/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
{
startRes = seqs[i].getStart();
endRes = seqs[i].getEnd();
-
if (startEnd != null)
{
startIndex = startEnd[0];
}
startRes = seqs[i].findPosition(startIndex);
- startRes = seqs[i].getStart() > 1 ? startRes - seqs[i].getStart()
- : startRes;
- endRes = seqs[i].findPosition(endIndex) - seqs[i].getStart();
+ endRes = seqs[i].findPosition(endIndex);
}
tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
return this.formatSequences(format, alignment, suffix);
}
- public AlignmentI readFile(String inFile, String type, String format)
- throws java.io.IOException
- {
- AlignmentI al = super.readFile(inFile, type, format);
- return al;
- }
-
- public AlignmentI readFromFile(FileParse source, String format)
- throws java.io.IOException
- {
- AlignmentI al = super.readFromFile(source, format);
- return al;
- }
-
/**
* validate format is valid for IO in Application. This is basically the
* AppletFormatAdapter.isValidFormat call with additional checks for