X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FShiftList.java;h=1dd18ec2f75987f6944cb012561aea4a8f0398ca;hb=afffa24481a7d3cb65ae41e0948c16a5f490f302;hp=0c78ca13d74f0db7bfd9fbdc88f3bdaa5527d042;hpb=b2d54d33d6313efd9da96bd7586dfaa7a0d7a182;p=jalview.git
diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index 0c78ca1..1dd18ec 100644
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -1,74 +1,90 @@
/*
- * 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
+ * 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
-import jalview.datamodel.SequenceI;
-
-import java.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
+ * 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;
+ private List shifts;
+
public ShiftList()
{
- shifts = new Vector();
+ shifts = new ArrayList();
}
/**
* addShift
- * @param pos start position for shift (in original reference frame)
- * @param shift length of shift
+ *
+ * @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 (sidx0) {
- shiftList=new ShiftList();
- for (int i=0,p=0; i 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;
+ }
}