JAL-2103 - refactored msa transformation routines and added (failing) test for new...

[jalview.git] / test / jalview / ws / jws1 / JPredWSUtilsTest.java

diff --git a/test/jalview/ws/jws1/JPredWSUtilsTest.java b/test/jalview/ws/jws1/JPredWSUtilsTest.java
index 0563647..e930e55 100644 (file)
--- a/test/jalview/ws/jws1/JPredWSUtilsTest.java
+++ b/test/jalview/ws/jws1/JPredWSUtilsTest.java
@@ -1,5 +1,11 @@
 package jalview.ws.jws1;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import org.testng.Assert;
 import org.testng.annotations.Test;
 
 public class JPredWSUtilsTest
@@ -28,4 +34,34 @@ public class JPredWSUtilsTest
 
   }
 
+  @Test(groups = { "Functional" })
+  public void testInsertHiddenResidues()
+  {
+    // orig: asdfPPPPPPPasdfPPPPasdf
+    // pred: PPPPPPPPPPP
+    // al: -----P-P-P---P---P----P---P-P--PP---P---
+    // s1: SSSSSSS-SS---S---SSSSSS---S-S--SSSSSSSSS
+    // s2: SSSSSSS-SSSSSSSSSSS----SSS-S-SSS-----SSS
+    SequenceI orig = new Sequence("orig", "asdfPPPPPPPasdfPPPPasdf"), pred = new Sequence(
+            "pred", "PPPPPPPPPPP"), al = new Sequence("al/5-23",
+            "-----P-P-P---P---P----P---P-P--PP---P---"), s1 = new Sequence(
+            "s1", "SSSSSSS-SS---S---SSSSSS---S-S--SSSSSSSSS"), s2 = new Sequence(
+            "s2", "SSSSSSS-SSSSSSSSSSS----SSS-S-SSS-----SSS");
+
+    AlignmentI alpred = new Alignment(new SequenceI[] { al, s1, s2 });
+    JPredWSUtils.insertHiddenResidues(alpred, '.', new int[] { 5, 6, 7, 8,
+        9, 10, 11, 16, 17, 18, 19 }, orig);
+    Assert.assertEquals(alpred.getSequenceAt(2).getSequenceAsString(),
+            "....SSSSSSS-SS---S---SSSSSS---S....-S--SSSSSSSSS....");
+    Assert.assertEquals(alpred.getSequenceAt(1).getSequenceAsString(),
+            "....SSSSSSS-SSSSSSSSSSS----SSS-....S-SSS-----SSS....");
+    Assert.assertEquals(alpred.getSequenceAt(0).getSequenceAsString(),
+            "asdf-----P-P-P---P---P----P---Pasdf-P--PP---P---asdf");
+
+    // result:
+    //
+    // al: asdf-----P-P-P---P---P----P---Pasdf-P--PP---P---asdf
+    // s1: ....SSSSSSS-SS---S---SSSSSS---S....-S--SSSSSSSSS....
+    // s2: ....SSSSSSS-SSSSSSSSSSS----SSS-....S-SSS-----SSS....
+  }
 }