X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FResidueCountTest.java;fp=test%2Fjalview%2Fdatamodel%2FResidueCountTest.java;h=6c6e36a29696d95c72482e0fc7ccbfe396474095;hb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;hp=0000000000000000000000000000000000000000;hpb=02e38bb826828ab2991584cf4b737c0138cb6c44;p=jalview.git

diff --git a/test/jalview/datamodel/ResidueCountTest.java b/test/jalview/datamodel/ResidueCountTest.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+
+import jalview.datamodel.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');
+    
+    /*
+     * percentages are rounded (0.5 rounded up)
+     * 10/40 9/40 7/40 6/40 1/40
+     */
+    assertEquals(rc.getTooltip(40, 0),
+            "P 25%; W 23%; C 18%; Q 18%; K 15%; F 3%");
+
+    rc.add('Q');
+    /*
+     * 10/30 9/30 8/30 7/30 6/30 1/30
+     */
+    assertEquals(rc.getTooltip(30, 1),
+            "P 33.3%; W 30.0%; Q 26.7%; C 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);
+  }
+}