/*
* 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
*
* 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.
*
* 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 .
*/
package jalview.io;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
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.factories.RNAFactory;
import fr.orsay.lri.varna.models.rna.RNA;
public class RnamlFile extends AlignFile
{
public String id;
protected ArrayList result;
public RnamlFile()
{
super();
}
public RnamlFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
public RnamlFile(FileParse source) throws IOException
{
super(source);
}
// public RnamlFile(BufferedReader r) throws IOException,
// ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException,
// ExceptionPermissionDenied, ExceptionLoadingFailed
// {
// super();
// parse(r);
// // sets the index of each sequence in the alignment
// for( int i=0,c=seqs.size(); i -1 && b < dataName.length())
{
dataName = dataName.substring(b + 1).trim();
}
int e = (dataName.length() - dataName.indexOf(".")) + 1;
dataName = dataName.substring(1, e).trim();
return dataName;
}
}