/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview 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 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.util;\r
\r
-import jalview.datamodel.SequenceI;\r
-\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
+ 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() && (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
* 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
{\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
- &&\r
- (rshift=((int[]) shifts.elementAt(sidx++)))[0]<=pos) {\r
+ while (sidx < shifts.size()\r
+ && (rshift = ((int[]) shifts.elementAt(sidx++)))[0] <= pos)\r
+ {\r
shifted += rshift[1];\r
}\r
return shifted;\r
{\r
shifts.removeAllElements();\r
}\r
+\r
/**\r
* invert the shifts\r
+ * \r
* @return ShiftList with inverse shift operations\r
*/\r
- public ShiftList getInverse() {\r
- ShiftList inverse=new ShiftList();\r
- if (shifts!=null) {\r
- for (int i=0,j=shifts.size(); i<j; i++) {\r
- int[] sh=(int[]) shifts.elementAt(i);\r
- if (sh!=null)\r
- inverse.shifts.addElement(new int[] {sh[0], -sh[1]});\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
+ * parse a 1d map of position 1<i<n to L<pos[i]<N such as that returned from\r
+ * SequenceI.gapMap()\r
+ * \r
* @param gapMap\r
* @return shifts from map index to mapped position\r
*/\r
- public static ShiftList parseMap(int[] gapMap) {\r
+ public static ShiftList parseMap(int[] gapMap)\r
+ {\r
ShiftList shiftList = null;\r
- if (gapMap!=null && gapMap.length>0) {\r
- shiftList=new ShiftList();\r
- for (int i=0,p=0; i<gapMap.length; p++,i++) {\r
- if (p!=gapMap[i]) {\r
- shiftList.addShift(p, gapMap[i]-p);\r
- p=gapMap[i];\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
git://source.jalview.org / jalview.git / blobdiff