/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
refseq.getSequenceAsString(start, end), GapChar);
if (edit_result == null)
{
- throw new Error(
- "Implementation Error - unexpected null from getSequenceAndDeletions");
+ 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("Implementation Error - _setSeq(null,...)");
+ throw new Error(MessageManager.getString("error.implementation_error_set_seq_null"));
}
if (_s < 0)
{
- throw new Error("Implementation Error: _s=" + _s);
+ 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(
- "SeqCigar: Possible implementation error: sequence is longer than dataset sequence");
+ throw new Error(MessageManager.getString("error.implementation_error_seqcigar_possible"));
// end = ds.getLength();
}
super();
if (seq == null)
{
- throw new Error("Implementation Bug. Null seq !");
+ throw new Error(MessageManager.getString("error.implmentation_bug_seq_null"));
}
if (operation.length != range.length)
{
- throw new 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(
- "NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
+ 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("Implementation Bug. Cigar Operation '" + j
- + "' '" + op + "' not one of '" + M + "', '" + I
- + "', or '" + 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()}));
}
this.operation[i] = op;
this.range[i] = range[j];
this.length = 0;
if (_setSeq(seq, false, 0, 0))
{
- throw new Error(
- "NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
+ throw new Error(MessageManager.getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
}
}
}
super();
if (seq == null)
{
- throw new Error("Implementation error for new Cigar(SequenceI)");
+ 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("Implementation error for new Cigar(SequenceI)");
+ 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("Implementation error: " + i
- + "'th sequence Cigar has no operations.");
+ 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