/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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:
seqs[i] = align.getSequenceAt(i);
}
- QuickSort.sort(scores, 0, scores.length - 1, seqs);
+ QuickSort.sortFloat(scores, seqs);
setReverseOrder(align, seqs);
}
}
// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
- for (int i = 0; i < len; i++)
+ List<SequenceI> 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]);
+ }
}
}
* @param tmp
* sequences as a vector
*/
- private static void setOrder(AlignmentI align, Vector tmp)
+ private static void setOrder(AlignmentI align, List<SequenceI> tmp)
{
setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
}
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<SequenceI> algn;
+ synchronized (algn = align.getSequences())
{
- if (algn.contains(seqs[i]))
+ List<SequenceI> tmp = new ArrayList<SequenceI>();
+
+ 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));
+ }
}
-
}
/**
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);
+ QuickSort.sortFloat(length, seqs);
if (sortLengthAscending)
{
{
// MAINTAINS ORIGNAL SEQUENCE ORDER,
// ORDERS BY GROUP SIZE
- Vector groups = new Vector();
+ List<SequenceGroup> groups = new ArrayList<SequenceGroup>();
if (groups.hashCode() != lastGroupHash)
{
// 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);
+ SequenceGroup sg2 = groups.get(j);
if (sg.getSize() > sg2.getSize())
{
- groups.insertElementAt(sg, j);
+ groups.add(j, sg);
break;
}
if (!groups.contains(sg))
{
- groups.addElement(sg);
+ groups.add(sg);
}
}
// NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
// /////////////////////////////////////////////
- Vector seqs = new Vector();
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
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]);
}
}
}
/**
- * Converts Vector to array. java 1.18 does not have Vector.toArray()
+ * Select sequences in order from tmp that is present in mask, and any
+ * remaining sequences in mask not in tmp
*
* @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;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @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<SequenceI> tmp,
+ List<SequenceI> mask)
{
- Vector seqs = new Vector();
+ // or?
+ // tmp2 = tmp.retainAll(mask);
+ // return tmp2.addAll(mask.removeAll(tmp2))
+
+ ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
int i, idx;
boolean[] tmask = new boolean[mask.size()];
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);
}
}
{
if (tmask[i])
{
- seqs.addElement(mask.elementAt(i));
+ seqs.add(mask.get(i));
}
}
- return vectorToArray(seqs);
+ return seqs.toArray(new SequenceI[seqs.size()]);
}
/**
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<SequenceI> tmp = order.getOrder();
if (lastOrder == order)
{
*
* @return DOCUMENT ME!
*/
- private static Vector getOrderByTree(AlignmentI align, NJTree tree)
+ private static List<SequenceI> getOrderByTree(AlignmentI align,
+ NJTree tree)
{
int nSeq = align.getHeight();
- Vector tmp = new Vector();
+ List<SequenceI> tmp = new ArrayList<SequenceI>();
tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
// 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");
}
}
*/
public static void sortByTree(AlignmentI align, NJTree tree)
{
- Vector tmp = getOrderByTree(align, tree);
+ List<SequenceI> tmp = getOrderByTree(align, tree);
// tmp should properly permute align with tree.
if (lastTree != tree)
*
* @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<SequenceI> 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");
*
* @return DOCUMENT ME!
*/
- private static Vector _sortByTree(SequenceNode node, Vector tmp,
- Vector seqset)
+ private static List<SequenceI> _sortByTree(SequenceNode node,
+ List<SequenceI> tmp,
+ List<SequenceI> seqset)
{
if (node == null)
{
{
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.add((SequenceI) node.element());
}
}
}
.floatValue();
}
- jalview.util.QuickSort.sort(ids, alignment);
+ jalview.util.QuickSort.sortFloat(ids, alignment);
}
/**
}
}
- jalview.util.QuickSort.sort(scores, seqs);
+ jalview.util.QuickSort.sortDouble(scores, seqs);
if (lastSortByScore != scoreLabel)
{
lastSortByScore = scoreLabel;
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();
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];
// 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
}
}
- jalview.util.QuickSort.sort(scores, seqs);
+ jalview.util.QuickSort.sortDouble(scores, seqs);
}
else if (method == FEATURE_DENSITY)
{
// System.err.println("Sorting on Density: seq "+seqs[i].getName()+
// " Feats: "+nf+" Score : "+scores[i]);
}
- jalview.util.QuickSort.sort(scores, seqs);
+ jalview.util.QuickSort.sortDouble(scores, seqs);
}
else
{
if (method == FEATURE_LABEL)
{
- throw new Error("Not yet implemented.");
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
}
if (lastSortByFeatureScore == null
git://source.jalview.org / jalview.git / blobdiff