X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FShiftList.java;h=1dd18ec2f75987f6944cb012561aea4a8f0398ca;hb=afffa24481a7d3cb65ae41e0948c16a5f490f302;hp=7b13045fbe6063877320bc3a7344fa940a09a724;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index 7b13045..1dd18ec 100644
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -1,143 +1,154 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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 .
- */
-package jalview.util;
-
-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.elementAt(i);
- if (sh != null)
- {
- inverse.shifts.addElement(new int[]
- { sh[0], -sh[1] });
- }
- }
- }
- return inverse;
- }
-
- /**
- * parse a 1d map of position 1 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;
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * 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 shifts;
+
+ public ShiftList()
+ {
+ shifts = new ArrayList();
+ }
+
+ /**
+ * 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 getShifts()
+ {
+ return shifts;
+ }
+}