1 package jalview.analysis;
5 import jalview.datamodel.Alignment;
6 import jalview.datamodel.AlignmentI;
7 import jalview.datamodel.Sequence;
8 import jalview.datamodel.SequenceI;
9 import jalview.io.AppletFormatAdapter;
11 public class AlignmentUtilsTests
13 public static Sequence ts=new Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");
15 public void testExpandFlanks()
17 AlignmentI al = new Alignment(new Sequence[] {});
18 for (int i=4;i<14;i+=3)
20 SequenceI s1=ts.deriveSequence().getSubSequence(i, i+7);
23 System.out.println(new AppletFormatAdapter().formatSequences("Clustal", al, true));
24 for (int flnk=-1;flnk<25; flnk++)
26 System.out.println("\nFlank size: "+flnk);
27 System.out.println(new AppletFormatAdapter().formatSequences("Clustal", AlignmentUtils.expandContext(al, flnk), true));