/*
* 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 java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Vector;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import jalview.analysis.SecStrConsensus;
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;
/**
* @author jimp
*
*/
public class RnamlFile extends AlignFile {
public int id;
public String namefile;
public String name;
protected ArrayList result;
public RnamlFile() {
super();
}
public RnamlFile(String inFile, String type) throws Exception {
super(inFile, type);
}
public RnamlFile(FileParse source) throws Exception {
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
{
// 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 (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()];
namefile = inFile.getName();
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 = 1000;
id = i;
System.out.println("id=" + i);
name = this.safeName(namefile, i);
seqs[i] = new Sequence(name, 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));
char[] struc = align.getRNAStruc().toCharArray();
allarray.add(strucinarray);
this.annotations.addElement(align);
BP.add(align.bps);
}
this.setSeqs(seqs);
int[] tab = SecStrConsensus.extractConsensus(BP);
}
public void parse(BufferedReader r) throws ExceptionPermissionDenied,
ExceptionLoadingFailed, ExceptionFileFormatOrSyntax {
result = RNAFactory.loadSecStrRNAML(r);
ArrayList allarray = new ArrayList();
ArrayList> BP = new ArrayList();
ArrayList strucinarray = new ArrayList();
SequenceI[] seqs = new SequenceI[result.size()];
namefile = inFile.getName();
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 = 1000;
id = i;
name = this.safeName(namefile, i);
seqs[i] = new Sequence(name, 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));
char[] struc = align.getRNAStruc().toCharArray();
for (int y = 0; y < struc.length; y++) {
strucinarray.add(struc[y]);
// System.out.println("structy"+struc[y]);
}
// System.out.println("Sequence"+i+"\t : "+strucinarray.toString());
allarray.add(strucinarray);
this.annotations.addElement(align);
System.out.println(rna);
BP.add(align.bps);
System.out.println(align.bps.size());
}
this.setSeqs(seqs);
int[] tab = SecStrConsensus.extractConsensus(BP);
}
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 Vector getAnnot() {
return annotations;
}
// 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));
// }
public String safeName(String namefile, int id) {
Pattern p = Pattern.compile("(.*)[.][^.]+");
Matcher m = p.matcher(namefile);
name = m.group(1) + "_" + id;
return name;
}
}