/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.datamodel;
-import java.util.Enumeration;
-import java.util.Hashtable;
-
import jalview.analysis.AlignSeq;
import jalview.analysis.SeqsetUtils;
import jalview.util.MessageManager;
import jalview.util.ShiftList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+
public class SeqCigar extends CigarSimple
{
/**
refseq.getSequenceAsString(start, end), GapChar);
if (edit_result == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));
}
int bounds[] = (int[]) edit_result[1];
seq = new Sequence(refseq.getName(), (String) edit_result[0],
boolean hasgaps = false;
if (seq == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_set_seq_null"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_set_seq_null"));
}
if (_s < 0)
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_s", new String[]{Integer.valueOf(_s).toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_s", new String[] { Integer
+ .valueOf(_s).toString() }));
}
String seq_string = seq.getSequenceAsString();
if (_e == 0 || _e < _s || _e > seq_string.length())
// Check offsets
if (end > ds.getLength())
{
- throw new Error(MessageManager.getString("error.implementation_error_seqcigar_possible"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_seqcigar_possible"));
// end = ds.getLength();
}
super();
if (seq == null)
{
- throw new Error(MessageManager.getString("error.implmentation_bug_seq_null"));
+ throw new Error(
+ MessageManager.getString("error.implmentation_bug_seq_null"));
}
if (operation.length != range.length)
{
- throw new Error(MessageManager.getString("error.implementation_bug_cigar_operation_list_range_list"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_bug_cigar_operation_list_range_list"));
}
if (operation != null)
if (_setSeq(seq, false, 0, 0))
{
- throw new Error(MessageManager.getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
+ throw new Error(
+ MessageManager
+ .getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
}
for (int i = this.length, j = 0; j < operation.length; i++, j++)
{
char op = operation[j];
if (op != M && op != I && op != D)
{
- throw new Error(MessageManager.formatMessage("error.implementation_bug_cigar_operation", new String[]{Integer.valueOf(j).toString(),Integer.valueOf(op).toString(),Integer.valueOf(M).toString(),Integer.valueOf(I).toString(),Integer.valueOf(D).toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_bug_cigar_operation", new String[] {
+ Integer.valueOf(j).toString(),
+ Integer.valueOf(op).toString(),
+ Integer.valueOf(M).toString(),
+ Integer.valueOf(I).toString(),
+ Integer.valueOf(D).toString() }));
}
this.operation[i] = op;
this.range[i] = range[j];
this.length = 0;
if (_setSeq(seq, false, 0, 0))
{
- throw new Error(MessageManager.getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
+ throw new Error(
+ MessageManager
+ .getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
}
}
}
super();
if (seq == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_for_new_cigar"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_for_new_cigar"));
}
_setSeq(seq, false, 0, 0);
// there is still work to do
super();
if (seq == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_for_new_cigar"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_for_new_cigar"));
}
_setSeq(seq, false, start, end + 1);
// there is still work to do
// endcol}, hidden regions {{start, end, col}})
if (gs_regions[i] == null)
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_cigar_seq_no_operations", new String[]{Integer.valueOf(i).toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_cigar_seq_no_operations",
+ new String[] { Integer.valueOf(i).toString() }));
}
g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
// visible