/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * \r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
* as published by the Free Software Foundation; either version 2\r
* of the License, or (at your option) any later version.\r
- *\r
+ * \r
* This program is distributed in the hope that it will be useful,\r
* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
* GNU General Public License for more details.\r
- *\r
+ * \r
* You should have received a copy of the GNU General Public License\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
import java.util.*;\r
\r
/**\r
- * ShiftList\r
- * Simple way of mapping a linear series to a new linear range with new points introduced.\r
- * Use at your own risk!\r
- * Now growing to be used for interval ranges (position, offset) storing deletions/insertions\r
+ * ShiftList Simple way of mapping a linear series to a new linear range with\r
+ * new points introduced. Use at your own risk! Now growing to be used for\r
+ * interval ranges (position, offset) storing deletions/insertions\r
*/\r
public class ShiftList\r
{\r
public Vector shifts;\r
+\r
public ShiftList()\r
{\r
shifts = new Vector();\r
\r
/**\r
* addShift\r
- * @param pos start position for shift (in original reference frame)\r
- * @param shift length of shift\r
+ * \r
+ * @param pos\r
+ * start position for shift (in original reference frame)\r
+ * @param shift\r
+ * length of shift\r
*/\r
public void addShift(int pos, int shift)\r
{\r
int sidx = 0;\r
int[] rshift = null;\r
- while (sidx < shifts.size() &&\r
- (rshift = (int[]) shifts.elementAt(sidx))[0] < pos)\r
+ while (sidx < shifts.size()\r
+ && (rshift = (int[]) shifts.elementAt(sidx))[0] < pos)\r
{\r
sidx++;\r
}\r
if (sidx == shifts.size())\r
{\r
shifts.insertElementAt(new int[]\r
- {pos, shift}, sidx);\r
+ { pos, shift }, sidx);\r
}\r
else\r
{\r
\r
/**\r
* shift\r
- *\r
- * @param pos int\r
+ * \r
+ * @param pos\r
+ * int\r
* @return int shifted position\r
*/\r
public int shift(int pos)\r
int sidx = 0;\r
int rshift[];\r
while (sidx < shifts.size()\r
- &&\r
- (rshift = ( (int[]) shifts.elementAt(sidx++)))[0] <= pos)\r
+ && (rshift = ((int[]) shifts.elementAt(sidx++)))[0] <= pos)\r
{\r
shifted += rshift[1];\r
}\r
\r
/**\r
* invert the shifts\r
+ * \r
* @return ShiftList with inverse shift operations\r
*/\r
public ShiftList getInverse()\r
if (sh != null)\r
{\r
inverse.shifts.addElement(new int[]\r
- {sh[0], -sh[1]});\r
+ { sh[0], -sh[1] });\r
}\r
}\r
}\r
}\r
\r
/**\r
- * parse a 1d map of position 1<i<n to L<pos[i]<N\r
- * such as that returned from SequenceI.gapMap()\r
+ * parse a 1d map of position 1<i<n to L<pos[i]<N such as that returned\r
+ * from SequenceI.gapMap()\r
+ * \r
* @param gapMap\r
* @return shifts from map index to mapped position\r
*/\r