X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FShiftList.java;h=860a700fe1c09abfc6ea26f0da677f1f89f705d2;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=bcd8e7c24e9a58a1dbb54a43f65b5e6ece381afd;hpb=6fe4dc1cb082ea9df1c733d05e74ee1a187816cf;p=jalview.git

diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index bcd8e7c..860a700 100644
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -1,119 +1,154 @@
-/*
- * 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.elementAt(i);
-        if (sh!=null)
-          inverse.shifts.addElement(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;
-  }
-}
+/*
+ * 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&lt;i&lt;n to L&lt;pos[i]&lt;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;
+  }
+}