X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fanalysis%2FTestAlignSeq.java;h=44bea811761f89441dd095ff44945226bf985eb5;hb=261d2ca1b0eef309cd9d178e023c6bfecbd62017;hp=9fc88ead7cf2ce865feac8c6fa0bc4557191e5b0;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git

diff --git a/test/jalview/analysis/TestAlignSeq.java b/test/jalview/analysis/TestAlignSeq.java
index 9fc88ea..44bea81 100644
--- a/test/jalview/analysis/TestAlignSeq.java
+++ b/test/jalview/analysis/TestAlignSeq.java
@@ -29,11 +29,15 @@ 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
  * 
@@ -64,7 +68,7 @@ public class TestAlignSeq
     s2 = new Sequence("Seq2", "ASDFA");
     s2.setStart(5);
     s2.setEnd(9);
-    s3 = new Sequence("Seq1", "SDFAQQQSSS");
+    s3 = new Sequence("Seq3", "SDFAQQQSSS");
 
   }
 
@@ -83,16 +87,44 @@ 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" })
+  /**
+   * 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()
@@ -125,10 +157,9 @@ 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";
+    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());
   }
 }