/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
* 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.
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
import java.util.*;
/**
* ShiftList Simple way of mapping a linear series to a new linear range with
* new points introduced. Use at your own risk! Now growing to be used for
* interval ranges (position, offset) storing deletions/insertions
*/
public class ShiftList
{
public Vector shifts;
public ShiftList()
{
shifts = new Vector();
}
/**
* addShift
*
* @param pos
* start position for shift (in original reference frame)
* @param shift
* length of shift
*/
public void addShift(int pos, int shift)
{
int sidx = 0;
int[] rshift = null;
while (sidx < shifts.size()
&& (rshift = (int[]) shifts.elementAt(sidx))[0] < pos)
{
sidx++;
}
if (sidx == shifts.size())
{
shifts.insertElementAt(new int[]
{ pos, shift }, sidx);
}
else
{
rshift[1] += shift;
}
}
/**
* shift
*
* @param pos
* int
* @return int shifted position
*/
public int shift(int pos)
{
if (shifts.size() == 0)
{
return pos;
}
int shifted = pos;
int sidx = 0;
int rshift[];
while (sidx < shifts.size()
&& (rshift = ((int[]) shifts.elementAt(sidx++)))[0] <= pos)
{
shifted += rshift[1];
}
return shifted;
}
/**
* clear all shifts
*/
public void clear()
{
shifts.removeAllElements();
}
/**
* invert the shifts
*
* @return ShiftList with inverse shift operations
*/
public ShiftList getInverse()
{
ShiftList inverse = new ShiftList();
if (shifts != null)
{
for (int i = 0, j = shifts.size(); i < j; i++)
{
int[] sh = (int[]) shifts.elementAt(i);
if (sh != null)
{
inverse.shifts.addElement(new int[]
{ sh[0], -sh[1] });
}
}
}
return inverse;
}
/**
* parse a 1d map of position 1 0)
{
shiftList = new ShiftList();
for (int i = 0, p = 0; i < gapMap.length; p++, i++)
{
if (p != gapMap[i])
{
shiftList.addShift(p, gapMap[i] - p);
p = gapMap[i];
}
}
}
return shiftList;
}
}