Formatting

[jalview.git] / src / jalview / util / ShiftList.java

diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index 325a681..8885e2c 100644 (file)
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -28,7 +28,7 @@ import java.util.*;
  */\r
 public class ShiftList\r
 {\r
-    public Vector shifts;\r
+  public Vector shifts;\r
   public ShiftList()\r
   {\r
     shifts = new Vector();\r
@@ -42,13 +42,21 @@ public class ShiftList
   public void addShift(int pos, int shift)\r
   {\r
     int sidx = 0;\r
-    int[] rshift=null;\r
-    while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)\r
+    int[] rshift = null;\r
+    while (sidx < shifts.size() &&\r
+           (rshift = (int[]) shifts.elementAt(sidx))[0] < pos)\r
+    {\r
       sidx++;\r
-    if (sidx==shifts.size())\r
-      shifts.insertElementAt(new int[] { pos, shift}, sidx);\r
+    }\r
+    if (sidx == shifts.size())\r
+    {\r
+      shifts.insertElementAt(new int[]\r
+                             {pos, shift}, sidx);\r
+    }\r
     else\r
-      rshift[1]+=shift;\r
+    {\r
+      rshift[1] += shift;\r
+    }\r
   }\r
 \r
   /**\r
@@ -59,14 +67,17 @@ public class ShiftList
    */\r
   public int shift(int pos)\r
   {\r
-    if (shifts.size()==0)\r
+    if (shifts.size() == 0)\r
+    {\r
       return pos;\r
-    int shifted=pos;\r
-    int sidx=0;\r
+    }\r
+    int shifted = pos;\r
+    int sidx = 0;\r
     int rshift[];\r
-    while (sidx<shifts.size()\r
+    while (sidx < shifts.size()\r
            &&\r
-           (rshift=((int[]) shifts.elementAt(sidx++)))[0]<=pos) {\r
+           (rshift = ( (int[]) shifts.elementAt(sidx++)))[0] <= pos)\r
+    {\r
       shifted += rshift[1];\r
     }\r
     return shifted;\r
@@ -79,17 +90,24 @@ public class ShiftList
   {\r
     shifts.removeAllElements();\r
   }\r
+\r
   /**\r
    * invert the shifts\r
    * @return ShiftList with inverse shift operations\r
    */\r
-  public ShiftList getInverse() {\r
-    ShiftList inverse=new ShiftList();\r
-    if (shifts!=null) {\r
-      for (int i=0,j=shifts.size(); i<j; i++) {\r
-        int[] sh=(int[]) shifts.elementAt(i);\r
-        if (sh!=null)\r
-          inverse.shifts.addElement(new int[] {sh[0], -sh[1]});\r
+  public ShiftList getInverse()\r
+  {\r
+    ShiftList inverse = new ShiftList();\r
+    if (shifts != null)\r
+    {\r
+      for (int i = 0, j = shifts.size(); i < j; i++)\r
+      {\r
+        int[] sh = (int[]) shifts.elementAt(i);\r
+        if (sh != null)\r
+        {\r
+          inverse.shifts.addElement(new int[]\r
+                                    {sh[0], -sh[1]});\r
+        }\r
       }\r
     }\r
     return inverse;\r
@@ -101,14 +119,18 @@ public class ShiftList
    * @param gapMap\r
    * @return shifts from map index to mapped position\r
    */\r
-  public static ShiftList parseMap(int[] gapMap) {\r
+  public static ShiftList parseMap(int[] gapMap)\r
+  {\r
     ShiftList shiftList = null;\r
-    if (gapMap!=null && gapMap.length>0) {\r
-      shiftList=new ShiftList();\r
-      for (int i=0,p=0; i<gapMap.length; p++,i++) {\r
-        if (p!=gapMap[i]) {\r
-          shiftList.addShift(p, gapMap[i]-p);\r
-          p=gapMap[i];\r
+    if (gapMap != null && gapMap.length > 0)\r
+    {\r
+      shiftList = new ShiftList();\r
+      for (int i = 0, p = 0; i < gapMap.length; p++, i++)\r
+      {\r
+        if (p != gapMap[i])\r
+        {\r
+          shiftList.addShift(p, gapMap[i] - p);\r
+          p = gapMap[i];\r
         }\r
       }\r
     }\r