2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import java.io.BufferedReader;
24 import java.io.FileNotFoundException;
25 import java.io.FileReader;
26 import java.io.IOException;
27 import java.util.ArrayList;
29 import jalview.analysis.SecStrConsensus.SimpleBP;
30 import jalview.datamodel.AlignmentAnnotation;
31 import jalview.datamodel.Annotation;
32 import jalview.datamodel.Sequence;
33 import jalview.datamodel.SequenceI;
34 import jalview.util.MessageManager;
36 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
37 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
38 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
39 import fr.orsay.lri.varna.factories.RNAFactory;
40 import fr.orsay.lri.varna.models.rna.RNA;
42 public class RnamlFile extends AlignFile
46 protected ArrayList<RNA> result;
54 public RnamlFile(String inFile, String type) throws IOException
60 public RnamlFile(FileParse source) throws IOException
66 public BufferedReader CreateReader() throws FileNotFoundException
69 fr = new FileReader(inFile);
71 BufferedReader r = new BufferedReader(fr);
78 * @see jalview.io.AlignFile#parse()
80 public void parse() throws IOException
82 if (System.getProperty("java.version").indexOf("1.6") > -1
83 || System.getProperty("java.version").indexOf("1.5") > -1)
85 // patch for 'This parser does not support specification "null" version
87 // this hack ensures we get a properly updated SAXParserFactory on older
89 // thanks to Stefan Birkner over at https://coderwall.com/p/kqsrrw
90 System.setProperty("javax.xml.parsers.SAXParserFactory",
91 "com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl");
93 // rather than lose exception semantics whilst parsing RNAML with VARNA we
94 // wrap the routine and catch all exceptions before passing them up the
95 // chain as an IOException
99 } catch (ExceptionPermissionDenied pdx)
101 errormessage = MessageManager.formatMessage("exception.rnaml_couldnt_access_datasource", new String[]{pdx.getMessage()});
102 throw new IOException(pdx);
103 } catch (ExceptionLoadingFailed lf)
105 errormessage = MessageManager.formatMessage("exception.ranml_couldnt_process_data", new String[]{lf.getMessage()});
106 throw new IOException(lf);
107 } catch (ExceptionFileFormatOrSyntax iff)
109 errormessage = MessageManager.formatMessage("exception.ranml_invalid_file", new String[]{iff.getMessage()});
110 throw new IOException(iff);
111 } catch (Exception x)
114 errormessage = MessageManager.formatMessage("exception.ranml_problem_parsing_data", new String[]{x.getMessage()});
115 throw new IOException(errormessage , x);
119 @SuppressWarnings("unchecked")
120 public void _parse() throws FileNotFoundException,
121 ExceptionPermissionDenied, ExceptionLoadingFailed,
122 ExceptionFileFormatOrSyntax
125 result = RNAFactory.loadSecStrRNAML(getReader());
127 ArrayList<ArrayList> allarray = new ArrayList();
128 ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
129 ArrayList strucinarray = new ArrayList();
130 SequenceI[] seqs = new SequenceI[result.size()];
132 for (int i = 0; i < result.size(); i++)
135 RNA current = result.get(i);
136 String rna = current.getStructDBN(true);
137 String seq = current.getSeq();
139 int end = seq.length();
141 id = current.getName();
142 seqs[i] = new Sequence(id, seq, begin, end);
144 seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
145 String[] annot = new String[rna.length()];
146 Annotation[] ann = new Annotation[rna.length()];
148 for (int j = 0; j < rna.length(); j++)
150 annot[j] = "" + rna.charAt(j);
153 for (int k = 0; k < rna.length(); k++)
155 ann[k] = new Annotation(annot[k], "",
156 jalview.schemes.ResidueProperties.getRNASecStrucState(
157 annot[k]).charAt(0), 0f);
160 AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
161 current.getID(), ann);
163 seqs[i].addAlignmentAnnotation(align);
164 seqs[i].setRNA(result.get(i));
166 allarray.add(strucinarray);
168 annotations.addElement(align);
176 public static String print(SequenceI[] s)
178 return "not yet implemented";
181 public String print()
183 System.out.print("print :");
184 return print(getSeqsAsArray());
187 public ArrayList getRNA()
192 // public static void main(String[] args) {
193 // Pattern p= Pattern.compile("(.+)[.][^.]+");
194 // Matcher m = p.matcher("toto.xml.zip");
195 // System.out.println(m.matches());
196 // System.out.println(m.group(1));
199 * make a friendly ID string.
202 * @return truncated dataName to after last '/'
204 private String safeName(String dataName)
207 while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
209 dataName = dataName.substring(b + 1).trim();
212 int e = (dataName.length() - dataName.indexOf(".")) + 1;
213 dataName = dataName.substring(1, e).trim();