JAL-2909 Removed buggy CIGAR parsing code which was not used

[jalview.git] / test / jalview / datamodel / SeqCigarTest.java

diff --git a/test/jalview/datamodel/SeqCigarTest.java b/test/jalview/datamodel/SeqCigarTest.java
index 8d3c878..57f1156 100644 (file)
--- a/test/jalview/datamodel/SeqCigarTest.java
+++ b/test/jalview/datamodel/SeqCigarTest.java
@@ -23,8 +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;
 
 /**
@@ -32,6 +34,14 @@ 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()
   {
@@ -55,6 +65,7 @@ public class SeqCigarTest
       }
     }
   }
+
   /*
    * refactored 'as is' from main method
    * 
@@ -79,11 +90,6 @@ public class SeqCigarTest
     assertEquals("Failed to recover ungapped sequence cigar operations",
             "42M", cs_null);
     testCigar_string(s_gapped, ex_cs_gapped);
-    SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
-    assertEquals("Failed parseCigar", ex_cs_gapped,
-            gen_sgapped.getCigarstring());
-
-    testSeqRecovery(gen_sgapped, s_gapped);
 
     /*
      * Test dataset resolution
@@ -110,7 +116,7 @@ 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");
@@ -182,7 +188,8 @@ 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