X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=ad8dd4ab539b6f2d5373c7ebf261e1aed3d5f53d;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=3233cb1e76bedf6ece989b32f6e97d0b44e682a3;hpb=b13f521553582ef2fbfd7815ae25e23284babdea;p=jalview.git diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java index 3233cb1..ad8dd4a 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 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -33,7 +33,6 @@ import jalview.util.QuickSort; import java.util.ArrayList; import java.util.List; -import java.util.Vector; /** * Routines for manipulating the order of a multiple sequence alignment TODO: @@ -130,7 +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); } @@ -179,7 +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())); } @@ -295,7 +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) { @@ -313,11 +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; } @@ -325,22 +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]); } } @@ -356,28 +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 @@ -389,6 +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()]; @@ -431,7 +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) { @@ -462,11 +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()); @@ -504,7 +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) @@ -532,22 +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"); @@ -566,8 +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) { @@ -587,7 +571,7 @@ public class AlignmentSorter // seqset.size()==0 || // seqset.contains(tmp))) { - tmp.addElement(node.element()); + tmp.add((SequenceI) node.element()); } } } @@ -734,9 +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, @@ -767,7 +751,9 @@ 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(); @@ -835,7 +821,7 @@ 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) { @@ -943,7 +929,8 @@ public class AlignmentSorter { 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