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;
35 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
36 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
37 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
38 import fr.orsay.lri.varna.factories.RNAFactory;
39 import fr.orsay.lri.varna.models.rna.RNA;
41 public class RnamlFile extends AlignFile
45 protected ArrayList<RNA> result;
53 public RnamlFile(String inFile, String type) throws IOException
59 public RnamlFile(FileParse source) throws IOException
65 public BufferedReader CreateReader() throws FileNotFoundException
68 fr = new FileReader(inFile);
70 BufferedReader r = new BufferedReader(fr);
77 * @see jalview.io.AlignFile#parse()
79 public void parse() throws IOException
81 if (System.getProperty("java.version").indexOf("1.6") > -1
82 || System.getProperty("java.version").indexOf("1.5") > -1)
84 // patch for 'This parser does not support specification "null" version
86 // this hack ensures we get a properly updated SAXParserFactory on older
88 // thanks to Stefan Birkner over at https://coderwall.com/p/kqsrrw
89 System.setProperty("javax.xml.parsers.SAXParserFactory",
90 "com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl");
92 // rather than lose exception semantics whilst parsing RNAML with VARNA we
93 // wrap the routine and catch all exceptions before passing them up the
94 // chain as an IOException
98 } catch (ExceptionPermissionDenied pdx)
100 errormessage = "Couldn't access datasource (" + pdx.getMessage()
102 throw new IOException(pdx);
103 } catch (ExceptionLoadingFailed lf)
105 errormessage = "Couldn't process data as RNAML file ("
106 + lf.getMessage() + ")";
107 throw new IOException(lf);
108 } catch (ExceptionFileFormatOrSyntax iff)
110 errormessage = "Invalid RNAML file (" + iff.getMessage() + ")";
111 throw new IOException(iff);
112 } catch (Exception x)
115 errormessage = "Problem parsing data as RNAML (" + x.getMessage()
117 throw new IOException("Couldn't parse the datasource as RNAML", x);
121 @SuppressWarnings("unchecked")
122 public void _parse() throws FileNotFoundException,
123 ExceptionPermissionDenied, ExceptionLoadingFailed,
124 ExceptionFileFormatOrSyntax
127 result = RNAFactory.loadSecStrRNAML(getReader());
129 ArrayList<ArrayList> allarray = new ArrayList();
130 ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
131 ArrayList strucinarray = new ArrayList();
132 SequenceI[] seqs = new SequenceI[result.size()];
134 for (int i = 0; i < result.size(); i++)
137 RNA current = result.get(i);
138 String rna = current.getStructDBN(true);
139 String seq = current.getSeq();
141 int end = seq.length();
143 id = current.getName();
144 seqs[i] = new Sequence(id, seq, begin, end);
146 seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
147 String[] annot = new String[rna.length()];
148 Annotation[] ann = new Annotation[rna.length()];
150 for (int j = 0; j < rna.length(); j++)
152 annot[j] = "" + rna.charAt(j);
155 for (int k = 0; k < rna.length(); k++)
157 ann[k] = new Annotation(annot[k], "",
158 jalview.schemes.ResidueProperties.getRNASecStrucState(
159 annot[k]).charAt(0), 0f);
162 AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
163 current.getID(), ann);
165 seqs[i].addAlignmentAnnotation(align);
166 seqs[i].setRNA(result.get(i));
168 allarray.add(strucinarray);
170 annotations.addElement(align);
178 public static String print(SequenceI[] s)
180 return "not yet implemented";
183 public String print()
185 System.out.print("print :");
186 return print(getSeqsAsArray());
189 public ArrayList getRNA()
194 // public static void main(String[] args) {
195 // Pattern p= Pattern.compile("(.+)[.][^.]+");
196 // Matcher m = p.matcher("toto.xml.zip");
197 // System.out.println(m.matches());
198 // System.out.println(m.group(1));
201 * make a friendly ID string.
204 * @return truncated dataName to after last '/'
206 private String safeName(String dataName)
209 while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
211 dataName = dataName.substring(b + 1).trim();
214 int e = (dataName.length() - dataName.indexOf(".")) + 1;
215 dataName = dataName.substring(1, e).trim();