merge from 2_4_Release branch

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

diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index 8885e2c..be416dc 100644 (file)
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -1,17 +1,17 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 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
  * as published by the Free Software Foundation; either version 2\r
  * of the License, or (at your option) any later version.\r
- *\r
+ * \r
  * This program is distributed in the hope that it will be useful,\r
  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  * GNU General Public License for more details.\r
- *\r
+ * \r
  * You should have received a copy of the GNU General Public License\r
  * along with this program; if not, write to the Free Software\r
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
@@ -21,14 +21,14 @@ package jalview.util;
 import java.util.*;\r
 \r
 /**\r
- * ShiftList\r
- * Simple way of mapping a linear series to a new linear range with new points introduced.\r
- * Use at your own risk!\r
- * Now growing to be used for interval ranges (position, offset) storing deletions/insertions\r
+ * ShiftList Simple way of mapping a linear series to a new linear range with\r
+ * new points introduced. Use at your own risk! Now growing to be used for\r
+ * interval ranges (position, offset) storing deletions/insertions\r
  */\r
 public class ShiftList\r
 {\r
   public Vector shifts;\r
+\r
   public ShiftList()\r
   {\r
     shifts = new Vector();\r
@@ -36,22 +36,25 @@ public class ShiftList
 \r
   /**\r
    * addShift\r
-   * @param pos start position for shift (in original reference frame)\r
-   * @param shift length of shift\r
+   * \r
+   * @param pos\r
+   *                start position for shift (in original reference frame)\r
+   * @param shift\r
+   *                length of shift\r
    */\r
   public void addShift(int pos, int shift)\r
   {\r
     int sidx = 0;\r
     int[] rshift = null;\r
-    while (sidx < shifts.size() &&\r
-           (rshift = (int[]) shifts.elementAt(sidx))[0] < pos)\r
+    while (sidx < shifts.size()\r
+            && (rshift = (int[]) shifts.elementAt(sidx))[0] < pos)\r
     {\r
       sidx++;\r
     }\r
     if (sidx == shifts.size())\r
     {\r
       shifts.insertElementAt(new int[]\r
-                             {pos, shift}, sidx);\r
+      { pos, shift }, sidx);\r
     }\r
     else\r
     {\r
@@ -61,8 +64,9 @@ public class ShiftList
 \r
   /**\r
    * shift\r
-   *\r
-   * @param pos int\r
+   * \r
+   * @param pos\r
+   *                int\r
    * @return int shifted position\r
    */\r
   public int shift(int pos)\r
@@ -75,8 +79,7 @@ public class ShiftList
     int sidx = 0;\r
     int rshift[];\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
@@ -93,6 +96,7 @@ public class ShiftList
 \r
   /**\r
    * invert the shifts\r
+   * \r
    * @return ShiftList with inverse shift operations\r
    */\r
   public ShiftList getInverse()\r
@@ -106,7 +110,7 @@ public class ShiftList
         if (sh != null)\r
         {\r
           inverse.shifts.addElement(new int[]\r
-                                    {sh[0], -sh[1]});\r
+          { sh[0], -sh[1] });\r
         }\r
       }\r
     }\r
@@ -114,8 +118,9 @@ public class ShiftList
   }\r
 \r
   /**\r
-   * parse a 1d map of position 1<i<n to L<pos[i]<N\r
-   * such as that returned from SequenceI.gapMap()\r
+   * parse a 1d map of position 1<i<n to L<pos[i]<N such as that returned\r
+   * from SequenceI.gapMap()\r
+   * \r
    * @param gapMap\r
    * @return shifts from map index to mapped position\r
    */\r