1 package jalview.ext.jmol;
3 import jalview.datamodel.Alignment;
4 import jalview.datamodel.AlignmentI;
5 import jalview.datamodel.Sequence;
6 import jalview.datamodel.SequenceI;
7 import jalview.gui.AlignFrame;
8 import jalview.gui.SequenceRenderer;
9 import jalview.structure.StructureMappingcommandSet;
10 import jalview.structure.StructureSelectionManager;
12 import org.testng.annotations.Test;
14 public class JmolCommandsTest
17 @Test(groups = { "Functional" })
18 public void testGetColourBySequenceCommand_noFeatures()
20 SequenceI seq1 = new Sequence("seq1", "MHRSQTRALK");
21 SequenceI seq2 = new Sequence("seq2", "MRLEITQSGD");
22 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
23 AlignFrame af = new AlignFrame(al, 800, 500);
24 SequenceRenderer sr = new SequenceRenderer(af.getViewport());
25 SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
26 String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
27 StructureSelectionManager ssm = new StructureSelectionManager();
29 // need some mappings!
31 StructureMappingcommandSet[] commands = JmolCommands
32 .getColourBySequenceCommand(ssm, files, seqs, sr, null, al);