X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Futil%2FShiftList.java;h=2b3a8a40640c523904cedb4466c094cdb41807f4;hb=68dcaa7437590985b988a95338a36821c0ee641e;hp=e21392b19b104caca5c317c7213a66deeb323d1b;hpb=40643e496b01f691c747f01d39fb03b27118fcdb;p=jalview.git
diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index e21392b..2b3a8a4 100644
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -1,74 +1,146 @@
-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!
- *
Title: ShiftList
- *
- * Description:
- *
- * Copyright: Copyright (c) 2004
- *
- * Company: Dundee University
- *
- * @author not attributable
- * @version 1.0
- */
-public class ShiftList
-{
- 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.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+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;
+ }
+}