/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import java.io.*;
import java.util.*;
+import javax.xml.parsers.ParserConfigurationException;
+
+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 jalview.datamodel.*;
public class PIRFile extends AlignFile
{
}
- public PIRFile(String inFile, String type) throws IOException
+ public PIRFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
{
super(inFile, type);
}
- public PIRFile(FileParse source) throws IOException
+ public PIRFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
{
super(source);
}
// tRNA N3
// other functional RNA N1
- out.append(">N1;" + s[i].getName() + "\n");
+ out.append(">N1;" + s[i].getName());
+ out.append(newline);
if (s[i].getDescription() == null)
{
out.append(s[i].getName() + " "
+ (s[i].getEnd() - s[i].getStart() + 1));
- out.append(is_NA ? " bases\n" : " residues\n");
+ out.append(is_NA ? " bases" : " residues");
+ out.append(newline);
}
else
{
- out.append(s[i].getDescription() + "\n");
+ out.append(s[i].getDescription());
+ out.append(newline);
}
}
else
if (useModellerOutput)
{
- out.append(">P1;" + s[i].getName() + "\n");
+ out.append(">P1;" + s[i].getName());
+ out.append(newline);
md = new ModellerDescription(s[i]);
- out.append(md.getDescriptionLine() + "\n");
+ out.append(md.getDescriptionLine());
+ out.append(newline);
}
else
{
- out.append(">P1;" + printId(s[i]) + "\n");
+ out.append(">P1;" + printId(s[i]));
+ out.append(newline);
if (s[i].getDescription() != null)
{
- out.append(s[i].getDescription() + "\n");
+ out.append(s[i].getDescription());
+ out.append(newline);
}
else
{
- out
- .append(s[i].getName() + " "
- + (s[i].getEnd() - s[i].getStart() + 1)
- + " residues\n");
+ out.append(s[i].getName() + " "
+ + (s[i].getEnd() - s[i].getStart() + 1) + " residues");
+ out.append(newline);
}
}
}
if (end < seq.length())
{
- out.append(seq.substring(start, end) + "\n");
+ out.append(seq.substring(start, end));
+ out.append(newline);
}
else if (start < seq.length())
{
- out.append(seq.substring(start) + "\n");
+ out.append(seq.substring(start));
+ out.append(newline);
}
}