JAL-1067, JAL-1105 - refactor parser to fit Jalview's data parsing architecture

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

diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java
index 7257e14..85c0bff 100644 (file)
--- a/test/jalview/io/TCoffeeScoreFileTest.java
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@ -16,12 +16,15 @@ import org.junit.Test;
 
 public class TCoffeeScoreFileTest {
 
-       final static File SCORE_FILE = new File("./test/jalview/io/tcoffee.score_ascii");
+       final static File SCORE_FILE = new File("test/jalview/io/tcoffee.score_ascii");
+        final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
        
        @Test
-       public void testReadHeader() throws FileNotFoundException {
+       public void testReadHeader() throws IOException, FileNotFoundException {
 
-               Header header = TCoffeeScoreFile.readHeader( new BufferedReader(new FileReader(SCORE_FILE)) );
+               TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
+               assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
+               Header header = scoreFile.header;
                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 );
@@ -39,14 +42,19 @@ public class TCoffeeScoreFileTest {
        
        @Test
        public void testWrongFile() {
-               TCoffeeScoreFile result = TCoffeeScoreFile.load(new File("./test/jalview/io/tcoffee.fasta_aln"));
-               assertNull(result);
+           try {
+               TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
+               assertFalse(result.isValid());
+           } catch (IOException x)
+           {
+             assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
+           }
        } 
 
        @Test
-       public void testHeightAndWidth() {
-               TCoffeeScoreFile result = TCoffeeScoreFile.load(new File("./test/jalview/io/tcoffee.score_ascii"));
-               assertNotNull(result);
+       public void testHeightAndWidth() throws IOException {
+               TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
+               assertTrue(result.isValid());
                assertEquals( 8, result.getHeight() );
                assertEquals( 83, result.getWidth() );
        }       
@@ -68,9 +76,10 @@ public class TCoffeeScoreFileTest {
                                "cons   999999999999999999999999999851000110321100001134\n" +
                                "\n" +
                                "\n";
-               
-               Block block = TCoffeeScoreFile.readBlock(new BufferedReader(new StringReader(BLOCK)), 0);
-               assertNotNull(block);
+               FileParse source=new FileParse(BLOCK, FormatAdapter.PASTE);
+               Block block = TCoffeeScoreFile.readBlock(source, 0);
+
+                assertNotNull(block);
                assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
                assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
                assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
@@ -83,9 +92,9 @@ public class TCoffeeScoreFileTest {
        }
 
        @Test
-       public void testParse() throws FileNotFoundException {
+       public void testParse() throws IOException {
 
-               TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
+               TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
 
                assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
                assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
@@ -100,10 +109,10 @@ public class TCoffeeScoreFileTest {
 
        
        @Test
-       public void testGetAsList() throws FileNotFoundException {
+       public void testGetAsList() throws IOException {
                
-               TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
-
+          TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
+          assertTrue(parser.getWarningMessage(),parser.isValid());
                List<String> scores = parser.getScoresList();
                assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
                assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
@@ -119,10 +128,10 @@ public class TCoffeeScoreFileTest {
        
        
        @Test
-       public void testGetAsArray() throws FileNotFoundException {
+       public void testGetAsArray() throws IOException {
                
-               TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
-
+          TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
+          assertTrue(parser.getWarningMessage(),parser.isValid());
                byte[][] scores = parser.getScoresArray();
        
                assertEquals( 9, scores[0][0] );