From 85a66ca345b3831b9925bc421084db9c2af3054b Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 12 May 2017 14:22:03 +0100 Subject: [PATCH] JAL-2480 renamed java.util.RangeComparator to IntRangeComparator --- src/jalview/ext/ensembl/EnsemblSeqProxy.java | 87 ++++++++--------------- src/jalview/ext/rbvi/chimera/AtomSpecModel.java | 4 +- src/jalview/util/RangeComparator.java | 25 ------- 3 files changed, 32 insertions(+), 84 deletions(-) delete mode 100644 src/jalview/util/RangeComparator.java diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java index 2d0e3fe..dda77d7 100644 --- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java +++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java @@ -30,6 +30,7 @@ import jalview.datamodel.DBRefSource; import jalview.datamodel.Mapping; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.datamodel.features.SequenceFeatures; import jalview.exceptions.JalviewException; import jalview.io.FastaFile; import jalview.io.FileParse; @@ -37,8 +38,8 @@ import jalview.io.gff.SequenceOntologyFactory; import jalview.io.gff.SequenceOntologyI; import jalview.util.Comparison; import jalview.util.DBRefUtils; +import jalview.util.IntRangeComparator; import jalview.util.MapList; -import jalview.util.RangeComparator; import java.io.IOException; import java.net.MalformedURLException; @@ -46,7 +47,6 @@ import java.net.URL; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; -import java.util.Comparator; import java.util.List; /** @@ -536,8 +536,10 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence, String accId, int start) { - SequenceFeature[] sfs = sourceSequence.getSequenceFeatures(); - if (sfs == null) + // SequenceFeature[] sfs = sourceSequence.getSequenceFeatures(); + List sfs = sourceSequence.getFeatures() + .getPositionalFeatures(); + if (sfs.isEmpty()) { return null; } @@ -607,7 +609,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * a final sort is needed since Ensembl returns CDS sorted within source * (havana / ensembl_havana) */ - Collections.sort(regions, new RangeComparator(direction == 1)); + Collections.sort(regions, direction == 1 ? IntRangeComparator.ASCENDING + : IntRangeComparator.DESCENDING); List to = Arrays.asList(new int[] { start, start + mappedLength - 1 }); @@ -765,8 +768,10 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient return false; } - // long start = System.currentTimeMillis(); - SequenceFeature[] sfs = sourceSequence.getSequenceFeatures(); + long start = System.currentTimeMillis(); + // SequenceFeature[] sfs = sourceSequence.getSequenceFeatures(); + List sfs = sourceSequence.getFeatures() + .getPositionalFeatures(); MapList mapping = getGenomicRangesFromFeatures(sourceSequence, accessionId, targetSequence.getStart()); if (mapping == null) @@ -776,10 +781,10 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient boolean result = transferFeatures(sfs, targetSequence, mapping, accessionId); - // System.out.println("transferFeatures (" + (sfs.length) + " --> " - // + targetSequence.getSequenceFeatures().length + ") to " - // + targetSequence.getName() - // + " took " + (System.currentTimeMillis() - start) + "ms"); + System.out.println("transferFeatures (" + (sfs.size()) + " --> " + + targetSequence.getFeatures().getFeatureCount(true) + ") to " + + targetSequence.getName() + " took " + + (System.currentTimeMillis() - start) + "ms"); return result; } @@ -788,13 +793,13 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * converted using the mapping. Features which do not overlap are ignored. * Features whose parent is not the specified identifier are also ignored. * - * @param features + * @param sfs * @param targetSequence * @param mapping * @param parentId * @return */ - protected boolean transferFeatures(SequenceFeature[] features, + protected boolean transferFeatures(List sfs, SequenceI targetSequence, MapList mapping, String parentId) { final boolean forwardStrand = mapping.isFromForwardStrand(); @@ -804,10 +809,10 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * position descending if reverse strand) so as to add them in * 'forwards' order to the target sequence */ - sortFeatures(features, forwardStrand); + SequenceFeatures.sortFeatures(sfs, forwardStrand); boolean transferred = false; - for (SequenceFeature sf : features) + for (SequenceFeature sf : sfs) { if (retainFeature(sf, parentId)) { @@ -819,33 +824,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient } /** - * Sort features by start position ascending (if on forward strand), or end - * position descending (if on reverse strand) - * - * @param features - * @param forwardStrand - */ - protected static void sortFeatures(SequenceFeature[] features, - final boolean forwardStrand) - { - Arrays.sort(features, new Comparator() - { - @Override - public int compare(SequenceFeature o1, SequenceFeature o2) - { - if (forwardStrand) - { - return Integer.compare(o1.getBegin(), o2.getBegin()); - } - else - { - return Integer.compare(o2.getEnd(), o1.getEnd()); - } - } - }); - } - - /** * Answers true if the feature type is one we want to keep for the sequence. * Some features are only retrieved in order to identify the sequence range, * and may then be discarded as redundant information (e.g. "CDS" feature for @@ -887,35 +865,30 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient /** * Returns a (possibly empty) list of features on the sequence which have the - * specified sequence ontology type (or a sub-type of it), and the given + * specified sequence ontology term (or a sub-type of it), and the given * identifier as parent * * @param sequence - * @param type + * @param term * @param parentId * @return */ protected List findFeatures(SequenceI sequence, - String type, String parentId) + String term, String parentId) { List result = new ArrayList(); - SequenceFeature[] sfs = sequence.getSequenceFeatures(); - if (sfs != null) + List sfs = sequence.getFeatures() + .getFeaturesByOntology(term); + for (SequenceFeature sf : sfs) { - SequenceOntologyI so = SequenceOntologyFactory.getInstance(); - for (SequenceFeature sf : sfs) + String parent = (String) sf.getValue(PARENT); + if (parent != null && parent.equals(parentId)) { - if (so.isA(sf.getType(), type)) - { - String parent = (String) sf.getValue(PARENT); - if (parent.equals(parentId)) - { - result.add(sf); - } - } + result.add(sf); } } + return result; } diff --git a/src/jalview/ext/rbvi/chimera/AtomSpecModel.java b/src/jalview/ext/rbvi/chimera/AtomSpecModel.java index d62cc3c..f3c9c1e 100644 --- a/src/jalview/ext/rbvi/chimera/AtomSpecModel.java +++ b/src/jalview/ext/rbvi/chimera/AtomSpecModel.java @@ -1,6 +1,6 @@ package jalview.ext.rbvi.chimera; -import jalview.util.RangeComparator; +import jalview.util.IntRangeComparator; import java.util.ArrayList; import java.util.Collections; @@ -107,7 +107,7 @@ public class AtomSpecModel /* * sort ranges into ascending start position order */ - Collections.sort(rangeList, new RangeComparator(true)); + Collections.sort(rangeList, IntRangeComparator.ASCENDING); int start = rangeList.isEmpty() ? 0 : rangeList.get(0)[0]; int end = rangeList.isEmpty() ? 0 : rangeList.get(0)[1]; diff --git a/src/jalview/util/RangeComparator.java b/src/jalview/util/RangeComparator.java deleted file mode 100644 index f911a9b..0000000 --- a/src/jalview/util/RangeComparator.java +++ /dev/null @@ -1,25 +0,0 @@ -package jalview.util; - -import java.util.Comparator; - -/** - * A comparator to order [from, to] ranges into ascending or descending order of - * their start position - */ -public class RangeComparator implements Comparator -{ - boolean forwards; - - public RangeComparator(boolean forward) - { - forwards = forward; - } - - @Override - public int compare(int[] o1, int[] o2) - { - int compared = Integer.compare(o1[0], o2[0]); - return forwards ? compared : -compared; - } - -} \ No newline at end of file -- 1.7.10.2