formatting

[jalview.git] / src / jalview / datamodel / ColumnSelection.java

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 589c19b..fd3d897 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,6 +1,6 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
  * \r
  * This file is part of Jalview.\r
  * \r
@@ -1118,38 +1118,45 @@ public class ColumnSelection
    * AlignmentView\r
    * \r
    * @param profileseq\r
-   * @param al - alignment to have gaps inserted into it\r
-   * @param input - alignment view where sequence corresponding to profileseq is first entry\r
-   * @return new Column selection for new alignment view, with insertions into profileseq marked as hidden.\r
+   * @param al\r
+   *          - alignment to have gaps inserted into it\r
+   * @param input\r
+   *          - alignment view where sequence corresponding to profileseq is\r
+   *          first entry\r
+   * @return new Column selection for new alignment view, with insertions into\r
+   *         profileseq marked as hidden.\r
    */\r
   public static ColumnSelection propagateInsertions(SequenceI profileseq,\r
           Alignment al, AlignmentView input)\r
   {\r
-    int profsqpos=0;\r
-    \r
-//    return propagateInsertions(profileseq, al, )\r
+    int profsqpos = 0;\r
+\r
+    // return propagateInsertions(profileseq, al, )\r
     char gc = al.getGapCharacter();\r
     Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);\r
     ColumnSelection nview = (ColumnSelection) alandcolsel[1];\r
     SequenceI origseq = ((SequenceI[]) alandcolsel[0])[profsqpos];\r
-    nview.propagateInsertions(profileseq,\r
-            al, origseq);\r
+    nview.propagateInsertions(profileseq, al, origseq);\r
     return nview;\r
   }\r
+\r
   /**\r
    * \r
-   * @param profileseq - sequence in al which corresponds to origseq \r
-   * @param al - alignment which is to have gaps inserted into it\r
-   * @param origseq - sequence corresponding to profileseq which defines gap map for modifying al\r
+   * @param profileseq\r
+   *          - sequence in al which corresponds to origseq\r
+   * @param al\r
+   *          - alignment which is to have gaps inserted into it\r
+   * @param origseq\r
+   *          - sequence corresponding to profileseq which defines gap map for\r
+   *          modifying al\r
    */\r
-  public void propagateInsertions(SequenceI profileseq, AlignmentI al, SequenceI origseq)\r
+  public void propagateInsertions(SequenceI profileseq, AlignmentI al,\r
+          SequenceI origseq)\r
   {\r
     char gc = al.getGapCharacter();\r
-    // recover mapping between sequence's non-gap positions and positions \r
+    // recover mapping between sequence's non-gap positions and positions\r
     // mapping to view.\r
-    pruneDeletions(ShiftList\r
-            .parseMap(origseq\r
-                    .gapMap())); \r
+    pruneDeletions(ShiftList.parseMap(origseq.gapMap()));\r
     int[] viscontigs = getVisibleContigs(0, profileseq.getLength());\r
     int spos = 0;\r
     int offset = 0;\r
@@ -1181,15 +1188,18 @@ public class ColumnSelection
                 sq = sq + sb;\r
                 while ((diff = spos + offset - sq.length() - 1) > 0)\r
                 {\r
-                  //sq = sq\r
-                  //        + ((diff >= sb.length()) ? sb.toString() : sb\r
-                  //                .substring(0, diff));\r
-                  if (diff>=sb.length()) {\r
-                    sq+=sb.toString();\r
-                  } else {\r
+                  // sq = sq\r
+                  // + ((diff >= sb.length()) ? sb.toString() : sb\r
+                  // .substring(0, diff));\r
+                  if (diff >= sb.length())\r
+                  {\r
+                    sq += sb.toString();\r
+                  }\r
+                  else\r
+                  {\r
                     char[] buf = new char[diff];\r
                     sb.getChars(0, diff, buf, 0);\r
-                    sq+=buf.toString();\r
+                    sq += buf.toString();\r
                   }\r
                 }\r
               }\r
@@ -1218,7 +1228,7 @@ public class ColumnSelection
       for (int s = 0, ns = al.getHeight(); s < ns; s++)\r
       {\r
         SequenceI sqobj = al.getSequenceAt(s);\r
-        if (sqobj==profileseq)\r
+        if (sqobj == profileseq)\r
         {\r
           continue;\r
         }\r
@@ -1227,9 +1237,19 @@ public class ColumnSelection
         int diff = origseq.getLength() - sq.length();\r
         while (diff > 0)\r
         {\r
-          sq = sq\r
-                  + ((diff >= sb.length()) ? sb.toString() : sb\r
-                          .substring(0, diff));\r
+          // sq = sq\r
+          // + ((diff >= sb.length()) ? sb.toString() : sb\r
+          // .substring(0, diff));\r
+          if (diff >= sb.length())\r
+          {\r
+            sq += sb.toString();\r
+          }\r
+          else\r
+          {\r
+            char[] buf = new char[diff];\r
+            sb.getChars(0, diff, buf, 0);\r
+            sq += buf.toString();\r
+          }\r
           diff = origseq.getLength() - sq.length();\r
         }\r
       }\r