From b3f065b1e4604502ef60a0d5c83ac43f07ccec0f Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 9 Apr 2012 21:21:14 +0200
Subject: [PATCH] JAL-1067 - T-Coffee score file reader

---
 src/jalview/io/TCoffeeScoreFile.java      |   70 +++++++++++++++++------------
 test/jalview/io/TCoffeeScoreFileTest.java |   16 ++++---
 2 files changed, 51 insertions(+), 35 deletions(-)

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index df00986..7a3f2d9 100644
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -78,6 +78,44 @@ public class TCoffeeScoreFile {
 	
 
 	/**
+	 * Parse the specified file.
+	 * 
+	 * @param file The file to be parsed 
+	 */
+	public static TCoffeeScoreFile load(File file) {
+		try {
+			return load(new FileReader(file));
+		} 
+		catch (FileNotFoundException e) {
+			throw new RuntimeException(e);
+		}
+	}
+	
+	/**
+	 * Parse the provided reader for the T-Coffee scores file format
+	 * 
+	 * @param reader 
+	 */
+	public static TCoffeeScoreFile load(Reader reader) {
+
+		try {
+			BufferedReader in = (BufferedReader) (reader instanceof BufferedReader ? reader : new BufferedReader(reader));
+			TCoffeeScoreFile result = new TCoffeeScoreFile();
+			result.doParsing(in);
+			return result.header != null && result.scores != null ? result : null;
+		}
+		catch( Exception e) {
+			throw new RuntimeException(e);
+		}
+	}
+		
+	/**
+	 * The default constructor is marked as {@code protected} since this class is meant to created 
+	 * through the {@link #load(File)} or {@link #load(Reader)} factory methods
+	 */
+	protected TCoffeeScoreFile() { } 
+	
+	/**
 	 * Get the string of score values for the specified seqeunce ID. 
 	 * @param id The sequence ID 
 	 * @return The scores as a string of values e.g. {@code 99999987-------432}. 
@@ -122,43 +160,17 @@ public class TCoffeeScoreFile {
 		return result;
 	}
 	
-	/**
-	 * Parse the specified file.
-	 * 
-	 * @param file The file to be parsed 
-	 */
-	public void parse(File file) {
-		try {
-			parse(new FileReader(file));
-		} 
-		catch (FileNotFoundException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Parse the provided reader for the T-Coffee scores file format
-	 * 
-	 * @param reader 
-	 */
-	public void parse(Reader reader) {
 
-		try {
-			BufferedReader in = (BufferedReader) (reader instanceof BufferedReader ? reader : new BufferedReader(reader));
-			doParsing(in);
-		}
-		catch( Exception e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
 	private void doParsing(BufferedReader in) throws IOException {
 
 		/*
 		 * read the header
 		 */
 		header = readHeader(in);
+
+		if( header == null ) { return; }
 		
+	
 		/*
 		 * initilize the structure
 		 */
diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java
index f654ba1..27df5e0 100644
--- a/test/jalview/io/TCoffeeScoreFileTest.java
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@ -36,6 +36,13 @@ public class TCoffeeScoreFileTest {
 		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 {
 		
@@ -70,8 +77,7 @@ public class TCoffeeScoreFileTest {
 	@Test
 	public void testParse() throws FileNotFoundException {
 
-		TCoffeeScoreFile parser = new TCoffeeScoreFile();
-		parser.parse(new BufferedReader(new FileReader(SCORE_FILE)) );
+		TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
 
 		assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
 		assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
@@ -88,8 +94,7 @@ public class TCoffeeScoreFileTest {
 	@Test
 	public void testGetAsList() throws FileNotFoundException {
 		
-		TCoffeeScoreFile parser = new TCoffeeScoreFile();
-		parser.parse(new BufferedReader(new FileReader(SCORE_FILE)) );
+		TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
 
 		List<String> scores = parser.getScoresList();
 		assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
@@ -108,8 +113,7 @@ public class TCoffeeScoreFileTest {
 	@Test
 	public void testGetAsArray() throws FileNotFoundException {
 		
-		TCoffeeScoreFile parser = new TCoffeeScoreFile();
-		parser.parse(new BufferedReader(new FileReader(SCORE_FILE)) );
+		TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
 
 		byte[][] scores = parser.getScoresArray();
 	
-- 
1.7.10.2