From: Jim Procter Date: Fri, 7 Jun 2013 12:31:37 +0000 (+0100) Subject: JAL-1309 fix broken partition computation for adding in ungrouped sequences as final... X-Git-Tag: Jalview_2_9~248^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=85aca696b1e649b3a3f91bde9c542de7d026d52d;p=jalview.git JAL-1309 fix broken partition computation for adding in ungrouped sequences as final group --- diff --git a/src/jalview/ws/rest/params/SeqGroupIndexVector.java b/src/jalview/ws/rest/params/SeqGroupIndexVector.java index 766720b..0532035 100644 --- a/src/jalview/ws/rest/params/SeqGroupIndexVector.java +++ b/src/jalview/ws/rest/params/SeqGroupIndexVector.java @@ -88,7 +88,7 @@ public class SeqGroupIndexVector extends InputType implements // assume that alignment is properly ordered so groups form consecutive // blocks ArrayList gl = new ArrayList(); - int p = 0; + int p = 0,lowest=al.getHeight(), highest=0; List sgs; synchronized (sgs = al.getGroups()) { @@ -105,6 +105,14 @@ public class SeqGroupIndexVector extends InputType implements for (SequenceI sq : sg.getSequencesInOrder(al)) { p = al.findIndex(sq); + if (lowest>p) + { + lowest=p; + } + if (highest 0) { - int[] tail = gl.get(0); - if (tail[0] > 0) + if (lowest-1>minsize) { - if (1 + tail[0] > minsize) - { - gl.add(0, new int[] - { 0, tail[0] - 1 }); - } - else - { - // lets be intelligent here - if the remaining sequences aren't enough - // to make a final group, then don't make one. - // throw new - // NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences."); - } + gl.add(0, new int[] + { 0, lowest-2}); } - else + if ((al.getHeight()-1-highest)>minsize) { - tail = gl.get(gl.size() - 1); - if (1 + tail[1] < al.getHeight()) - { - if (al.getHeight() - (1 + tail[1]) > minsize) - { - gl.add(new int[] - { tail[1] + 1, al.getHeight() - 1 }); - } - else - { - // lets be intelligent here - if the remaining sequences aren't - // enough to make a final group, then don't make one. - // throw new - // NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences."); - } - } + gl.add(new int[] { highest+1, al.getHeight()-1}); } } else