/*
- * 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 2.8)
+ * 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
// 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);
}
}