+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
-
-
-
-
+import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
-import jalview.datamodel.SecondaryStructureAnnotation;
import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.ws.jws1.Annotate3D;
+import jalview.util.MessageManager;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.Reader;
import java.io.FileReader;
-import java.lang.reflect.Array;
+import java.io.IOException;
import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.parsers.SAXParser;
-import javax.xml.parsers.SAXParserFactory;
-
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
import com.stevesoft.pat.Regex;
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 fr.orsay.lri.varna.factories.RNAFactory;
-import fr.orsay.lri.varna.factories.RNAFactory.RNAFileType;
import fr.orsay.lri.varna.models.rna.RNA;
-import fr.orsay.lri.varna.utils.RNAMLParser;
-
-
-
public class RnamlFile extends AlignFile
{
- public String id;
- protected ArrayList<RNA> result;
-
- public RnamlFile()
- {
- super();
-
- }
-
- public RnamlFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
- {
- super(inFile, type);
-
- }
-
- public RnamlFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
- {
- 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<c; i++ ) {
-// seqs.get(i).setIndex(i);
-// }
-//
-//
-// }
-
- public BufferedReader CreateReader() throws FileNotFoundException
- {
- FileReader fr = null;
- fr = new FileReader(inFile);
-
- BufferedReader r = new BufferedReader (fr);
- return r;
- }
-
-
- @SuppressWarnings("unchecked")
- public void parse() throws FileNotFoundException, ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
- {
- result = RNAFactory.loadSecStrRNAML(getReader());
-
- System.out.println("this is the secondary scructure:" +result.size());
- //System.out.println("this is the secondary scructure:" +result.toString());
- //System.out.println("this is the secondary scructure:" +result.size());
- SequenceI[] seqs = new SequenceI[result.size()];
- System.out.println(type); //the type is "File"
- System.out.println(inFile );//inFile is the path
-
- for(int i=0;i<result.size();i++)
- {
- RNA current = result.get(i);
- System.out.println(current.getSeq());
- //System.out.println(result.get(i).getStructBPSEQ());
- System.out.println(result.get(i).getStructDBN(true));
- System.out.println(i);
- String rna =current.getStructDBN(true);
- //System.out.println(result.get(0).getAnnotations());
- String seq = current.getSeq();
-
- int begin=0;
- int end = seq.length()-1;
-
- id = safeName(getDataName());
- seqs[i] = new Sequence(id, seq, begin, end);
- //System.out.println(seq);
- System.out.println("Rna is still "+rna);
- //SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
- //seqs[i].addSequenceFeature(feat);
-
- 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);
-
- }
-
- 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));
- this.annotations.addElement(align);
- }
- this.setSeqs(seqs);
-
-
-
-
- }
-
-
- public void parse(BufferedReader r) throws ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
- {
- System.out.println("parse with Buffer (RnamlFile");
- Hashtable seqhash = new Hashtable();
- Vector headers = new Vector();
- //ArrayList<String> seq =new ArrayList();
- //System.out.println(r);
-
- result = RNAFactory.loadSecStr(r,RNAFileType.FILE_TYPE_RNAML);
-
- System.out.println("this is the secondary scructure:" +result.toArray());
- System.out.println("this is the secondary scructure:" +result.toString());
- System.out.println("this is the secondary scructure:" +result.size());
- for(int i=0;i<result.size();i++)
- {
- System.out.println(result.get(0).getSeq());
- System.out.println(result.get(0).getStructBPSEQ());
- System.out.println(result.get(0).getStructDBN(true));
- String rna1 =result.get(0).getStructDBN(true);
- System.out.println(result.get(0).getAnnotations());
- String seq = result.get(0).getSeq();
- System.out.println(type); //the type is "File"
- System.out.println(inFile );//inFile is the path
- int begin=0;
- int end = seq.length()-1;
- SequenceI[] seqs = new SequenceI[1];
- id = safeName(getDataName());
- seqs[0] = new Sequence(id, seq, begin, end);
- SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
- seqs[0].addSequenceFeature(feat);
- this.setSeqs(seqs);
-
- String[] annot=new String[10000] ;
- Annotation[] ann = new Annotation[1000];
- for(int j=0;j<rna1.length();j++)
- {
- annot[j] =rna1.substring(j,j+1);
- //System.out.println(annot[j]);
- }
-
- for(int k=0;k<rna1.length();k++)
- {
- ann[k] = new Annotation(annot[k], "", ' ', 0f);
-
- ann[k].secondaryStructure = jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0);
-
- }
- AlignmentAnnotation align = new AlignmentAnnotation("Secondary structure","",ann);
- seqs[0].addAlignmentAnnotation(align);
- this.annotations.addElement(align);
- }
- //Annotate3D tintin = new Annotate3D();
-
- //System.out.println(tintin);
-
-
-
-
-
-
-
-
-// for(RNAMLParser.RNATmp rnaTmp : RNAMLData.getMolecules())
-// {
-// // Retrieving parsed data
-// seq = rnaTmp.getSequence(); //contient la séquence sous forme de liste
-// System.out.println(seq);
-// String seqAsStr = "";
-// for(String s:seq)
-// {
-// // Only consider last character, e.g. in case of modified nucleotide
-// seqAsStr += s.charAt(s.length()-1);
-// }
-// int begin=0;
-// int end = seqAsStr.length()-1;
-// SequenceI[] seqs = new SequenceI[1];
-// id = safeName(getDataName());
-// seqs[0] = new Sequence(id, seqAsStr, begin, end);
-// SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
-//
-// seqs[0].addSequenceFeature(feat);
-// this.setSeqs(seqs);
-
- //String pos = annot.substring(1, 2);
- //System.out.println(annot);
- //System.out.println(pos);
-
- // ann[1] = new Annotation(pos, "", ' ', 0f);
- // ann[1].secondaryStructure = 'A';
- //System.out.println(ann[1]);
-
- // toto.annotations=ann;
-
-
-
-//// Annotation[] els = new Annotation[seq.size()];
-//
-// //System.err.println(""+seq.size());
-// Vector<RNAMLParser.BPTemp> allbpsTmp = rnaTmp.getStructure();
-// String[] annot = new String[10000];
-//
-// //Annotation[] ann = new Annotation[allbpsTmp.size()];
-// for (int i = 0; i < allbpsTmp.size(); i++) {
-// RNAMLParser.BPTemp bp = allbpsTmp.get(i);
-// //System.err.println("toto ="+bp);
-// int bp5 = bp.pos5;
-// annot[bp5]= "(";
-// //annot[bp5]= '(';
-// System.out.println(annot[bp5]);
-// //System.out.println("bp5 ="+bp5);
-// int bp3 = bp.pos3;
-//
-// annot[bp3]= ")";
-// System.out.println(annot[bp3]);
-// //System.out.println(annot.get(bp3));
-//
-// //String pos1 = annot.substring(bp5, bp5+1);
-// //String pos2 = annot.substring(bp3, bp3+1);
-// //ann[i] = new Annotation(pos1, "", ' ', 0f);
-// //ann[i+1] = new Annotation(pos2, "", ' ', 0f);
-// //System.out.println(pos1);
-//
-// //System.out.println("bp3 ="+bp3);
-// //ModeleBP newStyle = bp.createBPStyle(mb, part);
-// }
-// Annotation[] ann = new Annotation[annot.length+1];
-// for(int i=0;i<annot.length;i++)
-// {
-// if(annot[i]==null)
-// {
-// annot[i]=".";
-// }
-//
-// ann[i] = new Annotation(annot[i], "", ' ', 0f);
-// //System.out.print(annot[i]);
-// }
-//
-// AlignmentAnnotation toto = new AlignmentAnnotation("Secondary structure","",ann);
-// this.annotations.addElement(toto);
-
- // Creating empty structure of suitable size
-// int[] str = new int[seq.size()];
-// for (int i=0;i<str.length;i++)
-// { str[i] = -1; }
-// Vector<RNAMLParser.BPTemp> allbpsTmp = rnaTmp.getStructure();
-// for (int i = 0; i < allbpsTmp.size(); i++) {
-// RNAMLParser.BPTemp bp = allbpsTmp.get(i);
-// //System.err.println("toto ="+bp);
-// int bp5 = bp.pos5;
-// //System.out.println("bp5 ="+bp5);
-// int bp3 = bp.pos3;
- //System.out.println("bp3 ="+bp3);
- //ModeleBP newStyle = bp.createBPStyle(mb, part);
-// }
- //Annotation ann;
- //ann = new Annotation(bp5, "", ' ', 0f);
-
- //}
-
-
-
-// return result;
-
-}
-
-
- public static String print(SequenceI[] s)
- {
- return "not yet implemented";
- }
-
- public String print()
- {
- System.out.print("affiche :");
- return print(getSeqsAsArray());
- }
-
- /**
- * 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;
- }
-
- public ArrayList getRNA()
- {
- return result;
- }
-
- public Vector getAnnot()
- {
- return annotations;
- }
+ public String id;
+
+ protected ArrayList<RNA> 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 = MessageManager.formatMessage(
+ "exception.rnaml_couldnt_access_datasource",
+ new String[] { pdx.getMessage() });
+ throw new IOException(pdx);
+ } catch (ExceptionLoadingFailed lf)
+ {
+ errormessage = MessageManager.formatMessage(
+ "exception.ranml_couldnt_process_data",
+ new String[] { lf.getMessage() });
+ throw new IOException(lf);
+ } catch (ExceptionFileFormatOrSyntax iff)
+ {
+ errormessage = MessageManager.formatMessage(
+ "exception.ranml_invalid_file",
+ new String[] { iff.getMessage() });
+ throw new IOException(iff);
+ } catch (Exception x)
+ {
+ error = true;
+ errormessage = MessageManager.formatMessage(
+ "exception.ranml_problem_parsing_data",
+ new String[] { x.getMessage() });
+ throw new IOException(errormessage, 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++)
+ {
+
+ RNA current = result.get(i);
+ String rna = current.getStructDBN(true);
+ String seq = current.getSeq();
+ int begin = 1;
+ int end = seq.length();
+
+ id = current.getName();
+ if (id == null || id.trim().length() == 0)
+ {
+ id = safeName(getDataName());
+ if (result.size() > 1)
+ {
+ id += "." + i;
+ }
+ }
+ 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(
+ "Secondary Structure",
+ current.getID().trim().length() > 0 ? "Secondary Structure for "
+ + 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;
+ if ((b = dataName.lastIndexOf(".")) > 0)
+ {
+ dataName = dataName.substring(0, b - 1);
+ }
+ b = 0;
+ Regex m = new Regex("[\\/]?([-A-Za-z0-9]+)\\.?");
+ String mm = dataName;
+ while (m.searchFrom(dataName, b))
+ {
+ mm = m.stringMatched();
+ b = m.matchedTo();
+ }
+ return mm;
+ }
}
git://source.jalview.org / jalview.git / blobdiff