/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 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.
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
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 BufferedReader CreateReader() throws FileNotFoundException
{
FileReader fr = null;
fr = new FileReader(inFile);
BufferedReader r = new BufferedReader(fr);
return r;
}
/*
* (non-Javadoc)
*
* @see jalview.io.AlignFile#parse()
*/
public void parse() throws IOException
{
if (System.getProperty("java.version").indexOf("1.6") > -1
|| System.getProperty("java.version").indexOf("1.5") > -1)
{
// patch for 'This parser does not support specification "null" version
// "null"' error
// this hack ensures we get a properly updated SAXParserFactory on older
// JVMs
// thanks to Stefan Birkner over at https://coderwall.com/p/kqsrrw
System.setProperty("javax.xml.parsers.SAXParserFactory",
"com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl");
}
// rather than lose exception semantics whilst parsing RNAML with VARNA we
// wrap the routine and catch all exceptions before passing them up the
// chain as an IOException
try
{
_parse();
} catch (ExceptionPermissionDenied pdx)
{
errormessage = "Couldn't access datasource (" + pdx.getMessage()
+ ")";
throw new IOException(pdx);
} catch (ExceptionLoadingFailed lf)
{
errormessage = "Couldn't process data as RNAML file ("
+ lf.getMessage() + ")";
throw new IOException(lf);
} catch (ExceptionFileFormatOrSyntax iff)
{
errormessage = "Invalid RNAML file (" + iff.getMessage() + ")";
throw new IOException(iff);
} catch (Exception x)
{
error = true;
errormessage = "Problem parsing data as RNAML (" + x.getMessage()
+ ")";
throw new IOException("Couldn't parse the datasource as RNAML", x);
}
}
@SuppressWarnings("unchecked")
public void _parse() throws FileNotFoundException,
ExceptionPermissionDenied, ExceptionLoadingFailed,
ExceptionFileFormatOrSyntax
{
result = RNAFactory.loadSecStrRNAML(getReader());
ArrayList allarray = new ArrayList();
ArrayList> BP = new ArrayList();
ArrayList strucinarray = new ArrayList();
SequenceI[] seqs = new SequenceI[result.size()];
for (int i = 0; i < result.size(); i++)
{
RNA current = result.get(i);
String rna = current.getStructDBN(true);
String seq = current.getSeq();
int begin = 1;
int end = seq.length();
id = current.getName();
seqs[i] = new Sequence(id, seq, begin, end);
seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
String[] annot = new String[rna.length()];
Annotation[] ann = new Annotation[rna.length()];
for (int j = 0; j < rna.length(); j++)
{
annot[j] = "" + rna.charAt(j);
}
for (int k = 0; k < rna.length(); k++)
{
ann[k] = new Annotation(annot[k], "",
jalview.schemes.ResidueProperties.getRNASecStrucState(
annot[k]).charAt(0), 0f);
}
AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
current.getID(), ann);
seqs[i].addAlignmentAnnotation(align);
seqs[i].setRNA(result.get(i));
allarray.add(strucinarray);
annotations.addElement(align);
BP.add(align.bps);
}
setSeqs(seqs);
}
public static String print(SequenceI[] s)
{
return "not yet implemented";
}
public String print()
{
System.out.print("print :");
return print(getSeqsAsArray());
}
public ArrayList getRNA()
{
return result;
}
// public static void main(String[] args) {
// Pattern p= Pattern.compile("(.+)[.][^.]+");
// Matcher m = p.matcher("toto.xml.zip");
// System.out.println(m.matches());
// System.out.println(m.group(1));
// }
/**
* make a friendly ID string.
*
* @param dataName
* @return truncated dataName to after last '/'
*/
private String safeName(String dataName)
{
int b = 0;
while ((b = dataName.indexOf("/")) > -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;
}
}