/*
- * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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
+ *
* @author jimp
- *
+ *
*/
public class TestAlignSeq
{
- SequenceI s1,s2,s3;
+ @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 = 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("Seq3", "SDFAQQQSSS");
}
- @Test
+ @Test(groups = { "Functional" })
/**
* simple test that mapping from alignment corresponds identical positions.
*/
- public void TestGetMappingForS1()
+ public void testGetMappingForS1()
+ {
+ 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)
{
- 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)));
+ 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());
+ }
}