X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FTCoffeeScoreFile.java;h=ca8a22ab7e9c1867ffd7157319142d3910be892d;hb=a23cc416cd520ac6dec6052591575b264f5d25bc;hp=1455c63cdf13c0716166d81c09811e863255ee05;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index 1455c63..ca8a22a 100644
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
@@ -24,17 +27,14 @@ import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
import java.awt.Color;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
import java.io.IOException;
-import java.io.Reader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
/**
* A file parse for T-Coffee score ascii format. This file contains the
@@ -91,7 +91,6 @@ import java.util.Map;
*/
public class TCoffeeScoreFile extends AlignFile
{
-
public TCoffeeScoreFile(String inFile, String type) throws IOException
{
super(inFile, type);
@@ -143,7 +142,7 @@ public class TCoffeeScoreFile extends AlignFile
/**
* @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,
+ * the score value are supposed to be calculated for an 'aligned' MSA,
* all the entries have to have the same width.
*/
public int getWidth()
@@ -398,6 +397,9 @@ public class TCoffeeScoreFile extends AlignFile
}
}
+ static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
+ .compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
+
/**
* Read a scores block ihe provided stream.
*
@@ -457,6 +459,12 @@ public class TCoffeeScoreFile extends AlignFile
String id = line.substring(0, p).trim();
String val = line.substring(p + 1).trim();
+ Matcher m = SCORES_WITH_RESIDUE_NUMS.matcher(val);
+ if (m.matches())
+ {
+ val = m.group(1);
+ }
+
result.items.put(id, val);
} while ((line = reader.nextLine()) != null);
@@ -545,7 +553,11 @@ public class TCoffeeScoreFile extends AlignFile
{
if (al.getHeight() != getHeight() || al.getWidth() != getWidth())
{
- warningMessage = "Alignment shape does not match T-Coffee score file shape.";
+ String info = String.format(
+ "align w: %s, h: %s; score: w: %s; h: %s ", al.getWidth(),
+ al.getHeight(), getWidth(), getHeight());
+ warningMessage = "Alignment shape does not match T-Coffee score file shape -- "
+ + info;
return false;
}
boolean added = false;