-/*\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
- */\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
- * <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
- */\r
-public class ShiftList\r
-{\r
- public Vector shifts;\r
- public ShiftList()\r
- {\r
- shifts = new Vector();\r
- }\r
-\r
- /**\r
- * addShift\r
- * @param pos start position for shift (in original reference frame)\r
- * @param shift 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
- sidx++;\r
- if (sidx==shifts.size())\r
- shifts.insertElementAt(new int[] { pos, shift}, sidx);\r
- else\r
- rshift[1]+=shift;\r
- }\r
-\r
- /**\r
- * shift\r
- *\r
- * @param pos int\r
- * @return int shifted position\r
- */\r
- public int shift(int pos)\r
- {\r
- if (shifts.size()==0)\r
- return pos;\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
- shifted += rshift[1];\r
- }\r
- return shifted;\r
- }\r
-\r
- /**\r
- * clear all shifts\r
- */\r
- public void clear()\r
- {\r
- shifts.removeAllElements();\r
- }\r
- /**\r
- * invert the shifts\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
- }\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\r
- */\r
- public static ShiftList parseMap(int[] gapMap) {\r
- ShiftList shiftList = null;\r
- if (gapMap!=null && gapMap.length>0) {\r
- shiftList=new ShiftList();\r
-\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
- }\r
- }\r
- }\r
- return shiftList;\r
- }\r
-}\r
+/*
+ * 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
+ * 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.
+ *
+ * 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
+ */
+package jalview.util;
+
+import jalview.datamodel.SequenceI;
+
+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.get(i);
+ 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()
+ * @param gapMap
+ * @return shifts from map index to mapped position
+ */
+ 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];
+ }
+ }
+ }
+ return shiftList;
+ }
+}