*/
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()
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
- return print(getSeqsAsArray());
- }
-
- public String print(SequenceI[] s)
- {
- boolean is_NA = jalview.util.Comparison.isNucleotide(s);
+ boolean is_NA = Comparison.isNucleotide(s);
int len = 72;
StringBuffer out = new StringBuffer();
int i = 0;
}
else
{
- out.append(">P1;" + printId(s[i]));
+ out.append(">P1;" + printId(s[i], jvsuffix));
out.append(newline);
if (s[i].getDescription() != null)
{
}
}
}
- int nochunks = (seq.length() / len) + 1;
+ int nochunks = (seq.length() / len)
+ + (seq.length() % len > 0 ? 1 : 0);
for (int j = 0; j < nochunks; j++)
{