/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
*
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
/**
* parse a simple blast report. Attempt to cope with query anchored and pairwise
{
}
- 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;
if (seqentry == null)
{
padseq = true; // prepend gaps to new sequences in this block
- seqentry = new Object[]
- { new StringBuffer(), new long[]
- { rstart, rend } };
+ seqentry = new Object[] { new StringBuffer(),
+ new long[] { rstart, rend } };
seqentries.addElement(seqentry);
seqhash.put(sqid, seqentry);
}
}
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
return new String("Not Implemented.");
}
-
- public String print()
- {
- return print(getSeqsAsArray());
- }
}