X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FTestAlignSeq.java;h=955cca7a21708d7865c1d2ffd66203d4c094ec80;hb=447c5c1b22bd12a78730640321264fb38c39ec7b;hp=9fc88ead7cf2ce865feac8c6fa0bc4557191e5b0;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git

diff --git a/test/jalview/analysis/TestAlignSeq.java b/test/jalview/analysis/TestAlignSeq.java
index 9fc88ea..955cca7 100644
--- a/test/jalview/analysis/TestAlignSeq.java
+++ b/test/jalview/analysis/TestAlignSeq.java
@@ -64,7 +64,7 @@ public class TestAlignSeq
     s2 = new Sequence("Seq2", "ASDFA");
     s2.setStart(5);
     s2.setEnd(9);
-    s3 = new Sequence("Seq1", "SDFAQQQSSS");
+    s3 = new Sequence("Seq3", "SDFAQQQSSS");
 
   }
 
@@ -108,13 +108,19 @@ public class TestAlignSeq
   public void testPrintAlignment()
   {
     AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s3, AlignSeq.PEP);
+
+    // s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
+    // s1.setStart(3);
+    // s1.setEnd(18);
+    // s3 = new Sequence("Seq3", "SDFAQQQSSS");
+    //
     final StringBuilder baos = new StringBuilder();
     PrintStream ps = new PrintStream(System.out)
     {
       @Override
       public void print(String x)
       {
-        baos.append(x);
+        baos.append(x.replaceAll("\r", ""));
       }
 
       @Override
@@ -125,10 +131,17 @@ public class TestAlignSeq
     };
 
     as.printAlignment(ps);
-    String expected = "Score = 320\nLength of alignment = 10\nSequence Seq1 :  3 - 18 (Sequence length = 14)\nSequence Seq1 :  1 - 10 (Sequence length = 10)\n\n"
-            + "Seq1 SDFAQQQRRR\n"
-            + "     |||||||   \n"
-            + "Seq1 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n";
-    assertEquals(expected, baos.toString());
+    String expected = "Score = 320.0\n" + "Length of alignment = 10\n"
+            + "Sequence Seq1/4-13 (Sequence length = 14)\n"
+            + "Sequence Seq3/1-10 (Sequence length = 10)\n" + "\n"
+            + "Seq1/4-13 SDFAQQQRRR\n"
+            + "          |||||||   \n"
+            + "Seq3/1-10 SDFAQQQSSS\n" + "\n" + "Percentage ID = 70.00\n"
+            + "\n";
+
+    String s = baos.toString();
+    System.out.println(s);
+
+    assertEquals(expected, s);
   }
 }