+/*
+ * 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
+ *
+ * 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.
+ *
+ * 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/>.
+ */
package jalview.io;
-
-
-
-
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.SecondaryStructureAnnotation;
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;
}
- public RnamlFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public RnamlFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, type);
}
- public RnamlFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public RnamlFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
}
+ @SuppressWarnings("unchecked")
public void parse() throws FileNotFoundException, ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
{
- FileReader fr = null;
- fr = new FileReader(inFile);
-
- BufferedReader r = new BufferedReader (fr);
- Hashtable seqhash = new Hashtable();
- Vector headers = new Vector();
- //ArrayList<String> seq =new ArrayList();
- //System.out.println(r);
-
+ result = RNAFactory.loadSecStrRNAML(getReader());
- result = RNAFactory.loadSecStrRNAML(r);
-
- System.out.println("this is the secondary scructure:" +result.toArray());
+ System.out.println("this is the secondary scructure:" +result.size());
//System.out.println("this is the secondary scructure:" +result.toString());
//System.out.println("this is the secondary scructure:" +result.size());
- for(int i=0;i<result.size();i++)
- {
- //System.out.println(result.get(0).getSeq());
- //System.out.println(result.get(0).getStructBPSEQ());
- //System.out.println(result.get(0).getStructDBN(true));
- String rna1 =result.get(0).getStructDBN(true);
- //System.out.println(result.get(0).getAnnotations());
- String seq = result.get(0).getSeq();
+ SequenceI[] seqs = new SequenceI[result.size()];
System.out.println(type); //the type is "File"
System.out.println(inFile );//inFile is the path
- int begin=0;
- int end = seq.length()-1;
- SequenceI[] seqs = new SequenceI[1];
- id = safeName(getDataName());
- seqs[0] = new Sequence(id, seq, begin, end);
- SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
- seqs[0].addSequenceFeature(feat);
- this.setSeqs(seqs);
- String[] annot=new String[10000] ;
- Annotation[] ann = new Annotation[1000];
- for(int j=0;j<rna1.length();j++)
+ for(int i=0;i<result.size();i++)
{
- annot[j] =rna1.substring(j,j+1);
- System.out.println(annot[j]);
+ RNA current = result.get(i);
+ System.out.println(current.getSeq());
+ //System.out.println(result.get(i).getStructBPSEQ());
+ System.out.println(result.get(i).getStructDBN(true));
+ System.out.println(i);
+ String rna =current.getStructDBN(true);
+ //System.out.println(result.get(0).getAnnotations());
+ String seq = current.getSeq();
+
+ int begin=1;
+ int end = seq.length();
+
+ id = current.getName();
+ seqs[i] = new Sequence(id, seq, begin, end);
+ //System.out.println(seq);
+ System.out.println("Rna is still "+rna);
+ //SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
+ //seqs[i].addSequenceFeature(feat);
+
+ 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);
+
}
- for(int k=0;k<rna1.length();k++)
+ for(int k=0;k<rna.length();k++)
{
- ann[k] = new Annotation(annot[k], "", ' ', 0f);
-
- ann[k].secondaryStructure = jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0);
-
+ ann[k] = new Annotation(annot[k], "", jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0), 0f);
+
}
- AlignmentAnnotation align = new AlignmentAnnotation("Secondary structure","",ann);
- seqs[0].addAlignmentAnnotation(align);
- seqs[0].setRNA(result.get(begin));
- this.annotations.addElement(align);
-
+ AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",current.getID(),ann);
+ seqs[i].addAlignmentAnnotation(align);
+ seqs[i].setRNA(result.get(i));
+ this.annotations.addElement(align);
}
+ this.setSeqs(seqs);
+
+
- //Annotate3D tintin = new Annotate3D();
-
- //System.out.println(tintin);
+
}
return annotations;
}
}
-
git://source.jalview.org / jalview.git / blobdiff