From a4a68a8b10217312efe5f2ea4746f1cfc9da155d Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 21 Aug 2009 11:12:27 +0000 Subject: [PATCH] new sortbyPID for specific start/end region --- src/jalview/analysis/AlignmentSorter.java | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java index e16e2ab..bb55426 100755 --- a/src/jalview/analysis/AlignmentSorter.java +++ b/src/jalview/analysis/AlignmentSorter.java @@ -79,6 +79,23 @@ public class AlignmentSorter public static void sortByPID(AlignmentI align, SequenceI s, SequenceI[] tosort) { + sortByPID(align,s,tosort,0,-1); + } + /** + * Sort by Percentage Identity w.r.t. s + * + * @param align + * AlignmentI + * @param s + * SequenceI + * @param tosort + * sequences from align that are to be sorted. + * @param start start column (0 for beginning + * @param end + */ + public static void sortByPID(AlignmentI align, SequenceI s, + SequenceI[] tosort,int start, int end) + { int nSeq = align.getHeight(); float[] scores = new float[nSeq]; -- 1.7.10.2