X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=48dbb6a55cdac0a69c092d705c1a5a27e1c8c127;hb=c3583f7ab67ddb450f61af4d36af839ddf485a09;hp=881dc74b8020887d88325b805dfe58b7f0204b56;hpb=f52f7b378972cc884b5d3e5cc250f89667f558f7;p=jalview.git
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 881dc74..48dbb6a 100755
--- 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
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 .
*/
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
*/
@@ -274,7 +274,7 @@ public class AlignmentSorter
* Sorts the alignment by size of group.
* Maintains the order of sequences in each group by order in given alignment
* object.
- *
+ *
* @param align
* sorts the given alignment object by group
*/
@@ -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)
@@ -365,12 +365,12 @@ public class AlignmentSorter
/**
* Select sequences in order from tmp that is present in mask, and any
* remaining seqeunces in mask not in tmp
- *
+ *
* @param tmp
* thread safe collection of sequences
* @param mask
* thread safe collection of sequences
- *
+ *
* @return intersect(tmp,mask)+intersect(complement(tmp),mask)
*/
private static SequenceI[] vectorSubsetToArray(List 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)
@@ -483,7 +483,7 @@ public class AlignmentSorter
/**
* Sorts the alignment by a given tree
- *
+ *
* @param align
* alignment to order
* @param tree
@@ -516,7 +516,7 @@ public class AlignmentSorter
/**
* DOCUMENT ME!
- *
+ *
* @param align
* DOCUMENT ME!
* @param seqs
@@ -543,14 +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,
@@ -615,7 +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.
@@ -703,7 +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