+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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
+ * 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
+ * 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
+ */\r
package jalview.util;\r
\r
import java.util.*;\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
- * <p>Title: ShiftList</p>\r
- *\r
- * <p>Description: </p>\r
- *\r
- * <p>Copyright: Copyright (c) 2004</p>\r
- *\r
- * <p>Company: Dundee University</p>\r
- *\r
- * @author not attributable\r
- * @version 1.0\r
+ * Now growing to be used for interval ranges (position, offset) storing deletions/insertions\r
*/\r
public class ShiftList\r
{\r
- Vector shifts;\r
+ public Vector shifts;\r
public ShiftList()\r
{\r
shifts = new Vector();\r
public void addShift(int pos, int shift)\r
{\r
int sidx = 0;\r
- int[] rshift=null;\r
- while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)\r
+ int[] rshift = null;\r
+ while (sidx < shifts.size() &&\r
+ (rshift = (int[]) shifts.elementAt(sidx))[0] < pos)\r
+ {\r
sidx++;\r
- if (sidx==shifts.size())\r
- shifts.insertElementAt(new int[] { pos, shift}, sidx);\r
+ }\r
+ if (sidx == shifts.size())\r
+ {\r
+ shifts.insertElementAt(new int[]\r
+ {pos, shift}, sidx);\r
+ }\r
else\r
- rshift[1]+=shift;\r
+ {\r
+ rshift[1] += shift;\r
+ }\r
}\r
\r
/**\r
*/\r
public int shift(int pos)\r
{\r
- if (shifts.size()==0)\r
+ if (shifts.size() == 0)\r
+ {\r
return pos;\r
- int shifted=pos;\r
- int sidx=0;\r
+ }\r
+ int shifted = pos;\r
+ int sidx = 0;\r
int rshift[];\r
- while (sidx<shifts.size()\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
return shifted;\r
shifts.removeAllElements();\r
}\r
\r
+ /**\r
+ * invert the shifts\r
+ * @return ShiftList with inverse shift operations\r
+ */\r
+ public ShiftList getInverse()\r
+ {\r
+ ShiftList inverse = new ShiftList();\r
+ if (shifts != null)\r
+ {\r
+ for (int i = 0, j = shifts.size(); i < j; i++)\r
+ {\r
+ int[] sh = (int[]) shifts.elementAt(i);\r
+ if (sh != null)\r
+ {\r
+ inverse.shifts.addElement(new int[]\r
+ {sh[0], -sh[1]});\r
+ }\r
+ }\r
+ }\r
+ return inverse;\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
+ * @param gapMap\r
+ * @return shifts from map index to mapped position\r
+ */\r
+ public static ShiftList parseMap(int[] gapMap)\r
+ {\r
+ ShiftList shiftList = null;\r
+ if (gapMap != null && gapMap.length > 0)\r
+ {\r
+ shiftList = new ShiftList();\r
+ for (int i = 0, p = 0; i < gapMap.length; p++, i++)\r
+ {\r
+ if (p != gapMap[i])\r
+ {\r
+ shiftList.addShift(p, gapMap[i] - p);\r
+ p = gapMap[i];\r
+ }\r
+ }\r
+ }\r
+ return shiftList;\r
+ }\r
}\r