javatidy

[jalview.git] / src / jalview / analysis / AlignmentSorter.java

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 3c3feb3..881dc74 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,18 +1,18 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- * 
+ *
  * This file is part of Jalview.
- * 
+ *
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
+ * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
- * Jalview 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 
+ *
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.analysis;
@@ -75,7 +75,7 @@ public class AlignmentSorter
 
   /**
    * Sort by Percentage Identity w.r.t. s
-   * 
+   *
    * @param align
    *          AlignmentI
    * @param s
@@ -91,7 +91,7 @@ public class AlignmentSorter
 
   /**
    * Sort by Percentage Identity w.r.t. s
-   * 
+   *
    * @param align
    *          AlignmentI
    * @param s
@@ -124,7 +124,7 @@ public class AlignmentSorter
 
   /**
    * Reverse the order of the sort
-   * 
+   *
    * @param align
    *          DOCUMENT ME!
    * @param seqs
@@ -160,7 +160,7 @@ public class AlignmentSorter
 
   /**
    * Sets the Alignment object with the given sequences
-   * 
+   *
    * @param align
    *          Alignment object to be updated
    * @param tmp
@@ -173,7 +173,7 @@ public class AlignmentSorter
 
   /**
    * Sets the Alignment object with the given sequences
-   * 
+   *
    * @param align
    *          DOCUMENT ME!
    * @param seqs
@@ -206,7 +206,7 @@ public class AlignmentSorter
 
   /**
    * Sorts by ID. Numbers are sorted before letters.
-   * 
+   *
    * @param align
    *          The alignment object to sort
    */
@@ -239,7 +239,7 @@ public class AlignmentSorter
 
   /**
    * Sorts by sequence length
-   * 
+   *
    * @param align
    *          The alignment object to sort
    */
@@ -253,7 +253,7 @@ public class AlignmentSorter
     for (int i = 0; i < nSeq; i++)
     {
       seqs[i] = align.getSequenceAt(i);
-      length[i] = (float) (seqs[i].getEnd() - seqs[i].getStart());
+      length[i] = (seqs[i].getEnd() - seqs[i].getStart());
     }
 
     QuickSort.sort(length, seqs);
@@ -274,7 +274,7 @@ public class AlignmentSorter
    * Sorts the alignment by size of group. <br>
    * Maintains the order of sequences in each group by order in given alignment
    * object.
-   * 
+   *
    * @param align
    *          sorts the given alignment object by group
    */
@@ -296,7 +296,7 @@ public class AlignmentSorter
 
     // SORTS GROUPS BY SIZE
     // ////////////////////
-    for (SequenceGroup sg:align.getGroups())
+    for (SequenceGroup sg : align.getGroups())
     {
       for (int j = 0; j < groups.size(); j++)
       {
@@ -344,10 +344,10 @@ public class AlignmentSorter
 
   /**
    * Converts Vector to array. java 1.18 does not have Vector.toArray()
-   * 
+   *
    * @param tmp
    *          Vector of SequenceI objects
-   * 
+   *
    * @return array of Sequence[]
    */
   private static SequenceI[] vectorToArray(Vector tmp)
@@ -409,7 +409,7 @@ public class AlignmentSorter
 
   /**
    * Sorts by a given AlignmentOrder object
-   * 
+   *
    * @param align
    *          Alignment to order
    * @param order
@@ -441,12 +441,12 @@ public class AlignmentSorter
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param align
    *          alignment to order
    * @param tree
    *          tree which has
-   * 
+   *
    * @return DOCUMENT ME!
    */
   private static Vector getOrderByTree(AlignmentI align, NJTree tree)
@@ -469,8 +469,12 @@ public class AlignmentSorter
 
       if (tmp.size() != nSeq)
       {
-        System.err.println("WARNING: tmp.size()=" + tmp.size() + " != nseq="
-                + nSeq + " in getOrderByTree - tree contains sequences not in alignment");
+        System.err
+                .println("WARNING: tmp.size()="
+                        + tmp.size()
+                        + " != nseq="
+                        + nSeq
+                        + " in getOrderByTree - tree contains sequences not in alignment");
       }
     }
 
@@ -479,7 +483,7 @@ public class AlignmentSorter
 
   /**
    * Sorts the alignment by a given tree
-   * 
+   *
    * @param align
    *          alignment to order
    * @param tree
@@ -512,7 +516,7 @@ public class AlignmentSorter
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param align
    *          DOCUMENT ME!
    * @param seqs
@@ -539,14 +543,14 @@ public class AlignmentSorter
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param node
    *          DOCUMENT ME!
    * @param tmp
    *          DOCUMENT ME!
    * @param seqset
    *          DOCUMENT ME!
-   * 
+   *
    * @return DOCUMENT ME!
    */
   private static Vector _sortByTree(SequenceNode node, Vector tmp,
@@ -566,9 +570,11 @@ public class AlignmentSorter
       {
         if (node.element() instanceof SequenceI)
         {
-          if (!tmp.contains(node.element())) //  && (seqset==null || seqset.size()==0 || seqset.contains(tmp)))
+          if (!tmp.contains(node.element())) // && (seqset==null ||
+                                             // seqset.size()==0 ||
+                                             // seqset.contains(tmp)))
           {
-            tmp.addElement((SequenceI) node.element());
+            tmp.addElement(node.element());
           }
         }
       }
@@ -609,7 +615,7 @@ public class AlignmentSorter
   /**
    * Sort sequence in order of increasing score attribute for annotation with a
    * particular scoreLabel. Or reverse if same label was used previously
-   * 
+   *
    * @param scoreLabel
    *          exact label for sequence associated AlignmentAnnotation scores to
    *          use for sorting.
@@ -697,7 +703,7 @@ public class AlignmentSorter
   /**
    * sort the alignment using the features on each sequence found between start
    * and stop with the given featureLabel (and optional group qualifier)
-   * 
+   *
    * @param featureLabel
    *          (may not be null)
    * @param groupLabel