-/*\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
-\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
- */\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() &&\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
- }\r
- else\r
- {\r
- rshift[1] += shift;\r
- }\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
- {\r
- return pos;\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
- {\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
- /**\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
+/*
+ * 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.
+ *
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.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
+ */
+public class ShiftList
+{
+ private List<int[]> shifts;
+
+ public ShiftList()
+ {
+ shifts = new ArrayList<int[]>();
+ }
+
+ /**
+ * addShift
+ *
+ * @param pos
+ * start position for shift (in original reference frame)
+ * @param shift
+ * length of shift
+ */
+ public void addShift(int pos, int 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
+ * @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 = (shifts.get(sidx++)))[0] <= pos)
+ {
+ shifted += rshift[1];
+ }
+ return shifted;
+ }
+
+ /**
+ * clear all shifts
+ */
+ public synchronized void clear()
+ {
+ shifts.clear();
+ }
+
+ /**
+ * invert the shifts
+ *
+ * @return ShiftList with inverse shift operations
+ */
+ 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()
+ *
+ * @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;
+ }
+
+ public List<int[]> getShifts()
+ {
+ return shifts;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff