/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+
+import java.io.PrintStream;
+import java.nio.charset.Charset;
+import java.util.Locale;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import com.google.common.base.Charsets;
/**
* Test the alignment -> Mapping routines
public class TestAlignSeq
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
SequenceI s1, s2, s3;
/**
* @throws java.lang.Exception
*/
- @Before
+ @BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
{
s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
s1.setStart(3);
+ s1.setEnd(18);
s2 = new Sequence("Seq2", "ASDFA");
s2.setStart(5);
- s3 = new Sequence("Seq1", "SDFAQQQSSS");
+ s2.setEnd(9);
+ s3 = new Sequence("Seq3", "SDFAQQQSSS");
}
- @Test
+ @Test(groups = { "Functional" })
/**
* 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);
+ 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);
+ checkMapping(s1tos2, s1, s2);
+ }
+
+ public void checkMapping(Mapping s1tos2, SequenceI _s1, SequenceI _s2)
+ {
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)));
+ int p = s1tos2.getPosition(i);
+ char s2c = _s2.getCharAt(i - _s2.getStart());
+ char s1c = _s1.getCharAt(p - _s1.getStart());
+ System.out.println("Position in s2: " + i + s2c
+ + " maps to position in s1: " + p + s1c);
+ assertEquals(s1c, s2c);
}
}
+ @Test(groups = { "Functional" })
+ /**
+ * simple test that mapping from alignment corresponds identical positions.
+ */
+ public void testGetMappingForS1_withLowerCase()
+ {
+ // make one of the sequences lower case
+ SequenceI ns2 = new Sequence(s2);
+ ns2.replace('D', 'd');
+ AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, ns2, 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().toUpperCase(Locale.ROOT));
+
+ Mapping s1tos2 = as.getMappingFromS1(false);
+ assertEquals("ASdFA", as.getAStr2());
+ // verify mapping is consistent between original all-caps sequences
+ checkMapping(s1tos2, s1, s2);
+ }
+
+ @Test(groups = { "Functional" })
+ 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."));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testPrintAlignment()
+ {
+ AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s3, AlignSeq.PEP);
+ final StringBuilder baos = new StringBuilder();
+ PrintStream ps = new PrintStream(System.out)
+ {
+ @Override
+ public void print(String x)
+ {
+ baos.append(x);
+ }
+
+ @Override
+ public void println()
+ {
+ baos.append("\n");
+ }
+ };
+
+ as.printAlignment(ps);
+ String expected = "Score = 320.0\nLength of alignment = 10\nSequence Seq1/4-13 (Sequence length = 14)\nSequence 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";
+ assertEquals(expected, baos.toString());
+ }
}