/*
- * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import java.awt.Color;
import java.io.IOException;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
-
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
/**
* A file parse for T-Coffee score ascii format. This file contains the
* @author Paolo Di Tommaso
*
*/
-public class TCoffeeScoreFile extends AlignFile {
-
- public TCoffeeScoreFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+public class TCoffeeScoreFile extends AlignFile
+{
+ public TCoffeeScoreFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
- public TCoffeeScoreFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public TCoffeeScoreFile(FileParse source) throws IOException
{
super(source);
}
/**
* @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;
for (int j = 0; j < jSize; j++)
{
byte val = srow[j];
- if (s != null && jalview.util.Comparison.isGap(s.getCharAt(j)))
+ if (s != null && Comparison.isGap(s.getCharAt(j)))
{
annotations[j] = null;
if (val > 0)