X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Futil%2FShiftList.java;h=8885e2c9607706b8b2e9816a4c88fd1769a39382;hb=77e9dc41516acc93470931bcc5f344c67e819e70;hp=7792287b12e2a095ef83d00f774ae07e521717e1;hpb=279f73359584dd952a06668b034d2ed98818e315;p=jalview.git

diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index 7792287..8885e2c 100644
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -1,27 +1,34 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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!
- * <p>Title: ShiftList</p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
+ * Now growing to be used for interval ranges (position, offset) storing deletions/insertions
  */
 public class ShiftList
 {
-    public Vector shifts;
+  public Vector shifts;
   public ShiftList()
   {
     shifts = new Vector();
@@ -35,13 +42,21 @@ public class ShiftList
   public void addShift(int pos, int shift)
   {
     int sidx = 0;
-    int[] rshift=null;
-    while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
+    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);
+    }
+    if (sidx == shifts.size())
+    {
+      shifts.insertElementAt(new int[]
+                             {pos, shift}, sidx);
+    }
     else
-      rshift[1]+=shift;
+    {
+      rshift[1] += shift;
+    }
   }
 
   /**
@@ -52,14 +67,17 @@ public class ShiftList
    */
   public int shift(int pos)
   {
-    if (shifts.size()==0)
+    if (shifts.size() == 0)
+    {
       return pos;
-    int shifted=pos;
-    int sidx=0;
+    }
+    int shifted = pos;
+    int sidx = 0;
     int rshift[];
-    while (sidx<shifts.size()
+    while (sidx < shifts.size()
            &&
-           (rshift=((int[]) shifts.elementAt(sidx++)))[0]<=pos) {
+           (rshift = ( (int[]) shifts.elementAt(sidx++)))[0] <= pos)
+    {
       shifted += rshift[1];
     }
     return shifted;
@@ -72,17 +90,24 @@ public class ShiftList
   {
     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]});
+  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;
@@ -92,17 +117,20 @@ public class ShiftList
    * parse a 1d map of position 1<i<n to L<pos[i]<N
    * such as that returned from SequenceI.gapMap()
    * @param gapMap
-   * @return
+   * @return shifts from map index to mapped position
    */
-  public static ShiftList parseMap(int[] gapMap) {
+  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];
+    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];
         }
       }
     }