+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program is free software; you can redistribute it and/or\r
+* modify it under the terms of the GNU General Public License\r
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+*/\r
+\r
package jalview.analysis;\r
\r
import jalview.datamodel.*;\r
}\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