import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
import javax.xml.parsers.ParserConfigurationException;
/**
* @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()
}
}
+ static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern.compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
+
/**
* Read a scores block ihe provided stream.
*
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);
{
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;