/*
- * 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.
*
int[][] deletions = new int[length][];
int[][] trunc_deletions = null;
StringBuffer sq = new StringBuffer();
- int cursor = 0, alcursor = 0, start = 0, startpos = 0, end = 0, endpos = 0, delcount = -1;
+ int cursor = 0, alcursor = 0, start = 0, startpos = 0, end = 0,
+ endpos = 0, delcount = -1;
boolean consecutive_del = false;
if (length == 0)
{
break;
default:
throw new Error(MessageManager.formatMessage(
- "error.unknown_seq_cigar_operation",
- new String[] { new StringBuffer(operation[i]).toString() }));
+ "error.unknown_seq_cigar_operation", new String[]
+ { new StringBuffer(operation[i]).toString() }));
}
}
if (++delcount > 0)
}
deletions = null;
return new Object[] { ((reference != null) ? sq.toString() : null),
- new int[] { start, startpos, end, endpos }, trunc_deletions };
+ new int[]
+ { start, startpos, end, endpos }, trunc_deletions };
}
protected void compact_operations()
} while (c >= '0' && c <= '9' && j < l);
if (j >= l && c >= '0' && c <= '9')
{
- throw new Exception(
- MessageManager
- .getString("exception.unterminated_cigar_string"));
+ throw new Exception(MessageManager
+ .getString("exception.unterminated_cigar_string"));
}
try
{
i = j;
} catch (Exception e)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_bug_parse_cigar_string"));
+ throw new Error(MessageManager
+ .getString("error.implementation_bug_parse_cigar_string"));
}
if (c >= 'a' && c <= 'z')
{
{
throw new Exception(MessageManager.formatMessage(
"exception.unexpected_operation_cigar_string_pos",
- new String[] { new StringBuffer(c).toString(),
+ new String[]
+ { new StringBuffer(c).toString(),
Integer.valueOf(i).toString(), cigarString }));
}
}
}
if (op != M && op != D && op != I)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_invalid_operation_string"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_invalid_operation_string"));
}
if (range == 0)
{
* int public void addOperationAt(int pos, char op, int range) { int
* cursor = -1; // mark the position for the current operation being
* edited. int o = 0; boolean last_d = false; // previous op was a
- * deletion. if (pos < -1) throw new
- * Error("pos<-1 is not supported."); while (o<length) { if
- * (operation[o] != D) { if ( (cursor + this.range[o]) < pos) {
- * cursor += this.range[o]; o++; last_d=false; } else { break; } }
- * else { last_d=true; o++; } } if (o==length) { // must insert more
- * operations before pos if (pos-cursor>0) addInsertion(pos-cursor);
- * // then just add the new operation. Regardless of what it is.
- * addOperation(op, range); } else { int diff = pos - cursor;
+ * deletion. if (pos < -1) throw new Error("pos<-1 is not
+ * supported."); while (o<length) { if (operation[o] != D) { if (
+ * (cursor + this.range[o]) < pos) { cursor += this.range[o]; o++;
+ * last_d=false; } else { break; } } else { last_d=true; o++; } } if
+ * (o==length) { // must insert more operations before pos if
+ * (pos-cursor>0) addInsertion(pos-cursor); // then just add the new
+ * operation. Regardless of what it is. addOperation(op, range); }
+ * else { int diff = pos - cursor;
*
* int e_length = length-o; // new edit operation array length. //
* diff<0 - can only happen before first insertion or match. -
}
if (start < 0 || start > end)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_delete_range_out_of_bounds"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_delete_range_out_of_bounds"));
}
// find beginning
int cursor = 0; // mark the position for the current operation being edited.
default:
throw new Error(MessageManager.formatMessage(
"error.implementation_error_unknown_operation",
- new String[] { new StringBuffer(oldops[o]).toString() }));
+ new String[]
+ { new StringBuffer(oldops[o]).toString() }));
}
rlength -= remain;
remain = oldrange[++o]; // number of op characters left to edit
{
case M:
cursor += range[i];
+ break;
case I:
vcursor += range[i];
break;