X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FTCoffeeScoreFile.java;h=2de4573125b1c52000033e2a93b8d9e35af3977b;hb=1379350f04bc63ca05bd428afb86717c4764755d;hp=7a3f2d9deaae376cd55d360b1f3eb8a4e7437095;hpb=b3f065b1e4604502ef60a0d5c83ac43f07ccec0f;p=jalview.git

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index 7a3f2d9..2de4573 100644
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -75,7 +75,8 @@ public class TCoffeeScoreFile {
 	 * insertion order. 
 	 */
 	LinkedHashMap<String,StringBuilder> scores = new LinkedHashMap<String,StringBuilder>();
-	
+
+	Integer fWidth;
 
 	/**
 	 * Parse the specified file.
@@ -110,6 +111,25 @@ public class TCoffeeScoreFile {
 	}
 		
 	/**
+	 * @return The 'height' of the score matrix i.e. the numbers of score rows that should matches 
+	 * the number of sequences in the alignment
+	 */
+	public int getHeight() {
+		// the last entry will always be the 'global' alingment consensus scores, so it is removed 
+		// from the 'height' count to make this value compatible with the number of sequences in the MSA
+		return scores != null && scores.size() > 0 ? scores.size()-1 : 0;
+	}
+	
+	/**
+	 * @return The 'width' of the score matrix i.e. the number of columns. 
+	 * Since teh score value are supposd to be calculated for an 'aligned' MSA, all the entries 
+	 * have to have the same width.  
+	 */
+	public int getWidth() {
+		return fWidth != null ? fWidth : 0;
+	}
+	
+	/**
 	 * 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
 	 */
@@ -190,14 +210,27 @@ public class TCoffeeScoreFile {
 			for( Map.Entry<String,String> entry : block.items.entrySet() ) {
 				StringBuilder scoreStringBuilder = scores.get(entry.getKey());
 				if( scoreStringBuilder == null ) {
-					throw new RuntimeException(String.format("Invalid T-Coffee score file. Sequence ID '%s' is not declared in header section", entry.getKey()));
+					throw new RuntimeException(String.format("Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section", entry.getKey()));
 				}
 				
 				scoreStringBuilder.append( entry.getValue() );
 			}
-			
 		}
 		
+		/*
+		 * verify that all rows have the same width
+		 */
+		for( StringBuilder str : scores.values() ) {
+			if( fWidth == null ) {
+				fWidth = str.length();
+			}
+			else if( fWidth != str.length() ) {
+				throw new RuntimeException("Invalid T-Coffee score file: All the score sequences must have the same length");
+			}
+		}
+		
+		
+		
 	}