X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=881dc74b8020887d88325b805dfe58b7f0204b56;hb=f52f7b378972cc884b5d3e5cc250f89667f558f7;hp=3c3feb3a0b352046b623bcccf3e2de44f8c62d8f;hpb=6357db6c20614a666b7b446aeb3260c5379637eb;p=jalview.git
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 3c3feb3..881dc74 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
- *
+ *
* 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
*/
@@ -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.
* 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