JAL-98 ResidueCount 100% test coverage (and bug fixes!)

[jalview.git] / test / jalview / analysis / ResidueCountTest.java

diff --git a/test/jalview/analysis/ResidueCountTest.java b/test/jalview/analysis/ResidueCountTest.java
index a26252c..4a71f89 100644 (file)
--- a/test/jalview/analysis/ResidueCountTest.java
+++ b/test/jalview/analysis/ResidueCountTest.java
@@ -71,6 +71,7 @@ public class ResidueCountTest
      * overflow from add
      */
     ResidueCount rc = new ResidueCount(true);
+    rc.addGap();
     rc.put('A', Short.MAX_VALUE - 1);
     assertFalse(rc.isCountingInts());
     rc.add('A');
@@ -78,6 +79,12 @@ public class ResidueCountTest
     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
@@ -86,6 +93,17 @@ public class ResidueCountTest
     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);
   }
 
   /**
@@ -135,6 +153,9 @@ public class ResidueCountTest
 
     rc.put('J', 4);
     assertTrue(rc.isUsingOtherData());
+    assertEquals(rc.getCount('J'), 4);
+    rc.add('j');
+    assertEquals(rc.getCount('J'), 5);
   }
 
   @Test(groups = "Functional")
@@ -162,7 +183,7 @@ public class ResidueCountTest
   @Test(groups = "Functional")
   public void testGetModalCount()
   {
-    ResidueCount rc = new ResidueCount();
+    ResidueCount rc = new ResidueCount(true);
     rc.add('c');
     rc.add('g');
     rc.add('c');
@@ -176,7 +197,7 @@ public class ResidueCountTest
     assertEquals(rc.getModalCount(), Short.MAX_VALUE + 1);
 
     // modal count is in the 'other data' counts
-    rc = new ResidueCount();
+    rc = new ResidueCount(false);
     rc.add('Q');
     rc.add('{');
     rc.add('{');
@@ -196,7 +217,7 @@ public class ResidueCountTest
   @Test(groups = "Functional")
   public void testGetResiduesForCount()
   {
-    ResidueCount rc = new ResidueCount();
+    ResidueCount rc = new ResidueCount(true);
     rc.add('c');
     rc.add('g');
     rc.add('c');
@@ -207,12 +228,20 @@ public class ResidueCountTest
     assertEquals(rc.getResiduesForCount(-1), "");
 
     // modal count is in the 'short overflow' counts
-    rc = new ResidueCount();
+    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();
@@ -248,27 +277,52 @@ public class ResidueCountTest
   }
 
   @Test(groups = "Functional")
-  public void testGetSymbolCounts()
+  public void testGetSymbolCounts_nucleotide()
   {
-    ResidueCount rc = new ResidueCount();
-    rc.add('q');
+    ResidueCount rc = new ResidueCount(true);
+    rc.add('g');
     rc.add('c');
-    rc.add('Q');
+    rc.add('G');
     rc.add('J'); // 'otherData'
-    rc.add('q');
-    rc.add('x');
+    rc.add('g');
+    rc.add('N');
+    rc.put('[', 0); // 'otherdata'
 
     SymbolCounts sc = rc.getSymbolCounts();
-    Assert.assertArrayEquals(new char[] { 'C', 'Q', 'X', 'J' }, sc.symbols);
-    Assert.assertArrayEquals(new int[] { 1, 3, 1, 1 }, sc.values);
+    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('g', Short.MAX_VALUE);
-    rc.add('g');
+    rc.put('U', Short.MAX_VALUE);
+    rc.add('u');
     sc = rc.getSymbolCounts();
-    Assert.assertArrayEquals(new char[] { 'C', 'G', 'Q', 'X', 'J' },
+    Assert.assertArrayEquals(new char[] { 'C', 'G', 'N', 'U', 'J', '[' },
             sc.symbols);
-    Assert.assertArrayEquals(new int[] { 1, 32768, 3, 1, 1 }, sc.values);
+    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")
@@ -289,4 +343,62 @@ public class ResidueCountTest
     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);
+  }
 }