JAL-4090 JAL-1551 spotlessApply

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

diff --git a/test/jalview/analysis/TestAlignSeq.java b/test/jalview/analysis/TestAlignSeq.java
index 81514a4..05575f4 100644 (file)
--- a/test/jalview/analysis/TestAlignSeq.java
+++ b/test/jalview/analysis/TestAlignSeq.java
@@ -26,12 +26,18 @@ import static org.testng.AssertJUnit.assertNull;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 
 import java.io.PrintStream;
+import java.nio.charset.Charset;
+import java.util.Locale;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import com.google.common.base.Charsets;
+
 /**
  * Test the alignment -> Mapping routines
  * 
@@ -41,12 +47,19 @@ import org.testng.annotations.Test;
 public class TestAlignSeq
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   SequenceI s1, s2, s3;
 
   /**
    * @throws java.lang.Exception
    */
-  @BeforeMethod
+  @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
   {
     s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
@@ -55,18 +68,17 @@ public class TestAlignSeq
     s2 = new Sequence("Seq2", "ASDFA");
     s2.setStart(5);
     s2.setEnd(9);
-    s3 = new Sequence("Seq1", "SDFAQQQSSS");
+    s3 = new Sequence("Seq3", "SDFAQQQSSS");
 
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   /**
    * simple test that mapping from alignment corresponds identical positions.
    */
   public void testGetMappingForS1()
   {
-    AlignSeq as = AlignSeq
-            .doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
+    AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
     System.out.println("s1: " + as.getAStr1());
     System.out.println("s2: " + as.getAStr2());
 
@@ -75,18 +87,47 @@ public class TestAlignSeq
     assertEquals(as.getAStr1(), as.getAStr2());
 
     Mapping s1tos2 = as.getMappingFromS1(false);
+    checkMapping(s1tos2, s1, s2);
+  }
+
+  public void checkMapping(Mapping s1tos2, SequenceI _s1, SequenceI _s2)
+  {
     System.out.println(s1tos2.getMap().toString());
-    for (int i = s2.getStart(); i < s2.getEnd(); i++)
+    for (int i = _s2.getStart(); i < _s2.getEnd(); i++)
     {
-      System.out.println("Position in s2: " + i
-              + " maps to position in s1: " + s1tos2.getPosition(i));
-      // TODO fails: getCharAt doesn't allow for the start position??
-      // assertEquals(String.valueOf(s2.getCharAt(i)),
-      // String.valueOf(s1.getCharAt(s1tos2.getPosition(i))));
+      int p = s1tos2.getPosition(i);
+      char s2c = _s2.getCharAt(i - _s2.getStart());
+      char s1c = _s1.getCharAt(p - _s1.getStart());
+      System.out.println("Position in s2: " + i + s2c
+              + " maps to position in s1: " + p + s1c);
+      assertEquals(s1c, s2c);
     }
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
+  /**
+   * simple test that mapping from alignment corresponds identical positions.
+   */
+  public void testGetMappingForS1_withLowerCase()
+  {
+    // make one of the sequences lower case
+    SequenceI ns2 = new Sequence(s2);
+    ns2.replace('D', 'd');
+    AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, ns2, AlignSeq.PEP);
+    System.out.println("s1: " + as.getAStr1());
+    System.out.println("s2: " + as.getAStr2());
+
+    // aligned results match
+    assertEquals("ASDFA", as.getAStr1());
+    assertEquals(as.getAStr1(), as.getAStr2().toUpperCase(Locale.ROOT));
+
+    Mapping s1tos2 = as.getMappingFromS1(false);
+    assertEquals("ASdFA", as.getAStr2());
+    // verify mapping is consistent between original all-caps sequences
+    checkMapping(s1tos2, s1, s2);
+  }
+
+  @Test(groups = { "Functional" })
   public void testExtractGaps()
   {
     assertNull(AlignSeq.extractGaps(null, null));
@@ -96,7 +137,7 @@ public class TestAlignSeq
     assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D."));
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testPrintAlignment()
   {
     AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s3, AlignSeq.PEP);
@@ -117,10 +158,9 @@ public class TestAlignSeq
     };
 
     as.printAlignment(ps);
-    String expected = "Score = 320\nLength of alignment = 10\nSequence Seq1 :  3 - 18 (Sequence length = 14)\nSequence Seq1 :  1 - 10 (Sequence length = 10)\n\n"
-            + "Seq1 SDFAQQQRRR\n"
-            + "     |||||||   \n"
-            + "Seq1 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n\n";
+    String expected = "Score = 320.0\nLength of alignment = 10\nSequence Seq1/4-13 (Sequence length = 14)\nSequence Seq3/1-10 (Sequence length = 10)\n\n"
+            + "Seq1/4-13 SDFAQQQRRR\n" + "          |||||||   \n"
+            + "Seq3/1-10 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n\n";
     assertEquals(expected, baos.toString());
   }
 }