X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=a993e26c772d3a885f097b5a5eb7d155bfd3ad86;hb=d197025c26793dc26ef790633ee6ab394c8eff85;hp=39af6490320efa7072e49f8fc5966c3087cb4565;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 39af649..a993e26 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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;
@@ -146,11 +149,15 @@ public class AlignmentSorter
}
// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
- for (int i = 0; i < len; i++)
+ List asq;
+ synchronized (asq = align.getSequences())
{
- // SequenceI tmp = seqs[i];
- align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
- align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
+ for (int i = 0; i < len; i++)
+ {
+ // SequenceI tmp = seqs[i];
+ asq.set(i, seqs[nSeq - i - 1]);
+ asq.set(nSeq - i - 1, seqs[i]);
+ }
}
}
@@ -178,24 +185,26 @@ public class AlignmentSorter
public static void setOrder(AlignmentI align, SequenceI[] seqs)
{
// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
- Vector algn = align.getSequences();
- Vector tmp = new Vector();
-
- for (int i = 0; i < seqs.length; i++)
+ List algn;
+ synchronized (algn = align.getSequences())
{
- if (algn.contains(seqs[i]))
+ List tmp = new ArrayList();
+
+ for (int i = 0; i < seqs.length; i++)
{
- tmp.addElement(seqs[i]);
+ if (algn.contains(seqs[i]))
+ {
+ tmp.add(seqs[i]);
+ }
}
- }
- algn.removeAllElements();
- // User may have hidden seqs, then clicked undo or redo
- for (int i = 0; i < tmp.size(); i++)
- {
- algn.addElement(tmp.elementAt(i));
+ algn.clear();
+ // User may have hidden seqs, then clicked undo or redo
+ for (int i = 0; i < tmp.size(); i++)
+ {
+ algn.add(tmp.get(i));
+ }
}
-
}
/**
@@ -247,7 +256,7 @@ 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);
@@ -290,10 +299,8 @@ public class AlignmentSorter
// SORTS GROUPS BY SIZE
// ////////////////////
- for (int i = 0; i < align.getGroups().size(); i++)
+ for (SequenceGroup sg : align.getGroups())
{
- SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
-
for (int j = 0; j < groups.size(); j++)
{
SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
@@ -359,18 +366,20 @@ public class AlignmentSorter
}
/**
- * DOCUMENT ME!
+ * Select sequences in order from tmp that is present in mask, and any
+ * remaining seqeunces in mask not in tmp
*
* @param tmp
- * DOCUMENT ME!
+ * thread safe collection of sequences
* @param mask
- * DOCUMENT ME!
+ * thread safe collection of sequences
*
- * @return DOCUMENT ME!
+ * @return intersect(tmp,mask)+intersect(complement(tmp),mask)
*/
- private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
+ private static SequenceI[] vectorSubsetToArray(List tmp,
+ List mask)
{
- Vector seqs = new Vector();
+ ArrayList seqs = new ArrayList();
int i, idx;
boolean[] tmask = new boolean[mask.size()];
@@ -381,12 +390,12 @@ public class AlignmentSorter
for (i = 0; i < tmp.size(); i++)
{
- Object sq = tmp.elementAt(i);
+ SequenceI sq = tmp.get(i);
idx = mask.indexOf(sq);
if (idx > -1 && tmask[idx])
{
tmask[idx] = false;
- seqs.addElement(sq);
+ seqs.add(sq);
}
}
@@ -394,11 +403,11 @@ public class AlignmentSorter
{
if (tmask[i])
{
- seqs.addElement(mask.elementAt(i));
+ seqs.add(mask.get(i));
}
}
- return vectorToArray(seqs);
+ return seqs.toArray(new SequenceI[seqs.size()]);
}
/**
@@ -456,15 +465,19 @@ public class AlignmentSorter
// TODO: JBPNote - decide if this is always an error
// (eg. not when a tree is associated to another alignment which has more
// sequences)
- if (tmp.size() < nSeq)
+ if (tmp.size() != nSeq)
{
addStrays(align, tmp);
}
if (tmp.size() != nSeq)
{
- System.err.println("ERROR: tmp.size()=" + tmp.size() + " != nseq="
- + nSeq + " in getOrderByTree");
+ System.err
+ .println("WARNING: tmp.size()="
+ + tmp.size()
+ + " != nseq="
+ + nSeq
+ + " in getOrderByTree - tree contains sequences not in alignment");
}
}
@@ -544,7 +557,7 @@ public class AlignmentSorter
* @return DOCUMENT ME!
*/
private static Vector _sortByTree(SequenceNode node, Vector tmp,
- Vector seqset)
+ List seqset)
{
if (node == null)
{
@@ -560,9 +573,11 @@ public class AlignmentSorter
{
if (node.element() instanceof SequenceI)
{
- if (!tmp.contains(node.element()))
+ if (!tmp.contains(node.element())) // && (seqset==null ||
+ // seqset.size()==0 ||
+ // seqset.contains(tmp)))
{
- tmp.addElement((SequenceI) node.element());
+ tmp.addElement(node.element());
}
}
}
@@ -798,9 +813,8 @@ public class AlignmentSorter
// filter for selection criteria
if (
// ignore features outwith alignment start-stop positions.
- (sf[f].end < sstart || sf[f].begin > sstop)
- ||
- // or ignore based on selection criteria
+ (sf[f].end < sstart || sf[f].begin > sstop) ||
+ // or ignore based on selection criteria
(featureLabels != null && !AlignmentSorter
.containsIgnoreCase(sf[f].type, featureLabels))
|| (groupLabels != null