");
-    assertEquals(rc.getResiduesForCount(1), "G");
-    assertEquals(rc.getResiduesForCount(3), "");
-    assertEquals(rc.getResiduesForCount(0), "");
-    assertEquals(rc.getResiduesForCount(-1), "");
-
-    // modal count is in the 'short overflow' counts
-    rc = new ResidueCount(true);
-    rc.add('c');
-    rc.put('g', Short.MAX_VALUE);
-    rc.add('G');
-    assertEquals(rc.getResiduesForCount(Short.MAX_VALUE + 1), "G");
-    assertEquals(rc.getResiduesForCount(1), "C");
-
-    // peptide modal count is in the 'short overflow' counts
-    rc = new ResidueCount(false);
-    rc.add('c');
-    rc.put('p', Short.MAX_VALUE);
-    rc.add('P');
-    assertEquals(rc.getResiduesForCount(Short.MAX_VALUE + 1), "P");
-    assertEquals(rc.getResiduesForCount(1), "C");
-  
-    // modal count is in the 'other data' counts
-    rc = new ResidueCount();
-    rc.add('Q');
-    rc.add('{');
-    rc.add('{');
-    assertEquals(rc.getResiduesForCount(1), "Q");
-    assertEquals(rc.getResiduesForCount(2), "{");
-
-    // residues share modal count
-    rc = new ResidueCount();
-    rc.add('G');
-    rc.add('G');
-    rc.add('c');
-    rc.add('C');
-    rc.add('U');
-    assertEquals(rc.getResiduesForCount(1), "U");
-    assertEquals(rc.getResiduesForCount(2), "CG");
-
-    // expected and unexpected symbols share modal count
-    rc = new ResidueCount();
-    rc.add('G');
-    rc.add('t');
-    rc.add('[');
-    rc.add('[');
-    rc.add('t');
-    rc.add('G');
-    rc.add('c');
-    rc.add('C');
-    rc.add('U');
-    assertEquals(rc.getResiduesForCount(1), "U");
-    assertEquals(rc.getResiduesForCount(2), "CGT[");
-  }
-
-  @Test(groups = "Functional")
-  public void testGetSymbolCounts_nucleotide()
-  {
-    ResidueCount rc = new ResidueCount(true);
-    rc.add('g');
-    rc.add('c');
-    rc.add('G');
-    rc.add('J'); // 'otherData'
-    rc.add('g');
-    rc.add('N');
-    rc.put('[', 0); // 'otherdata'
-
-    SymbolCounts sc = rc.getSymbolCounts();
-    Assert.assertArrayEquals(new char[] { 'C', 'G', 'N', 'J', '[' },
-            sc.symbols);
-    Assert.assertArrayEquals(new int[] { 1, 3, 1, 1, 0 }, sc.values);
-
-    // now with overflow to int counts
-    rc.put('U', Short.MAX_VALUE);
-    rc.add('u');
-    sc = rc.getSymbolCounts();
-    Assert.assertArrayEquals(new char[] { 'C', 'G', 'N', 'U', 'J', '[' },
-            sc.symbols);
-    Assert.assertArrayEquals(new int[] { 1, 3, 1, 32768, 1, 0 }, sc.values);
-  }
-
-  @Test(groups = "Functional")
-  public void testGetSymbolCounts_peptide()
-  {
-    ResidueCount rc = new ResidueCount(false);
-    rc.add('W');
-    rc.add('q');
-    rc.add('W');
-    rc.add('Z'); // 'otherData'
-    rc.add('w');
-    rc.add('L');
-
-    SymbolCounts sc = rc.getSymbolCounts();
-    Assert.assertArrayEquals(new char[] { 'L', 'Q', 'W', 'Z' }, sc.symbols);
-    Assert.assertArrayEquals(new int[] { 1, 1, 3, 1 }, sc.values);
-
-    // now with overflow to int counts
-    rc.put('W', Short.MAX_VALUE);
-    rc.add('W');
-    sc = rc.getSymbolCounts();
-    Assert.assertArrayEquals(new char[] { 'L', 'Q', 'W', 'Z' }, sc.symbols);
-    Assert.assertArrayEquals(new int[] { 1, 1, 32768, 1 }, sc.values);
-  }
-
-  @Test(groups = "Functional")
-  public void testToString()
-  {
-    ResidueCount rc = new ResidueCount();
-    rc.add('q');
-    rc.add('c');
-    rc.add('Q');
-    assertEquals(rc.toString(), "[ C:1 Q:2 ]");
-
-    // add 'other data'
-    rc.add('{');
-    assertEquals(rc.toString(), "[ C:1 Q:2 {:1 ]");
-
-    // switch from short to int counting:
-    rc.put('G', Short.MAX_VALUE);
-    rc.add('g');
-    assertEquals(rc.toString(), "[ C:1 G:32768 Q:2 {:1 ]");
-  }
-
-  @Test(groups = "Functional")
-  public void testGetTooltip()
-  {
-    ResidueCount rc = new ResidueCount();
-
-    // no counts!
-    assertEquals(rc.getTooltip(20, 1), "");
-
-    /*
-     * count 7 C, 6 K, 7 Q, 10 P, 9 W, 1 F (total 40)
-     */
-    for (int i = 0; i < 7; i++)
-    {
-      rc.add('c');
-      rc.add('q');
-    }
-    for (int i = 0; i < 10; i++)
-    {
-      rc.add('p');
-    }
-    for (int i = 0; i < 9; i++)
-    {
-      rc.add('W');
-    }
-    for (int i = 0; i < 6; i++)
-    {
-      rc.add('K');
-    }
-    rc.add('F');
-    
-    assertEquals(rc.getTooltip(40, 0),
-            "P 25%; W 22%; C 17%; Q 17%; K 15%; F 2%");
-
-    assertEquals(rc.getTooltip(30, 1),
-            "P 33.3%; W 30.0%; C 23.3%; Q 23.3%; K 20.0%; F 3.3%");
-  }
-
-  @Test(groups = "Functional")
-  public void testPut()
-  {
-    ResidueCount rc = new ResidueCount();
-    rc.put('q', 3);
-    assertEquals(rc.getCount('Q'), 3);
-    rc.put(' ', 4);
-    assertEquals(rc.getGapCount(), 4);
-    rc.put('.', 5);
-    assertEquals(rc.getGapCount(), 5);
-    rc.put('-', 6);
-    assertEquals(rc.getGapCount(), 6);
-
-    rc.put('?', 5);
-    assertEquals(rc.getCount('?'), 5);
-    rc.put('?', 6);
-    rc.put('!', 7);
-    assertEquals(rc.getCount('?'), 6);
-    assertEquals(rc.getCount('!'), 7);
-  }
-}