2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ext.jmol;
23 import jalview.datamodel.Alignment;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.Sequence;
26 import jalview.datamodel.SequenceI;
27 import jalview.gui.AlignFrame;
28 import jalview.gui.SequenceRenderer;
29 import jalview.structure.StructureMappingcommandSet;
30 import jalview.structure.StructureSelectionManager;
32 import org.testng.annotations.Test;
34 public class JmolCommandsTest
37 @Test(groups = { "Functional" })
38 public void testGetColourBySequenceCommand_noFeatures()
40 SequenceI seq1 = new Sequence("seq1", "MHRSQTRALK");
41 SequenceI seq2 = new Sequence("seq2", "MRLEITQSGD");
42 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
43 AlignFrame af = new AlignFrame(al, 800, 500);
44 SequenceRenderer sr = new SequenceRenderer(af.getViewport());
45 SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
46 String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
47 StructureSelectionManager ssm = new StructureSelectionManager();
49 // need some mappings!
51 StructureMappingcommandSet[] commands = JmolCommands
52 .getColourBySequenceCommand(ssm, files, seqs, sr, null, al);