X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FTestAlignSeq.java;h=4956bd8e7944c6fc144f146f01de9bd380b5d995;hb=0f26441e26325c728a3e9a108ac425d4d60dde1c;hp=59740dfad35134d364efb6699a8a8bd0fe9ac31c;hpb=aea8e62db4be70d2ebee5df313c285894f7ce342;p=jalview.git
diff --git a/test/jalview/analysis/TestAlignSeq.java b/test/jalview/analysis/TestAlignSeq.java
index 59740df..4956bd8 100644
--- a/test/jalview/analysis/TestAlignSeq.java
+++ b/test/jalview/analysis/TestAlignSeq.java
@@ -1,50 +1,61 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import static org.junit.Assert.*;
-import jalview.datamodel.Mapping;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
+import java.io.PrintStream;
import org.junit.Before;
import org.junit.Test;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
/**
* Test the alignment -> Mapping routines
+ *
* @author jimp
- *
+ *
*/
public class TestAlignSeq
{
- SequenceI s1,s2,s3;
+ SequenceI s1, s2, s3;
+
/**
* @throws java.lang.Exception
*/
@Before
public void setUp() throws Exception
{
- s1 = new Sequence("Seq1","ASDFAQQQRRRSSS");
+ s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
s1.setStart(3);
- s2 = new Sequence("Seq2","ASDFA");
+ s1.setEnd(18);
+ s2 = new Sequence("Seq2", "ASDFA");
s2.setStart(5);
- s3 = new Sequence("Seq1","SDFAQQQSSS");
+ s2.setEnd(9);
+ s3 = new Sequence("Seq1", "SDFAQQQSSS");
}
@@ -52,19 +63,64 @@ public class TestAlignSeq
/**
* simple test that mapping from alignment corresponds identical positions.
*/
- public void TestGetMappingForS1()
+ public void testGetMappingForS1()
{
- jalview.analysis.AlignSeq as = jalview.analysis.AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
- System.out.println("s1: "+as.getAStr1());
- System.out.println("s2: "+as.getAStr2());
-
- Mapping s1tos2=as.getMappingFromS1(false);
+ AlignSeq as = AlignSeq
+ .doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
+ System.out.println("s1: " + as.getAStr1());
+ System.out.println("s2: " + as.getAStr2());
+
+ // aligned results match
+ assertEquals("ASDFA", as.getAStr1());
+ assertEquals(as.getAStr1(), as.getAStr2());
+
+ Mapping s1tos2 = as.getMappingFromS1(false);
System.out.println(s1tos2.getMap().toString());
- for (int i=s2.getStart();i