2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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 jalview.analysis.SecStrConsensus.SimpleBP;
24 import jalview.datamodel.AlignmentAnnotation;
25 import jalview.datamodel.Annotation;
26 import jalview.datamodel.Sequence;
27 import jalview.datamodel.SequenceI;
28 import jalview.schemes.ResidueProperties;
29 import jalview.util.MessageManager;
31 import java.io.BufferedReader;
32 import java.io.FileNotFoundException;
33 import java.io.FileReader;
34 import java.io.IOException;
35 import java.util.ArrayList;
37 import com.stevesoft.pat.Regex;
39 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
40 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
41 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
42 import fr.orsay.lri.varna.factories.RNAFactory;
43 import fr.orsay.lri.varna.models.rna.RNA;
45 public class RnamlFile extends AlignFile
49 protected ArrayList<RNA> result;
57 public RnamlFile(String inFile, String type) throws IOException
63 public RnamlFile(FileParse source) throws IOException
69 public BufferedReader CreateReader() throws FileNotFoundException
72 fr = new FileReader(inFile);
74 BufferedReader r = new BufferedReader(fr);
81 * @see jalview.io.AlignFile#parse()
83 public void parse() throws IOException
85 if (System.getProperty("java.version").indexOf("1.6") > -1
86 || System.getProperty("java.version").indexOf("1.5") > -1)
88 // patch for 'This parser does not support specification "null" version
90 // this hack ensures we get a properly updated SAXParserFactory on older
92 // thanks to Stefan Birkner over at https://coderwall.com/p/kqsrrw
93 System.setProperty("javax.xml.parsers.SAXParserFactory",
94 "com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl");
96 // rather than lose exception semantics whilst parsing RNAML with VARNA we
97 // wrap the routine and catch all exceptions before passing them up the
98 // chain as an IOException
102 } catch (ExceptionPermissionDenied pdx)
104 errormessage = MessageManager.formatMessage("exception.rnaml_couldnt_access_datasource", new String[]{pdx.getMessage()});
105 throw new IOException(pdx);
106 } catch (ExceptionLoadingFailed lf)
108 errormessage = MessageManager.formatMessage("exception.ranml_couldnt_process_data", new String[]{lf.getMessage()});
109 throw new IOException(lf);
110 } catch (ExceptionFileFormatOrSyntax iff)
112 errormessage = MessageManager.formatMessage("exception.ranml_invalid_file", new String[]{iff.getMessage()});
113 throw new IOException(iff);
114 } catch (Exception x)
117 errormessage = MessageManager.formatMessage("exception.ranml_problem_parsing_data", new String[]{x.getMessage()});
118 throw new IOException(errormessage , x);
122 @SuppressWarnings("unchecked")
123 public void _parse() throws FileNotFoundException,
124 ExceptionPermissionDenied, ExceptionLoadingFailed,
125 ExceptionFileFormatOrSyntax
128 result = RNAFactory.loadSecStrRNAML(getReader());
130 ArrayList<ArrayList> allarray = new ArrayList();
131 ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
132 ArrayList strucinarray = new ArrayList();
133 SequenceI[] seqs = new SequenceI[result.size()];
135 for (int i = 0; i < result.size(); i++)
138 RNA current = result.get(i);
139 String rna = current.getStructDBN(true);
140 String seq = current.getSeq();
142 int end = seq.length();
144 id = current.getName();
145 if (id == null || id.trim().length() == 0)
147 id = safeName(getDataName());
148 if (result.size() > 1)
153 seqs[i] = new Sequence(id, seq, begin, end);
155 seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
156 String[] annot = new String[rna.length()];
157 Annotation[] ann = new Annotation[rna.length()];
159 for (int j = 0; j < rna.length(); j++)
161 annot[j] = "" + rna.charAt(j);
164 for (int k = 0; k < rna.length(); k++)
166 ann[k] = new Annotation(annot[k], "",
167 ResidueProperties.getRNASecStrucState(
168 annot[k]).charAt(0), 0f);
171 AlignmentAnnotation align = new AlignmentAnnotation(
172 "Secondary Structure",
173 current.getID().trim().length() > 0 ? "Secondary Structure for "
177 seqs[i].addAlignmentAnnotation(align);
178 seqs[i].setRNA(result.get(i));
180 allarray.add(strucinarray);
182 annotations.addElement(align);
190 public static String print(SequenceI[] s)
192 return "not yet implemented";
195 public String print()
197 System.out.print("print :");
198 return print(getSeqsAsArray());
201 public ArrayList getRNA()
206 // public static void main(String[] args) {
207 // Pattern p= Pattern.compile("(.+)[.][^.]+");
208 // Matcher m = p.matcher("toto.xml.zip");
209 // System.out.println(m.matches());
210 // System.out.println(m.group(1));
213 * make a friendly ID string.
216 * @return truncated dataName to after last '/'
218 private String safeName(String dataName)
221 if ((b = dataName.lastIndexOf(".")) > 0)
223 dataName = dataName.substring(0, b - 1);
226 Regex m = new Regex("[\\/]?([-A-Za-z0-9]+)\\.?");
227 String mm = dataName;
228 while (m.searchFrom(dataName, b))
230 mm = m.stringMatched();