/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import javax.xml.parsers.ParserConfigurationException;
-import jalview.datamodel.*;
+import org.xml.sax.SAXException;
+
+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;
/**
* DOCUMENT ME!
/**
* Sequences to be added to form a new alignment.
*/
- protected Vector seqs;
+ protected Vector<SequenceI> seqs;
/**
* annotation to be added to generated alignment object
*/
public AlignFile()
{
+ // Shouldn't we init data structures (JBPNote: not sure - initData is for initialising the structures used for reading from a datasource, and the bare constructor hasn't got any datasource)
+ initData();
}
/**
* Filename to read from.
* @param type
* What type of file to read from (File, URL)
+ * @throws SAXException
+ * @throws ParserConfigurationException
+ * @throws ExceptionFileFormatOrSyntax
+ * @throws ExceptionLoadingFailed
+ * @throws ExceptionPermissionDenied
+ * @throws InterruptedException
+ * @throws ExceptionUnmatchedClosingParentheses
*/
- public AlignFile(String inFile, String type) throws IOException
+ public AlignFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, type);
-
initData();
-
parse();
+ // sets the index of each sequence in the alignment
+ for (int i = 0, c = seqs.size(); i < c; i++)
+ {
+ seqs.get(i).setIndex(i);
+ }
}
/**
*
* @param source
* @throws IOException
+ * @throws SAXException
+ * @throws ParserConfigurationException
+ * @throws ExceptionFileFormatOrSyntax
+ * @throws ExceptionLoadingFailed
+ * @throws ExceptionPermissionDenied
+ * @throws InterruptedException
+ * @throws ExceptionUnmatchedClosingParentheses
*/
- public AlignFile(FileParse source) throws IOException
+ public AlignFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
initData();
parse();
+ // sets the index of each sequence in the alignment
+ for (int i = 0, c = seqs.size(); i < c; i++)
+ {
+ seqs.get(i).setIndex(i);
+ }
}
/**
* Return the seqs Vector
*/
- public Vector getSeqs()
+ public Vector<SequenceI> getSeqs()
{
return seqs;
}
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
{
- al.addAnnotation((AlignmentAnnotation) annotations.elementAt(i));
+ // detect if annotations.elementAt(i) rna secondary structure
+ // if so then do:
+ /*
+ * SequenceFeature[] pairArray =
+ * Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i));
+ * Rna.HelixMap(pairArray);
+ */
+ AlignmentAnnotation an = (AlignmentAnnotation) annotations
+ .elementAt(i);
+ an.validateRangeAndDisplay();
+ al.addAnnotation(an);
}
}
/**
* This method must be implemented to parse the contents of the file.
+ * @throws ExceptionFileFormatOrSyntax
+ * @throws SAXException
+ * @throws ParserConfigurationException
+ * @throws ExceptionLoadingFailed
+ * @throws ExceptionPermissionDenied
+ * @throws InterruptedException
+ * @throws ExceptionUnmatchedClosingParentheses
*/
- public abstract void parse() throws IOException;
+ public abstract void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses;
/**
* Print out in alignment file format the Sequences in the seqs Vector.