X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSeqCigarTest.java;h=89169d6dbb10cc387f372442133b575e8fa5d580;hb=490bea038483dcc853766de08a8971668930f43a;hp=c51a0803ec52f5409435204d636dce14e293e18e;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/test/jalview/datamodel/SeqCigarTest.java b/test/jalview/datamodel/SeqCigarTest.java
index c51a080..89169d6 100644
--- a/test/jalview/datamodel/SeqCigarTest.java
+++ b/test/jalview/datamodel/SeqCigarTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,6 +23,10 @@ package jalview.datamodel;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 
+import jalview.gui.JvOptionPane;
+import jalview.util.Comparison;
+
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 /**
@@ -30,6 +34,38 @@ import org.testng.annotations.Test;
  */
 public class SeqCigarTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @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
    * 
@@ -85,7 +121,7 @@ public class SeqCigarTest
     /*
      * TODO: can we add assertions to the sysouts that follow?
      */
-    System.out.println("Original sequence align:\n" + sub_gapped_s
+    System.out.println("\nOriginal sequence align:\n" + sub_gapped_s
             + "\nReconstructed window from 8 to 48\n" + "XXXXXXXX"
             + sub_se_gp.getSequenceString('-') + "..." + "\nCigar String:"
             + sub_se_gp.getCigarstring() + "\n");
@@ -157,7 +193,8 @@ public class SeqCigarTest
     SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
     // assertEquals("Couldn't reconstruct sequence", s_gapped.getSequence(),
     // gen_sgapped_s);
-    if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
+    if (!gen_sgapped_s.getSequenceAsString().equals(
+            s_gapped.getSequenceAsString()))
     {
       // TODO: investigate errors reported here, to allow full conversion to
       // passing JUnit assertion form