1 package jalview.analysis;
3 import static org.junit.Assert.assertTrue;
7 import jalview.datamodel.Alignment;
8 import jalview.datamodel.AlignmentI;
9 import jalview.datamodel.Sequence;
10 import jalview.datamodel.SequenceI;
11 import jalview.io.AppletFormatAdapter;
13 public class AlignmentUtilsTests
15 public static Sequence ts=new Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");
17 public void testExpandFlanks()
19 AlignmentI al = new Alignment(new Sequence[] {});
20 for (int i=4;i<14;i+=3)
22 SequenceI s1=ts.deriveSequence().getSubSequence(i, i+7);
25 System.out.println(new AppletFormatAdapter().formatSequences("Clustal", al, true));
26 for (int flnk=-1;flnk<25; flnk++)
29 System.out.println("\nFlank size: "+flnk);
30 System.out.println(new AppletFormatAdapter().formatSequences("Clustal", exp=AlignmentUtils.expandContext(al, flnk), true));
32 for (SequenceI sq:exp.getSequences())
34 String ung = sq.getSequenceAsString().replaceAll("-+", "");
35 assertTrue("Flanking sequence not the same as original dataset sequence.\n"+ung+"\n"+sq.getDatasetSequence().getSequenceAsString(),ung.equalsIgnoreCase(sq.getDatasetSequence().getSequenceAsString()));