Merge branch 'Tcoffee_JAL-1065' of https://source.jalview.org/git/jalview into test_p...

[jalview.git] / test / jalview / io / TCoffeeScoreFileTest.java

diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java
new file mode 100644 (file)
index 0000000..27df5e0
--- /dev/null
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@ -0,0 +1,144 @@
+package jalview.io;
+
+import static org.junit.Assert.*;
+import jalview.io.TCoffeeScoreFile.Block;
+import jalview.io.TCoffeeScoreFile.Header;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.StringReader;
+import java.util.List;
+
+import org.junit.Test;
+
+public class TCoffeeScoreFileTest {
+
+       final static File SCORE_FILE = new File("./test/jalview/io/tcoffee.score_ascii");
+       
+       @Test
+       public void testReadHeader() throws FileNotFoundException {
+
+               Header header = TCoffeeScoreFile.readHeader( new BufferedReader(new FileReader(SCORE_FILE)) );
+               assertNotNull(header);
+               assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
+               assertEquals( 90, header.score );
+               assertEquals( 89, header.getScoreFor("1PHT") );
+               assertEquals( 90, header.getScoreFor("1BB9") );
+               assertEquals( 94, header.getScoreFor("1UHC") );
+               assertEquals( 94, header.getScoreFor("1YCS") );
+               assertEquals( 93, header.getScoreFor("1OOT") );
+               assertEquals( 94, header.getScoreFor("1ABO") );
+               assertEquals( 94, header.getScoreFor("1FYN") );
+               assertEquals( 94, header.getScoreFor("1QCF") );
+               assertEquals( 90, header.getScoreFor("cons") );
+       }
+       
+       
+       @Test
+       public void testWrongFile() {
+               TCoffeeScoreFile result = TCoffeeScoreFile.load(new File("./test/jalview/io/tcoffee.fasta_aln"));
+               assertNull(result);
+       } 
+       
+       @Test
+       public void testReadBlock( ) throws IOException {
+               
+               String BLOCK = "\n" +
+                               "\n" +
+                               "\n" +
+                               "1PHT   999999999999999999999999998762112222543211112134\n" +
+                               "1BB9   99999999999999999999999999987-------4322----2234  \n" +
+                               "1UHC   99999999999999999999999999987-------5321----2246\n" +
+                               "1YCS   99999999999999999999999999986-------4321----1-35\n" +
+                               "1OOT   999999999999999999999999999861-------3------1135  \n" +
+                               "1ABO   99999999999999999999999999986-------422-------34\n" +
+                               "1FYN   99999999999999999999999999985-------32--------35\n" +
+                               "1QCF   99999999999999999999999999974-------2---------24\n" +
+                               "cons   999999999999999999999999999851000110321100001134\n" +
+                               "\n" +
+                               "\n";
+               
+               Block block = TCoffeeScoreFile.readBlock(new BufferedReader(new StringReader(BLOCK)), 0);
+               assertNotNull(block);
+               assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
+               assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
+               assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
+               assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
+               assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
+               assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
+               assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
+               assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
+               assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
+       }
+
+       @Test
+       public void testParse() throws FileNotFoundException {
+
+               TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
+
+               assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
+               assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
+               assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
+               assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
+               assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
+               assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
+               assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
+               assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
+               assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );             
+       }
+
+       
+       @Test
+       public void testGetAsList() throws FileNotFoundException {
+               
+               TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
+
+               List<String> scores = parser.getScoresList();
+               assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
+               assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
+               assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
+               assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
+               assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
+               assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
+               assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
+               assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
+               assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );           
+               
+       } 
+       
+       
+       @Test
+       public void testGetAsArray() throws FileNotFoundException {
+               
+               TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
+
+               byte[][] scores = parser.getScoresArray();
+       
+               assertEquals( 9, scores[0][0] );
+               assertEquals( 9, scores[1][0] );
+               assertEquals( 9, scores[2][0] );
+               assertEquals( 9, scores[3][0] );
+               assertEquals( 9, scores[4][0] );
+               assertEquals( 9, scores[5][0] );
+               assertEquals( 9, scores[6][0] );
+               assertEquals( 9, scores[7][0] );
+               assertEquals( 9, scores[8][0] );
+               
+               assertEquals( 5, scores[0][36] );
+               assertEquals( 4, scores[1][36] );
+               assertEquals( 5, scores[2][36] );
+               assertEquals( 4, scores[3][36] );
+               assertEquals( -1, scores[4][36] );
+               assertEquals( 4, scores[5][36] );
+               assertEquals( 3, scores[6][36] );
+               assertEquals( 2, scores[7][36] );
+               assertEquals( 3, scores[8][36] );
+               
+       } 
+       
+       
+       
+}