/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 jalview.analysis.Rna;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
+import java.util.List;
+
+import com.stevesoft.pat.Regex;
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
}
- public RnamlFile(String inFile, String type) throws IOException
+ public RnamlFile(String inFile, DataSourceType type) throws IOException
{
super(inFile, type);
}
- // 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;
return r;
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.AlignFile#parse()
+ */
+ @Override
public void parse() throws IOException
{
- if (System.getProperty("java.version").indexOf("1.6")>-1 || System.getProperty("java.version").indexOf("1.5")>-1)
+ 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
+ // 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");
+ System.setProperty("javax.xml.parsers.SAXParserFactory",
+ "com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl");
}
- result = null;
+ // 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
{
- result = RNAFactory.loadSecStrRNAML(getReader());
-
+ _parse();
} catch (ExceptionPermissionDenied pdx)
{
- errormessage = "Couldn't access datasource (" + pdx.getMessage()
- + ")";
+ errormessage = MessageManager.formatMessage(
+ "exception.rnaml_couldnt_access_datasource", new String[]
+ { pdx.getMessage() });
throw new IOException(pdx);
} catch (ExceptionLoadingFailed lf)
{
- errormessage = "Couldn't process data as RNAML file ("
- + lf.getMessage() + ")";
+ errormessage = MessageManager.formatMessage(
+ "exception.ranml_couldnt_process_data", new String[]
+ { lf.getMessage() });
throw new IOException(lf);
} catch (ExceptionFileFormatOrSyntax iff)
{
- errormessage = "Invalid RNAML file (" + iff.getMessage() + ")";
+ 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);
}
+ }
- SequenceI[] seqs = new SequenceI[result.size()];
+ @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[] sqs = new SequenceI[result.size()];
for (int i = 0; i < result.size(); i++)
{
- // DEBUG System.err.println("RNAML entry "+i);
+
RNA current = result.get(i);
- String seq = current.getSeq();
- // DEBUG System.err.println(seq);
String rna = current.getStructDBN(true);
- // DEBUG System.err.println(rna);
-
+ String seq = current.getSeq();
int begin = 1;
- int end = seq.length(); // TODO: compute non-gapped length for sequence
+ int end = seq.length();
id = current.getName();
- seqs[i] = new Sequence(id, seq, begin, end);
+ if (id == null || id.trim().length() == 0)
+ {
+ id = safeName(getDataName());
+ if (result.size() > 1)
+ {
+ id += "." + i;
+ }
+ }
+ sqs[i] = new Sequence(id, seq, begin, end);
+ sqs[i].setEnd(sqs[i].findPosition(sqs[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.substring(j, j + 1);
+ 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);
-
+ Rna.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));
+ AlignmentAnnotation align = new AlignmentAnnotation(
+ "Secondary Structure",
+ current.getID().trim().length() > 0
+ ? "Secondary Structure for " + current.getID()
+ : "",
+ ann);
+
+ sqs[i].addAlignmentAnnotation(align);
+ sqs[i].setRNA(result.get(i));
+
+ // allarray.add(strucinarray);
+
annotations.addElement(align);
+ // BP.add(align.bps);
+
}
- setSeqs(seqs);
+
+ setSeqs(sqs);
}
- public static String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] s, boolean jvSuffix)
{
- // TODO: implement RNAML export option
return "not yet implemented";
}
- public String print()
+ public List<RNA> getRNA()
{
- return print(getSeqsAsArray());
+ 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.
*
private String safeName(String dataName)
{
int b = 0;
- while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
+ if ((b = dataName.lastIndexOf(".")) > 0)
{
- dataName = dataName.substring(b + 1).trim();
-
+ dataName = dataName.substring(0, b - 1);
+ }
+ b = 0;
+ Regex m = getSafeRegex();
+ String mm = dataName;
+ while (m.searchFrom(dataName, b))
+ {
+ mm = m.stringMatched();
+ b = m.matchedTo();
}
- int e = (dataName.length() - dataName.indexOf(".")) + 1;
- dataName = dataName.substring(1, e).trim();
- return dataName;
+ return mm;
+ }
+
+ private static Regex SAFE_REGEX;
+
+ private static Regex getSafeRegex()
+ {
+ return (SAFE_REGEX == null
+ ? SAFE_REGEX = Platform.newRegex("[\\/]?([-A-Za-z0-9]+)\\.?", null)
+ : SAFE_REGEX);
}
}
git://source.jalview.org / jalview.git / blobdiff