/*
- * 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 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.
+ * 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.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 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;
}
- // 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<c; i++ ) {
- // seqs.get(i).setIndex(i);
- // }
- //
- //
- // }
-
public BufferedReader CreateReader() throws FileNotFoundException
{
FileReader fr = null;
return r;
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.AlignFile#parse()
+ */
public void parse() throws IOException
{
- result = null;
+ 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
{
- result = RNAFactory.loadSecStrRNAML(getReader());
-
+ _parse();
} catch (ExceptionPermissionDenied pdx)
{
errormessage = "Couldn't access datasource (" + pdx.getMessage()
{
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<ArrayList> allarray = new ArrayList();
+ ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
+ ArrayList strucinarray = new ArrayList();
SequenceI[] seqs = new SequenceI[result.size()];
for (int i = 0; i < result.size(); i++)
{
- // DEBUG System.err.println("RNAML entry "+i);
+
RNA current = result.get(i);
- String seq = current.getSeq();
- // DEBUG System.err.println(seq);
String rna = current.getStructDBN(true);
- // DEBUG System.err.println(rna);
-
+ String seq = current.getSeq();
int begin = 1;
- int end = seq.length(); // TODO: compute non-gapped length for sequence
+ 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.substring(j, j + 1);
+ 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)
{
- // TODO: implement RNAML export option
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.
*
git://source.jalview.org / jalview.git / blobdiff