formatting

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

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index dea0d72..6e0ab9f 100644 (file)
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -74,24 +74,34 @@ public class CigarArray extends CigarBase
   }\r
 \r
   /**\r
-   * construct a cigar array from the current alignment, or just the subset of the current alignment specified by selectionGroup. Any columns marked as hidden in columnSelection will be marked as deleted in the array.\r
+   * construct a cigar array from the current alignment, or just the subset of\r
+   * the current alignment specified by selectionGroup. Any columns marked as\r
+   * hidden in columnSelection will be marked as deleted in the array.\r
+   * \r
    * @param alignment\r
-   * @param columnSelection \r
+   * @param columnSelection\r
    * @param selectionGroup\r
    */\r
-  public CigarArray(AlignmentI alignment, ColumnSelection columnSelection, SequenceGroup selectionGroup)\r
+  public CigarArray(AlignmentI alignment, ColumnSelection columnSelection,\r
+          SequenceGroup selectionGroup)\r
   {\r
     this(constructSeqCigarArray(alignment, selectionGroup));\r
-    constructFromAlignment(alignment, columnSelection!=null ? columnSelection.getHiddenColumns() : null, selectionGroup);\r
+    constructFromAlignment(alignment,\r
+            columnSelection != null ? columnSelection.getHiddenColumns()\r
+                    : null, selectionGroup);\r
   }\r
-  private static int[] _calcStartEndBounds(AlignmentI alignment, SequenceGroup selectionGroup)\r
+\r
+  private static int[] _calcStartEndBounds(AlignmentI alignment,\r
+          SequenceGroup selectionGroup)\r
   {\r
-    int[] startend = new int[] { 0,0,0};\r
+    int[] startend = new int[]\r
+    { 0, 0, 0 };\r
     if (selectionGroup != null)\r
     {\r
       startend[0] = selectionGroup.getSize();\r
       startend[1] = selectionGroup.getStartRes();\r
-      startend[2] = selectionGroup.getEndRes(); // inclusive for start and end in\r
+      startend[2] = selectionGroup.getEndRes(); // inclusive for start and end\r
+                                                // in\r
       // SeqCigar constructor\r
     }\r
     else\r
@@ -101,12 +111,14 @@ public class CigarArray extends CigarBase
     }\r
     return startend;\r
   }\r
-  public static SeqCigar[] constructSeqCigarArray(AlignmentI alignment, SequenceGroup selectionGroup)\r
+\r
+  public static SeqCigar[] constructSeqCigarArray(AlignmentI alignment,\r
+          SequenceGroup selectionGroup)\r
   {\r
     SequenceI[] seqs = null;\r
     int i, iSize;\r
     int _startend[] = _calcStartEndBounds(alignment, selectionGroup);\r
-    int start = _startend[1],end=_startend[2];\r
+    int start = _startend[1], end = _startend[2];\r
     if (selectionGroup != null)\r
     {\r
       iSize = selectionGroup.getSize();\r
@@ -128,18 +140,23 @@ public class CigarArray extends CigarBase
     }\r
     return selseqs;\r
   }\r
+\r
   /**\r
    * internal constructor function - called by CigarArray(AlignmentI, ...);\r
+   * \r
    * @param alignment\r
-   * @param columnSelection - vector of visible regions as returned from columnSelection.getHiddenColumns() \r
+   * @param columnSelection\r
+   *          - vector of visible regions as returned from\r
+   *          columnSelection.getHiddenColumns()\r
    * @param selectionGroup\r
    */\r
-  private void constructFromAlignment(AlignmentI alignment, Vector columnSelection, SequenceGroup selectionGroup)\r
+  private void constructFromAlignment(AlignmentI alignment,\r
+          Vector columnSelection, SequenceGroup selectionGroup)\r
   {\r
     int[] _startend = _calcStartEndBounds(alignment, selectionGroup);\r
-    int start = _startend[1],end=_startend[2];\r
+    int start = _startend[1], end = _startend[2];\r
     // now construct the CigarArray operations\r
-    if (columnSelection!=null)\r
+    if (columnSelection != null)\r
     {\r
       int[] region;\r
       int hideStart, hideEnd;\r