X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=0022af643dc36455ad4e05a901ce7023c65d66f4;hb=27f5f6fdfea52770ebd513c4607a6dde87821d48;hp=8aafcc206648cd2e94ed090c319a0c52f8120929;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 8aafcc2..0022af6 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,27 +1,38 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 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
* 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.QuickSort;
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.util.ArrayList;
+import java.util.List;
/**
* Routines for manipulating the order of a multiple sequence alignment TODO:
@@ -118,7 +129,7 @@ public class AlignmentSorter
seqs[i] = align.getSequenceAt(i);
}
- QuickSort.sort(scores, 0, scores.length - 1, seqs);
+ QuickSort.sort(scores, seqs);
setReverseOrder(align, seqs);
}
@@ -167,7 +178,7 @@ public class AlignmentSorter
* @param tmp
* sequences as a vector
*/
- private static void setOrder(AlignmentI align, Vector tmp)
+ private static void setOrder(AlignmentI align, List tmp)
{
setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
}
@@ -283,7 +294,7 @@ public class AlignmentSorter
{
// MAINTAINS ORIGNAL SEQUENCE ORDER,
// ORDERS BY GROUP SIZE
- Vector groups = new Vector();
+ List groups = new ArrayList();
if (groups.hashCode() != lastGroupHash)
{
@@ -301,11 +312,11 @@ public class AlignmentSorter
{
for (int j = 0; j < groups.size(); j++)
{
- SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
+ SequenceGroup sg2 = groups.get(j);
if (sg.getSize() > sg2.getSize())
{
- groups.insertElementAt(sg, j);
+ groups.add(j, sg);
break;
}
@@ -313,22 +324,22 @@ public class AlignmentSorter
if (!groups.contains(sg))
{
- groups.addElement(sg);
+ groups.add(sg);
}
}
// NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
// /////////////////////////////////////////////
- Vector seqs = new Vector();
+ List seqs = new ArrayList();
for (int i = 0; i < groups.size(); i++)
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ SequenceGroup sg = groups.get(i);
SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
for (int j = 0; j < orderedseqs.length; j++)
{
- seqs.addElement(orderedseqs[j]);
+ seqs.add(orderedseqs[j]);
}
}
@@ -344,28 +355,8 @@ 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)
- {
- SequenceI[] seqs = new SequenceI[tmp.size()];
-
- for (int i = 0; i < tmp.size(); i++)
- {
- seqs[i] = (SequenceI) tmp.elementAt(i);
- }
-
- return seqs;
- }
-
- /**
* Select sequences in order from tmp that is present in mask, and any
- * remaining seqeunces in mask not in tmp
+ * remaining sequences in mask not in tmp
*
* @param tmp
* thread safe collection of sequences
@@ -377,6 +368,10 @@ public class AlignmentSorter
private static SequenceI[] vectorSubsetToArray(List tmp,
List mask)
{
+ // or?
+ // tmp2 = tmp.retainAll(mask);
+ // return tmp2.addAll(mask.removeAll(tmp2))
+
ArrayList seqs = new ArrayList();
int i, idx;
boolean[] tmask = new boolean[mask.size()];
@@ -419,7 +414,7 @@ public class AlignmentSorter
public static void sortBy(AlignmentI align, AlignmentOrder order)
{
// Get an ordered vector of sequences which may also be present in align
- Vector tmp = order.getOrder();
+ List tmp = order.getOrder();
if (lastOrder == order)
{
@@ -450,11 +445,12 @@ public class AlignmentSorter
*
* @return DOCUMENT ME!
*/
- private static Vector getOrderByTree(AlignmentI align, NJTree tree)
+ private static List getOrderByTree(AlignmentI align,
+ NJTree tree)
{
int nSeq = align.getHeight();
- Vector tmp = new Vector();
+ List tmp = new ArrayList();
tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
@@ -492,7 +488,7 @@ public class AlignmentSorter
*/
public static void sortByTree(AlignmentI align, NJTree tree)
{
- Vector tmp = getOrderByTree(align, tree);
+ List tmp = getOrderByTree(align, tree);
// tmp should properly permute align with tree.
if (lastTree != tree)
@@ -520,22 +516,22 @@ public class AlignmentSorter
*
* @param align
* DOCUMENT ME!
- * @param seqs
+ * @param tmp
* DOCUMENT ME!
*/
- private static void addStrays(AlignmentI align, Vector seqs)
+ private static void addStrays(AlignmentI align, List tmp)
{
int nSeq = align.getHeight();
for (int i = 0; i < nSeq; i++)
{
- if (!seqs.contains(align.getSequenceAt(i)))
+ if (!tmp.contains(align.getSequenceAt(i)))
{
- seqs.addElement(align.getSequenceAt(i));
+ tmp.add(align.getSequenceAt(i));
}
}
- if (nSeq != seqs.size())
+ if (nSeq != tmp.size())
{
System.err
.println("ERROR: Size still not right even after addStrays");
@@ -554,7 +550,8 @@ public class AlignmentSorter
*
* @return DOCUMENT ME!
*/
- private static Vector _sortByTree(SequenceNode node, Vector tmp,
+ private static List _sortByTree(SequenceNode node,
+ List tmp,
List seqset)
{
if (node == null)
@@ -575,7 +572,7 @@ public class AlignmentSorter
// seqset.size()==0 ||
// seqset.contains(tmp)))
{
- tmp.addElement(node.element());
+ tmp.add((SequenceI) node.element());
}
}
}
@@ -755,8 +752,7 @@ public class AlignmentSorter
if (method != FEATURE_SCORE && method != FEATURE_LABEL
&& method != FEATURE_DENSITY)
{
- throw new Error(
- "Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY.");
+ throw new Error(MessageManager.getString("error.implementation_error_sortbyfeature"));
}
boolean ignoreScore = method != FEATURE_SCORE;
StringBuffer scoreLabel = new StringBuffer();
@@ -784,10 +780,6 @@ public class AlignmentSorter
for (int i = 0; i < seqs.length; i++)
{
SequenceFeature[] sf = seqs[i].getSequenceFeatures();
- if (sf == null && seqs[i].getDatasetSequence() != null)
- {
- sf = seqs[i].getDatasetSequence().getSequenceFeatures();
- }
if (sf == null)
{
sf = new SequenceFeature[0];
@@ -828,7 +820,7 @@ public class AlignmentSorter
else
{
// or, also take a look at the scores if necessary.
- if (!ignoreScore && sf[f].getScore() != Float.NaN)
+ if (!ignoreScore && !Float.isNaN(sf[f].getScore()))
{
if (seqScores[i] == 0)
{
@@ -936,7 +928,7 @@ public class AlignmentSorter
{
if (method == FEATURE_LABEL)
{
- throw new Error("Not yet implemented.");
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
}
if (lastSortByFeatureScore == null