/*
- * 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 2.9)
+ * 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.
+ * 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 java.io.BufferedReader;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-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.SecondaryStructureAnnotation;
import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+
+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 int id;
- public String namefile;
- public String name;
- protected ArrayList<RNA> 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;
- }
-
- @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()];
- 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<ArrayList> allarray = new ArrayList();
- ArrayList<ArrayList<SimpleBP>> 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;
-
- }
+public class RnamlFile extends AlignFile
+{
+ 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