1 |
|
|
2 |
|
|
3 |
|
|
4 |
|
|
5 |
|
|
6 |
|
|
7 |
|
|
8 |
|
|
9 |
|
|
10 |
|
|
11 |
|
|
12 |
|
|
13 |
|
|
14 |
|
|
15 |
|
|
16 |
|
|
17 |
|
|
18 |
|
|
19 |
|
|
20 |
|
|
21 |
|
package jalview.ext.jmol; |
22 |
|
|
23 |
|
import static org.testng.Assert.assertEquals; |
24 |
|
import static org.testng.Assert.assertTrue; |
25 |
|
|
26 |
|
import jalview.datamodel.Alignment; |
27 |
|
import jalview.datamodel.AlignmentI; |
28 |
|
import jalview.datamodel.ColumnSelection; |
29 |
|
import jalview.datamodel.Sequence; |
30 |
|
import jalview.datamodel.SequenceI; |
31 |
|
import jalview.gui.AlignFrame; |
32 |
|
import jalview.gui.JvOptionPane; |
33 |
|
import jalview.gui.SequenceRenderer; |
34 |
|
import jalview.schemes.JalviewColourScheme; |
35 |
|
import jalview.structure.StructureMapping; |
36 |
|
import jalview.structure.StructureMappingcommandSet; |
37 |
|
import jalview.structure.StructureSelectionManager; |
38 |
|
|
39 |
|
import java.util.HashMap; |
40 |
|
|
41 |
|
import org.testng.annotations.BeforeClass; |
42 |
|
import org.testng.annotations.Test; |
43 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (51) |
Complexity: 4 |
Complexity Density: 0.09 |
|
44 |
|
public class JmolCommandsTest |
45 |
|
{ |
46 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
47 |
1 |
@BeforeClass(alwaysRun = true)... |
48 |
|
public void setUpJvOptionPane() |
49 |
|
{ |
50 |
1 |
JvOptionPane.setInteractiveMode(false); |
51 |
1 |
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
52 |
|
} |
53 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
1PASS
|
|
54 |
1 |
@Test(groups = { "Functional" })... |
55 |
|
public void testGetColourBySequenceCommand_noFeatures() |
56 |
|
{ |
57 |
1 |
SequenceI seq1 = new Sequence("seq1", "MHRSQTRALK"); |
58 |
1 |
SequenceI seq2 = new Sequence("seq2", "MRLEITQSGD"); |
59 |
1 |
AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 }); |
60 |
1 |
AlignFrame af = new AlignFrame(al, 800, 500); |
61 |
1 |
SequenceRenderer sr = new SequenceRenderer(af.getViewport()); |
62 |
1 |
SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } }; |
63 |
1 |
String[] files = new String[] { "seq1.pdb", "seq2.pdb" }; |
64 |
1 |
StructureSelectionManager ssm = new StructureSelectionManager(); |
65 |
|
|
66 |
|
|
67 |
|
|
68 |
1 |
StructureMappingcommandSet[] commands = JmolCommands |
69 |
|
.getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel); |
70 |
|
} |
71 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (37) |
Complexity: 2 |
Complexity Density: 0.06 |
1PASS
|
|
72 |
1 |
@Test(groups = { "Functional" })... |
73 |
|
public void testGetColourBySequenceCommands_hiddenColumns() |
74 |
|
{ |
75 |
|
|
76 |
|
|
77 |
|
|
78 |
|
|
79 |
1 |
SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG"); |
80 |
1 |
SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS"); |
81 |
1 |
AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 }); |
82 |
1 |
AlignFrame af = new AlignFrame(al, 800, 500); |
83 |
1 |
af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString()); |
84 |
1 |
ColumnSelection cs = new ColumnSelection(); |
85 |
1 |
cs.addElement(2); |
86 |
1 |
cs.addElement(3); |
87 |
1 |
cs.addElement(4); |
88 |
1 |
af.getViewport().setColumnSelection(cs); |
89 |
1 |
af.hideSelColumns_actionPerformed(null); |
90 |
1 |
SequenceRenderer sr = new SequenceRenderer(af.getViewport()); |
91 |
1 |
SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } }; |
92 |
1 |
String[] files = new String[] { "seq1.pdb", "seq2.pdb" }; |
93 |
1 |
StructureSelectionManager ssm = new StructureSelectionManager(); |
94 |
|
|
95 |
|
|
96 |
|
|
97 |
|
|
98 |
1 |
HashMap<Integer, int[]> map = new HashMap<Integer, int[]>(); |
99 |
11 |
for (int pos = 1; pos <= seq1.getLength(); pos++) |
100 |
|
{ |
101 |
10 |
map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) }); |
102 |
|
} |
103 |
1 |
StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1", |
104 |
|
"A", map, null); |
105 |
1 |
ssm.addStructureMapping(sm1); |
106 |
1 |
StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2", |
107 |
|
"B", map, null); |
108 |
1 |
ssm.addStructureMapping(sm2); |
109 |
|
|
110 |
1 |
StructureMappingcommandSet[] commands = JmolCommands |
111 |
|
.getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel); |
112 |
1 |
assertEquals(commands.length, 2); |
113 |
1 |
assertEquals(commands[0].commands.length, 1); |
114 |
|
|
115 |
1 |
String chainACommand = commands[0].commands[0]; |
116 |
|
|
117 |
1 |
assertTrue(chainACommand |
118 |
|
.contains("select 21:A/1.1;color[130,130,125]")); |
119 |
|
|
120 |
1 |
assertTrue(chainACommand.contains(";select 22:A/1.1;color[96,96,159]")); |
121 |
|
|
122 |
1 |
assertTrue(chainACommand |
123 |
|
.contains(";select 23-25:A/1.1;color[128,128,128]")); |
124 |
|
|
125 |
1 |
assertTrue(chainACommand |
126 |
|
.contains(";select 26-30:A/1.1;color[73,73,182]")); |
127 |
|
|
128 |
1 |
String chainBCommand = commands[1].commands[0]; |
129 |
|
|
130 |
1 |
assertTrue(chainBCommand |
131 |
|
.contains("select 21:B/2.1;color[130,130,125]")); |
132 |
|
|
133 |
1 |
assertTrue(chainBCommand |
134 |
|
.contains(";select 22:B/2.1;color[255,255,0]")); |
135 |
|
|
136 |
1 |
assertTrue(chainBCommand |
137 |
|
.contains(";select 23-25:B/2.1;color[128,128,128]")); |
138 |
|
|
139 |
1 |
assertTrue(chainBCommand |
140 |
|
.contains(";select 26-30:B/2.1;color[73,73,182]")); |
141 |
|
} |
142 |
|
} |