X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=007d538d55659bcf9f4f8f4bdb07d46ad73eb762;hb=0b1c761dfaa8242f122cf868e8897a06ec6eb727;hp=125ca15cd3dbb2b3af0cb4889f4c3f64fab3e0cb;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java index 125ca15..007d538 100755 --- a/src/jalview/analysis/AlignmentSorter.java +++ b/src/jalview/analysis/AlignmentSorter.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * 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. * @@ -20,10 +20,19 @@ */ 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: @@ -120,7 +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); } @@ -169,7 +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())); } @@ -285,7 +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) { @@ -303,11 +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; } @@ -315,22 +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]); } } @@ -346,28 +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 @@ -379,6 +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()]; @@ -421,7 +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) { @@ -452,11 +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()); @@ -494,7 +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) @@ -522,22 +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"); @@ -556,8 +550,8 @@ public class AlignmentSorter * * @return DOCUMENT ME! */ - private static Vector _sortByTree(SequenceNode node, Vector tmp, - List seqset) + private static List _sortByTree(SequenceNode node, + List tmp, List seqset) { if (node == null) { @@ -577,7 +571,7 @@ public class AlignmentSorter // seqset.size()==0 || // seqset.contains(tmp))) { - tmp.addElement(node.element()); + tmp.add((SequenceI) node.element()); } } } @@ -724,9 +718,9 @@ public class AlignmentSorter public static void sortByFeature(String featureLabel, String groupLabel, int start, int stop, AlignmentI alignment, String method) { - sortByFeature(featureLabel == null ? null : new String[] - { featureLabel }, groupLabel == null ? null : new String[] - { groupLabel }, start, stop, alignment, method); + sortByFeature(featureLabel == null ? null + : new String[] { featureLabel }, groupLabel == null ? null + : new String[] { groupLabel }, start, stop, alignment, method); } private static boolean containsIgnoreCase(final String lab, @@ -757,8 +751,11 @@ public class AlignmentSorter if (method != FEATURE_SCORE && method != FEATURE_LABEL && method != FEATURE_DENSITY) { - throw new Error(MessageManager.getString("error.implementation_error_sortbyfeature")); + throw new Error( + MessageManager + .getString("error.implementation_error_sortbyfeature")); } + boolean ignoreScore = method != FEATURE_SCORE; StringBuffer scoreLabel = new StringBuffer(); scoreLabel.append(start + stop + method); @@ -773,6 +770,21 @@ public class AlignmentSorter { scoreLabel.append(groupLabels[i] == null ? "null" : groupLabels[i]); } + + /* + * if resorting the same feature, toggle sort order + */ + if (lastSortByFeatureScore == null + || !scoreLabel.toString().equals(lastSortByFeatureScore)) + { + sortByFeatureScoreAscending = true; + } + else + { + sortByFeatureScoreAscending = !sortByFeatureScoreAscending; + } + lastSortByFeatureScore = scoreLabel.toString(); + SequenceI[] seqs = alignment.getSequencesArray(); boolean[] hasScore = new boolean[seqs.length]; // per sequence score @@ -785,10 +797,6 @@ 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]; @@ -829,7 +837,7 @@ 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) { @@ -863,7 +871,7 @@ public class AlignmentSorter labs[l] = (fs[l].getDescription() != null ? fs[l] .getDescription() : fs[l].getType()); } - jalview.util.QuickSort.sort(labs, ((Object[]) feats[i])); + QuickSort.sort(labs, ((Object[]) feats[i])); } } if (hasScore[i]) @@ -906,58 +914,38 @@ public class AlignmentSorter } else { - int nf = (feats[i] == null) ? 0 - : ((SequenceFeature[]) feats[i]).length; - // System.err.println("Sorting on Score: seq "+seqs[i].getName()+ - // " Feats: "+nf+" Score : "+scores[i]); + // int nf = (feats[i] == null) ? 0 + // : ((SequenceFeature[]) feats[i]).length; + // // System.err.println("Sorting on Score: seq " + + // seqs[i].getName() + // + " Feats: " + nf + " Score : " + scores[i]); } } } - - jalview.util.QuickSort.sort(scores, seqs); + QuickSort.sortByDouble(scores, seqs, sortByFeatureScoreAscending); } else if (method == FEATURE_DENSITY) { - - // break ties between equivalent numbers for adjacent sequences by adding - // 1/Nseq*i on the original order - double fr = 0.9 / (1.0 * seqs.length); for (int i = 0; i < seqs.length; i++) { - double nf; - scores[i] = (0.05 + fr * i) - + (nf = ((feats[i] == null) ? 0.0 - : 1.0 * ((SequenceFeature[]) feats[i]).length)); + int featureCount = feats[i] == null ? 0 + : ((SequenceFeature[]) feats[i]).length; + scores[i] = featureCount; // System.err.println("Sorting on Density: seq "+seqs[i].getName()+ - // " Feats: "+nf+" Score : "+scores[i]); + // " Feats: "+featureCount+" Score : "+scores[i]); } - jalview.util.QuickSort.sort(scores, seqs); + QuickSort.sortByDouble(scores, seqs, sortByFeatureScoreAscending); } else { if (method == FEATURE_LABEL) { - throw new Error(MessageManager.getString("error.not_yet_implemented")); + throw new Error( + MessageManager.getString("error.not_yet_implemented")); } } - if (lastSortByFeatureScore == null - || !scoreLabel.toString().equals(lastSortByFeatureScore)) - { - sortByFeatureScoreAscending = true; - } - else - { - sortByFeatureScoreAscending = !sortByFeatureScoreAscending; - } - if (sortByFeatureScoreAscending) - { - setOrder(alignment, seqs); - } - else - { - setReverseOrder(alignment, seqs); - } - lastSortByFeatureScore = scoreLabel.toString(); + + setOrder(alignment, seqs); } }