findKmers and fetchSequenceFeatures removed

diff --git a/src/jalview/analysis/AlignmentUtil.java b/src/jalview/analysis/AlignmentUtil.java
index 24d23b2..2192866 100755 (executable)
--- a/src/jalview/analysis/AlignmentUtil.java
+++ b/src/jalview/analysis/AlignmentUtil.java
@@ -194,39 +194,5 @@ public class AlignmentUtil {
        }\r
     }\r
 \r
-    public static Hashtable findKmers(SequenceI seq, int start, int end, Vector kmers) {\r
-\r
-         Hashtable pos = new Hashtable();\r
-\r
-         for (int j = 0; j < kmers.size(); j++) {\r
-\r
-           String   kmer    = ((Sequence)kmers.elementAt(j)).getSequence();\r
-           Sequence kmerseq = (Sequence)kmers.elementAt(j);\r
-\r
-           if (end < seq.getLength()) {\r
-\r
-              String str = seq.getSequence(start,end);\r
-\r
-              int i = 0;\r
-\r
-              while (str.indexOf(kmer,i) != -1) {\r
-\r
-              //               System.out.println("STring " + str + " " + i);\r
-                  int coord = str.indexOf(kmer,i);\r
-\r
-                  pos.put(new Integer(coord),new Integer(kmerseq.getLength()));\r
-\r
-                  i  = coord + 1;\r
-\r
-              }\r
-          }\r
-         }\r
-         return pos;\r
-    }\r
-\r
-    public static void fetchSequenceFeatures(AlignmentI al, jalview.gui.AlignmentPanel ap)\r
-    {\r
-      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al, ap);\r
-    }\r
 \r
 }\r