/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, 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 program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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;
// 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);
}
}