X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSeqCigarTest.java;fp=test%2Fjalview%2Fdatamodel%2FSeqCigarTest.java;h=8d3c878a5a37eb09139d2ff1836d987d7da09f51;hb=99d5f1d805e530f23a53dad4484d44ecd0fbfdf3;hp=705c773724c0ac9d87594bc80950ad5de21b2a30;hpb=e6134bccddc2c7faad28fad1a4e77ccd0ceb3d84;p=jalview.git

diff --git a/test/jalview/datamodel/SeqCigarTest.java b/test/jalview/datamodel/SeqCigarTest.java
index 705c773..8d3c878 100644
--- a/test/jalview/datamodel/SeqCigarTest.java
+++ b/test/jalview/datamodel/SeqCigarTest.java
@@ -23,6 +23,8 @@ package jalview.datamodel;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 
+import jalview.util.Comparison;
+
 import org.testng.annotations.Test;
 
 /**
@@ -30,6 +32,29 @@ import org.testng.annotations.Test;
  */
 public class SeqCigarTest
 {
+  @Test(groups = { "Functional" })
+  public void testFindPosition()
+  {
+    SequenceI oseq = new Sequence("MySeq", "ASD---ASD---ASD", 37, 45);
+    oseq.createDatasetSequence();
+    SeqCigar cs = new SeqCigar(oseq);
+    assertEquals(oseq.getSequenceAsString(), cs.getSequenceString('-'));
+    for (int c = 0, cLen = oseq.getLength(); c < cLen; c++)
+    {
+      int os_p = oseq.findPosition(c);
+      int cigar_p = cs.findPosition(c);
+      if (Comparison.isGap(oseq.getCharAt(c)))
+      {
+        assertEquals("Expected gap at position " + os_p + " column " + c,
+                -1, cigar_p);
+      }
+      else
+      {
+        assertEquals("Positions don't match for at column " + c, os_p,
+                cigar_p);
+      }
+    }
+  }
   /*
    * refactored 'as is' from main method
    *