X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FTCoffeeScoreFile.java;h=7a3f2d9deaae376cd55d360b1f3eb8a4e7437095;hb=b3f065b1e4604502ef60a0d5c83ac43f07ccec0f;hp=df009865cd405e68a66060ea5bb4eb88ea0b1afc;hpb=9d63632f20b8c8c2961601b0ab22ecea92059240;p=jalview.git

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
 		 */