/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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.
- *
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Vector;
public class PIRFile extends AlignFile
{
{
}
- public PIRFile(String inFile, String type) throws IOException
+ public PIRFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public PIRFile(FileParse source) throws IOException
super(source);
}
+ @Override
public void parse() throws IOException
{
StringBuffer sequence;
}
}
- public String print()
- {
- return print(getSeqsAsArray());
- }
-
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
- boolean is_NA = jalview.util.Comparison.isNucleotide(s);
+ boolean is_NA = Comparison.isNucleotide(s);
int len = 72;
StringBuffer out = new StringBuffer();
int i = 0;
// 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], jvsuffix));
+ 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);
}
}
}
- int nochunks = (seq.length() / len) + 1;
+ int nochunks = (seq.length() / len)
+ + (seq.length() % len > 0 ? 1 : 0);
for (int j = 0; j < nochunks; j++)
{
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);
}
}