/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
{
}
- public SimpleBlastFile(String inFile, String type) throws IOException
+ public SimpleBlastFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public SimpleBlastFile(FileParse source) throws IOException
super(source);
}
+ @Override
public void initData()
{
super.initData();
seqids = new Vector();
}
+ @Override
public void parse() throws IOException
{
String line;
rstart = Long.parseLong(stindx);
} catch (Exception e)
{
- System.err.println("Couldn't parse '" + stindx
- + "' as start of row");
+ System.err.println(
+ "Couldn't parse '" + stindx + "' as start of row");
// inAlignments = false;
// warn for this line
}
rend = Long.parseLong(endindx);
} catch (Exception e)
{
- System.err.println("Couldn't parse '" + endindx
- + "' as end of row");
+ System.err.println(
+ "Couldn't parse '" + endindx + "' as end of row");
// inAlignments = false;
// warn for this line
{
padseq = true; // prepend gaps to new sequences in this block
seqentry = new Object[] { new StringBuffer(),
- new long[] { rstart, rend } };
+ new long[]
+ { rstart, rend } };
seqentries.addElement(seqentry);
seqhash.put(sqid, seqentry);
{
Sequence newseq = new Sequence(idstring,
- ((StringBuffer) seqentry[0]).toString(),
+ ((StringBuffer) seqentry[0]).toString(),
(int) ((long[]) seqentry[1])[0],
(int) ((long[]) seqentry[1])[1]);
if (newseq.getEnd() == 0)
}
}
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
return new String("Not Implemented.");
}
-
- public String print()
- {
- return print(getSeqsAsArray());
- }
}