/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
*
*/
package jalview.analysis;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
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");
+ s2 = new Sequence("Seq2", "ASDFA");
s2.setStart(5);
- s3 = new Sequence("Seq1","SDFAQQQSSS");
+ s3 = new Sequence("Seq1", "SDFAQQQSSS");
}
*/
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);
+ 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);
System.out.println(s1tos2.getMap().toString());
- for (int i=s2.getStart();i<s2.getEnd();i++)
+ for (int i = s2.getStart(); i < s2.getEnd(); i++)
{
- System.out.println("Position in s2: "+i +" maps to position in s1: "+s1tos2.getPosition(i));
- assertTrue("",s2.getCharAt(i)==s1.getCharAt(s1tos2.getPosition(i)));
+ System.out.println("Position in s2: " + i
+ + " maps to position in s1: " + s1tos2.getPosition(i));
+ assertTrue("", s2.getCharAt(i) == s1.getCharAt(s1tos2.getPosition(i)));
}
}
+ @Test
+ public void testExtractGaps()
+ {
+ assertNull(AlignSeq.extractGaps(null, null));
+ assertNull(AlignSeq.extractGaps(". -", null));
+ assertNull(AlignSeq.extractGaps(null, "AB-C"));
+
+ assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D."));
+ }
}