se[1]) + se[1] = p; + } } - else + if (se != null) { - if (p < se[0]) - se[0] = p; - if (p > se[1]) - se[1] = p; + gl.add(se); } } - if (se != null) - { - gl.add(se); - } } // are there any more sequences ungrouped that should be added as a single // remaining group ? - these might be at the start or the end if (gl.size() > 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 @@ -277,8 +278,11 @@ public class SeqGroupIndexVector extends InputType implements "Separator character between elements of vector", true, ",", sep, Arrays.asList(new String[] { " ", ",", ";", "\t", "|" }), null)); - lst.add(new IntegerParameter("minsize", "Minimum size of partition allowed by service", true, 1, minsize, 1,0)); - lst.add(createMolTypeOption("type", "Sequence type", false, type, molType.MIX)); + lst.add(new IntegerParameter("minsize", + "Minimum size of partition allowed by service", true, 1, + minsize, 1, 0)); + lst.add(createMolTypeOption("type", "Sequence type", false, type, + molType.MIX)); return lst; }