X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FShiftList.java;h=15f455288cde6c0e164d05c30ad0fc3bffc7646b;hb=c16c1633e1a5acc9f44e4de40b9abbb8a59b99b4;hp=78b99ef1ff672670c3d68f603ddb7caad07776af;hpb=8906ee1e7c76cc694793097abbb0fefe4434bb5a;p=jalview.git

diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index 78b99ef..15f4552 100644
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -1,111 +1,144 @@
-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!
- * <p>Title: ShiftList</p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
-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.get(i);
-        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
-   */
-  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 (Development Version 2.4.1)
+ * Copyright (C) 2009 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 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;
+  }
+}