From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 22 Jun 2023 15:00:31 +0000 (+0200)
Subject: JAL-2292 - ensure mapping is built for equal symbols with mismatched case
X-Git-Tag: Release_2_11_4_0~253^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Fpatch%2FJAL-2292_caseSensitivePAE;p=jalview.git

JAL-2292 - ensure mapping is built for equal symbols with mismatched case
---

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 65fd110..02b3f41 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -890,7 +890,8 @@ public class AlignSeq
         pdbpos++;
       }
 
-      if (allowmismatch || c1 == c2)
+      // ignore case differences
+      if (allowmismatch || (c1 == c2) || (Math.abs(c2-c1)==('a'-'A')))
       {
         // extend mapping interval
         if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos)
diff --git a/test/jalview/analysis/TestAlignSeq.java b/test/jalview/analysis/TestAlignSeq.java
index 5134511..62250eb 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
  * 
@@ -83,16 +87,42 @@ 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);
+    checkMapping(s1tos2,s1,ns2);
+  }
 
   @Test(groups = { "Functional" })
   public void testExtractGaps()