From: gmungoc Date: Mon, 15 May 2017 08:43:05 +0000 (+0100) Subject: JAL-2490 use findFeatures() for efficient feature overlap lookup X-Git-Tag: Release_2_10_3b1~279 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a18b80e001441bc075c209fc1a757a9aa9fea0a5;p=jalview.git JAL-2490 use findFeatures() for efficient feature overlap lookup --- diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java index bc7f212..84036ab 100644 --- a/src/jalview/controller/AlignViewController.java +++ b/src/jalview/controller/AlignViewController.java @@ -238,85 +238,63 @@ public class AlignViewController implements AlignViewControllerI int nseq = 0; for (SequenceI sq : seqs) { - boolean sequenceHasFeature = false; if (sq != null) { - SequenceFeature[] sfs = sq.getSequenceFeatures(); - if (sfs != null) + int ist = sq.findPosition(sqcol.getStartRes()); + int iend = sq.findPosition(sqcol.getEndRes()); // see JAL-2526 + List sfs = sq.getFeatures().findFeatures(ist, + iend, featureType); + if (!sfs.isEmpty()) { - int ist = sq.findIndex(sq.getStart()); - int iend = sq.findIndex(sq.getEnd()); - if (iend < startPosition || ist > endPosition) - { - // sequence not in region - continue; - } - for (SequenceFeature sf : sfs) + nseq++; + } + for (SequenceFeature sf : sfs) + { + // future functionality - featureType == null means mark columns + // containing all displayed features + if (sf != null && (featureType.equals(sf.getType()))) { - // future functionality - featureType == null means mark columns - // containing all displayed features - if (sf != null && (featureType.equals(sf.getType()))) - { - // optimisation - could consider 'spos,apos' like cursor argument - // - findIndex wastes time by starting from first character and - // counting - - int sfStartCol = sq.findIndex(sf.getBegin()); - int sfEndCol = sq.findIndex(sf.getEnd()); - - if (sf.isContactFeature()) - { - /* - * 'contact' feature - check for 'start' or 'end' - * position within the selected region - */ - if (sfStartCol >= startPosition - && sfStartCol <= endPosition) - { - bs.set(sfStartCol - 1); - sequenceHasFeature = true; - } - if (sfEndCol >= startPosition && sfEndCol <= endPosition) - { - bs.set(sfEndCol - 1); - sequenceHasFeature = true; - } - continue; - } + int sfStartCol = sq.findIndex(sf.getBegin()); + int sfEndCol = sq.findIndex(sf.getEnd()); // inefficient - JAL-2526 + if (sf.isContactFeature()) + { /* - * contiguous feature - select feature positions (if any) - * within the selected region + * 'contact' feature - check for 'start' or 'end' + * position within the selected region */ - if (sfStartCol > endPosition || sfEndCol < startPosition) - { - // feature is outside selected region - continue; - } - sequenceHasFeature = true; - if (sfStartCol < startPosition) - { - sfStartCol = startPosition; - } - if (sfStartCol < ist) + if (sfStartCol >= startPosition && sfStartCol <= endPosition) { - sfStartCol = ist; + bs.set(sfStartCol - 1); } - if (sfEndCol > endPosition) + if (sfEndCol >= startPosition && sfEndCol <= endPosition) { - sfEndCol = endPosition; - } - for (; sfStartCol <= sfEndCol; sfStartCol++) - { - bs.set(sfStartCol - 1); // convert to base 0 + bs.set(sfEndCol - 1); } + continue; } - } - } - if (sequenceHasFeature) - { - nseq++; + /* + * contiguous feature - select feature positions (if any) + * within the selected region + */ + if (sfStartCol < startPosition) + { + sfStartCol = startPosition; + } + if (sfStartCol < ist) + { + sfStartCol = ist; + } + if (sfEndCol > endPosition) + { + sfEndCol = endPosition; + } + for (; sfStartCol <= sfEndCol; sfStartCol++) + { + bs.set(sfStartCol - 1); // convert to base 0 + } + } } } }