From be4614014839c44c1fafb3b84a71824625e5fa90 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Wed, 24 May 2017 09:17:07 +0100 Subject: [PATCH] JAL-2505 delete and readd modified feature after Cut or Paste --- src/jalview/commands/EditCommand.java | 54 ++++++++++++++++++++++----------- 1 file changed, 36 insertions(+), 18 deletions(-) diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java index 21ff841..98ac2d5 100644 --- a/src/jalview/commands/EditCommand.java +++ b/src/jalview/commands/EditCommand.java @@ -1122,51 +1122,69 @@ public class EditCommand implements CommandI return; } - SequenceFeature[] sf = sequence.getSequenceFeatures(); + List sf = sequence.getFeatures() + .getPositionalFeatures(); - if (sf == null) + if (sf.isEmpty()) { return; } - SequenceFeature[] oldsf = new SequenceFeature[sf.length]; + SequenceFeature[] oldsf = new SequenceFeature[sf.size()]; int cSize = j - i; - for (int s = 0; s < sf.length; s++) + int s = 0; + for (SequenceFeature feature : sf) { - SequenceFeature copy = new SequenceFeature(sf[s]); + SequenceFeature copy = new SequenceFeature(feature); - oldsf[s] = copy; + oldsf[s++] = copy; - if (sf[s].getEnd() < i) + if (feature.getEnd() < i) { continue; } - if (sf[s].getBegin() > j) + if (feature.getBegin() > j) { - sf[s].setBegin(copy.getBegin() - cSize); - sf[s].setEnd(copy.getEnd() - cSize); + int newBegin = copy.getBegin() - cSize; + int newEnd = copy.getEnd() - cSize; + SequenceFeature newSf = new SequenceFeature(feature, newBegin, + newEnd, feature.getFeatureGroup()); + sequence.deleteFeature(feature); + sequence.addSequenceFeature(newSf); + // feature.setBegin(newBegin); + // feature.setEnd(newEnd); continue; } - if (sf[s].getBegin() >= i) + int newBegin = feature.getBegin(); + int newEnd = feature.getEnd(); + if (newBegin >= i) { - sf[s].setBegin(i); + newBegin = i; + // feature.setBegin(i); } - if (sf[s].getEnd() < j) + if (newEnd < j) { - sf[s].setEnd(j - 1); + newEnd = j - 1; + // feature.setEnd(j - 1); } + newEnd = newEnd - cSize; + // feature.setEnd(feature.getEnd() - (cSize)); - sf[s].setEnd(sf[s].getEnd() - (cSize)); - - if (sf[s].getBegin() > sf[s].getEnd()) + sequence.deleteFeature(feature); + if (newEnd >= newBegin) { - sequence.deleteFeature(sf[s]); + sequence.addSequenceFeature(new SequenceFeature(feature, newBegin, + newEnd, feature.getFeatureGroup())); } + // if (feature.getBegin() > feature.getEnd()) + // { + // sequence.deleteFeature(feature); + // } } if (command.editedFeatures == null) -- 1.7.10.2