From 6f62124bf8277dd898f43f75e81bbde027fb2ebc Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Tue, 3 May 2005 12:39:06 +0000 Subject: [PATCH] findKmers and fetchSequenceFeatures removed --- src/jalview/analysis/AlignmentUtil.java | 34 ------------------------------- 1 file changed, 34 deletions(-) diff --git a/src/jalview/analysis/AlignmentUtil.java b/src/jalview/analysis/AlignmentUtil.java index 24d23b2..2192866 100755 --- a/src/jalview/analysis/AlignmentUtil.java +++ b/src/jalview/analysis/AlignmentUtil.java @@ -194,39 +194,5 @@ public class AlignmentUtil { } } - public static Hashtable findKmers(SequenceI seq, int start, int end, Vector kmers) { - - Hashtable pos = new Hashtable(); - - for (int j = 0; j < kmers.size(); j++) { - - String kmer = ((Sequence)kmers.elementAt(j)).getSequence(); - Sequence kmerseq = (Sequence)kmers.elementAt(j); - - if (end < seq.getLength()) { - - String str = seq.getSequence(start,end); - - int i = 0; - - while (str.indexOf(kmer,i) != -1) { - - // System.out.println("STring " + str + " " + i); - int coord = str.indexOf(kmer,i); - - pos.put(new Integer(coord),new Integer(kmerseq.getLength())); - - i = coord + 1; - - } - } - } - return pos; - } - - public static void fetchSequenceFeatures(AlignmentI al, jalview.gui.AlignmentPanel ap) - { - SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al, ap); - } } -- 1.7.10.2