/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
-import jalview.datamodel.SequenceI;
-
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
/**
- * 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
+ * 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;
+ private List<int[]> shifts;
+
public ShiftList()
{
- shifts = new Vector();
+ shifts = new ArrayList<int[]>();
}
/**
* addShift
- * @param pos start position for shift (in original reference frame)
- * @param shift length of shift
+ *
+ * @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;
+ synchronized (shifts)
+ {
+ int sidx = 0;
+ int[] rshift = null;
+ while (sidx < shifts.size() && (rshift = shifts.get(sidx))[0] < pos)
+ {
+ sidx++;
+ }
+ if (sidx == shifts.size())
+ {
+ shifts.add(sidx, new int[] { pos, shift });
+ }
+ else
+ {
+ rshift[1] += shift;
+ }
+ }
}
/**
* shift
- *
- * @param pos int
+ *
+ * @param pos
+ * int
* @return int shifted position
*/
public int shift(int pos)
{
- if (shifts.size()==0)
+ if (shifts.size() == 0)
+ {
return pos;
- int shifted=pos;
- int sidx=0;
+ }
+ int shifted = pos;
+ int sidx = 0;
int rshift[];
- while (sidx<shifts.size()
- &&
- (rshift=((int[]) shifts.elementAt(sidx++)))[0]<=pos) {
+ while (sidx < shifts.size()
+ && (rshift = (shifts.get(sidx++)))[0] <= pos)
+ {
shifted += rshift[1];
}
return shifted;
/**
* clear all shifts
*/
- public void clear()
+ public synchronized void clear()
{
- shifts.removeAllElements();
+ shifts.clear();
}
+
/**
* 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.get(i);
- if (sh!=null)
- inverse.shifts.add(new int[] {sh[0], -sh[1]});
+ public ShiftList getInverse()
+ {
+ ShiftList inverse = new ShiftList();
+ synchronized (shifts)
+ {
+ if (shifts != null)
+ {
+ for (int[] sh : shifts)
+ {
+ if (sh != null)
+ {
+ inverse.shifts.add(new int[] { sh[0], -sh[1] });
+ }
+ }
}
}
return inverse;
}
/**
- * parse a 1d map of position 1<i<n to L<pos[i]<N
- * such as that returned from SequenceI.gapMap()
+ * parse a 1d map of position 1<i<n to L<pos[i]<N such as that
+ * returned from SequenceI.gapMap()
+ *
* @param gapMap
* @return shifts from map index to mapped position
*/
- public static ShiftList parseMap(int[] gapMap) {
+ public static ShiftList parseMap(int[] gapMap)
+ {
ShiftList shiftList = null;
- if (gapMap!=null && gapMap.length>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];
+ if (gapMap != null && gapMap.length > 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;
}
+
+ public List<int[]> getShifts()
+ {
+ return shifts;
+ }
}
git://source.jalview.org / jalview.git / blobdiff