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package jalview.ext.jmol; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.Annotation; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.SequenceI; |
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import jalview.io.DataSourceType; |
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import jalview.io.FileParse; |
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import jalview.io.StructureFile; |
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import jalview.schemes.ResidueProperties; |
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import jalview.util.Format; |
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import jalview.util.MessageManager; |
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import java.io.IOException; |
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import java.util.ArrayList; |
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import java.util.HashMap; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.Vector; |
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import org.jmol.api.JmolStatusListener; |
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import org.jmol.api.JmolViewer; |
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import org.jmol.c.CBK; |
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import org.jmol.c.STR; |
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import org.jmol.modelset.ModelSet; |
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import org.jmol.viewer.Viewer; |
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import mc_view.Atom; |
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import mc_view.PDBChain; |
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import mc_view.Residue; |
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@author |
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|
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| 62.8% |
Uncovered Elements: 116 (312) |
Complexity: 97 |
Complexity Density: 0.46 |
|
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public class JmolParser extends StructureFile implements JmolStatusListener |
59 |
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{ |
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Viewer viewer = null; |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
62 |
76 |
public JmolParser(boolean immediate, Object inFile,... |
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DataSourceType sourceType) throws IOException |
64 |
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{ |
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|
66 |
76 |
super(immediate, inFile, sourceType); |
67 |
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} |
68 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
69 |
14 |
public JmolParser(Object inFile, DataSourceType sourceType)... |
70 |
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throws IOException |
71 |
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{ |
72 |
14 |
super(inFile, sourceType); |
73 |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
75 |
2 |
public JmolParser(FileParse fp) throws IOException... |
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{ |
77 |
2 |
super(fp); |
78 |
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} |
79 |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
80 |
1 |
public JmolParser()... |
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{ |
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} |
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@see |
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| 81.8% |
Uncovered Elements: 2 (11) |
Complexity: 3 |
Complexity Density: 0.43 |
|
92 |
92 |
@Override... |
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public void parse() throws IOException |
94 |
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{ |
95 |
92 |
setChains(new Vector<PDBChain>()); |
96 |
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Viewer jmolModel = getJmolData(); |
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jmolModel.openReader(getDataName(), getDataName(), getReader()); |
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waitForScript(jmolModel); |
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|
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101 |
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102 |
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103 |
92 |
if (jmolModel.ms.mc > 0) |
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{ |
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106 |
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109 |
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114 |
92 |
setStructureFileType(getDataName().toLowerCase().endsWith(".cif") |
115 |
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? PDBEntry.Type.MMCIF.toString() |
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: "PDB"); |
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118 |
92 |
transformJmolModelToJalview(jmolModel.ms); |
119 |
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} |
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} |
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124 |
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@return |
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| 75% |
Uncovered Elements: 2 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
127 |
92 |
private Viewer getJmolData()... |
128 |
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{ |
129 |
92 |
if (viewer == null) |
130 |
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{ |
131 |
92 |
try |
132 |
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{ |
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134 |
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135 |
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136 |
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137 |
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138 |
92 |
viewer = JalviewJmolBinding.getJmolData(this); |
139 |
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|
140 |
92 |
viewer.setBooleanProperty("defaultStructureDSSP", true); |
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} catch (ClassCastException x) |
142 |
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{ |
143 |
0 |
throw new Error(MessageManager.formatMessage( |
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"error.jmol_version_not_compatible_with_jalview_version", |
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new String[] |
146 |
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{ JmolViewer.getJmolVersion() }), x); |
147 |
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} |
148 |
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} |
149 |
92 |
return viewer; |
150 |
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} |
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| 88.9% |
Uncovered Elements: 5 (45) |
Complexity: 8 |
Complexity Density: 0.23 |
|
152 |
92 |
public void transformJmolModelToJalview(ModelSet ms) throws IOException... |
153 |
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{ |
154 |
92 |
try |
155 |
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{ |
156 |
92 |
String lastID = ""; |
157 |
92 |
List<SequenceI> rna = new ArrayList<SequenceI>(); |
158 |
92 |
List<SequenceI> prot = new ArrayList<SequenceI>(); |
159 |
92 |
PDBChain tmpchain; |
160 |
92 |
String pdbId = (String) ms.getInfo(0, "title"); |
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|
162 |
92 |
if (pdbId == null) |
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{ |
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setId(safeName(getDataName())); |
165 |
1 |
setPDBIdAvailable(false); |
166 |
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} |
167 |
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else |
168 |
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{ |
169 |
91 |
setId(pdbId); |
170 |
91 |
setPDBIdAvailable(true); |
171 |
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} |
172 |
92 |
List<Atom> significantAtoms = convertSignificantAtoms(ms); |
173 |
92 |
for (Atom tmpatom : significantAtoms) |
174 |
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{ |
175 |
19112 |
try |
176 |
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{ |
177 |
19112 |
tmpchain = findChain(tmpatom.chain); |
178 |
18975 |
if (tmpatom.resNumIns.trim().equals(lastID)) |
179 |
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{ |
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|
181 |
1 |
continue; |
182 |
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} |
183 |
18974 |
tmpchain.atoms.addElement(tmpatom); |
184 |
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} catch (Exception e) |
185 |
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{ |
186 |
137 |
tmpchain = new PDBChain(getId(), tmpatom.chain); |
187 |
137 |
getChains().add(tmpchain); |
188 |
137 |
tmpchain.atoms.addElement(tmpatom); |
189 |
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} |
190 |
19111 |
lastID = tmpatom.resNumIns.trim(); |
191 |
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} |
192 |
92 |
if (isParseImmediately()) |
193 |
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{ |
194 |
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|
195 |
92 |
xferSettings(); |
196 |
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} |
197 |
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|
198 |
92 |
makeResidueList(); |
199 |
92 |
makeCaBondList(); |
200 |
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|
201 |
92 |
for (PDBChain chain : getChains()) |
202 |
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{ |
203 |
137 |
SequenceI chainseq = postProcessChain(chain); |
204 |
137 |
if (isRNA(chainseq)) |
205 |
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{ |
206 |
0 |
rna.add(chainseq); |
207 |
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} |
208 |
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else |
209 |
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{ |
210 |
137 |
prot.add(chainseq); |
211 |
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} |
212 |
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|
213 |
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|
214 |
137 |
if (predictSecondaryStructure) |
215 |
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{ |
216 |
125 |
createAnnotation(chainseq, chain, ms.at); |
217 |
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} |
218 |
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} |
219 |
|
} catch (OutOfMemoryError er) |
220 |
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{ |
221 |
0 |
System.out.println( |
222 |
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"OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL"); |
223 |
0 |
throw new IOException(MessageManager |
224 |
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.getString("exception.outofmemory_loading_mmcif_file")); |
225 |
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} |
226 |
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} |
227 |
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|
|
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| 97.1% |
Uncovered Elements: 1 (34) |
Complexity: 7 |
Complexity Density: 0.29 |
|
228 |
92 |
private List<Atom> convertSignificantAtoms(ModelSet ms)... |
229 |
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{ |
230 |
92 |
List<Atom> significantAtoms = new ArrayList<Atom>(); |
231 |
92 |
HashMap<String, org.jmol.modelset.Atom> chainTerMap = new HashMap<String, org.jmol.modelset.Atom>(); |
232 |
92 |
org.jmol.modelset.Atom prevAtom = null; |
233 |
92 |
for (org.jmol.modelset.Atom atom : ms.at) |
234 |
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{ |
235 |
102399 |
if (atom.getAtomName().equalsIgnoreCase("CA") |
236 |
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|| atom.getAtomName().equalsIgnoreCase("P")) |
237 |
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{ |
238 |
19126 |
if (!atomValidated(atom, prevAtom, chainTerMap)) |
239 |
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{ |
240 |
12 |
continue; |
241 |
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} |
242 |
19114 |
Atom curAtom = new Atom(atom.x, atom.y, atom.z); |
243 |
19114 |
curAtom.atomIndex = atom.getIndex(); |
244 |
19114 |
curAtom.chain = atom.getChainIDStr(); |
245 |
19114 |
curAtom.insCode = atom.group.getInsertionCode() == '\000' ? ' ' |
246 |
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: atom.group.getInsertionCode(); |
247 |
19114 |
curAtom.name = atom.getAtomName(); |
248 |
19114 |
curAtom.number = atom.getAtomNumber(); |
249 |
19114 |
curAtom.resName = atom.getGroup3(true); |
250 |
19114 |
curAtom.resNumber = atom.getResno(); |
251 |
19114 |
curAtom.occupancy = ms.occupancies != null |
252 |
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? ms.occupancies[atom.getIndex()] |
253 |
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: Float.valueOf(atom.getOccupancy100()); |
254 |
19114 |
String fmt = new Format("%4i").form(curAtom.resNumber); |
255 |
19114 |
curAtom.resNumIns = (fmt + curAtom.insCode); |
256 |
19114 |
curAtom.tfactor = atom.getBfactor100() / 100f; |
257 |
19114 |
curAtom.type = 0; |
258 |
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|
259 |
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|
260 |
19114 |
if (!significantAtoms.contains(curAtom)) |
261 |
|
{ |
262 |
19112 |
significantAtoms.add(curAtom); |
263 |
|
} |
264 |
19114 |
prevAtom = atom; |
265 |
|
} |
266 |
|
} |
267 |
92 |
return significantAtoms; |
268 |
|
} |
269 |
|
|
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|
| 60% |
Uncovered Elements: 16 (40) |
Complexity: 11 |
Complexity Density: 0.5 |
|
270 |
19126 |
private boolean atomValidated(org.jmol.modelset.Atom curAtom,... |
271 |
|
org.jmol.modelset.Atom prevAtom, |
272 |
|
HashMap<String, org.jmol.modelset.Atom> chainTerMap) |
273 |
|
{ |
274 |
|
|
275 |
|
|
276 |
19126 |
if (chainTerMap == null || prevAtom == null) |
277 |
|
{ |
278 |
92 |
return true; |
279 |
|
} |
280 |
19034 |
String curAtomChId = curAtom.getChainIDStr(); |
281 |
19034 |
String prevAtomChId = prevAtom.getChainIDStr(); |
282 |
|
|
283 |
19034 |
if (!prevAtomChId.equals(curAtomChId)) |
284 |
|
{ |
285 |
|
|
286 |
57 |
if (!chainTerMap.containsKey(prevAtomChId)) |
287 |
|
{ |
288 |
51 |
chainTerMap.put(prevAtomChId, prevAtom); |
289 |
|
} |
290 |
|
|
291 |
|
|
292 |
57 |
if (chainTerMap.containsKey(curAtomChId)) |
293 |
|
{ |
294 |
12 |
if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno()) |
295 |
|
{ |
296 |
0 |
return false; |
297 |
|
} |
298 |
12 |
if ((curAtom.getResno() |
299 |
|
- chainTerMap.get(curAtomChId).getResno()) < 5) |
300 |
|
{ |
301 |
0 |
chainTerMap.put(curAtomChId, curAtom); |
302 |
0 |
return true; |
303 |
|
} |
304 |
12 |
return false; |
305 |
|
} |
306 |
|
} |
307 |
|
|
308 |
18977 |
else if (chainTerMap.containsKey(curAtomChId)) |
309 |
|
{ |
310 |
0 |
if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno()) |
311 |
|
{ |
312 |
0 |
return false; |
313 |
|
} |
314 |
0 |
if ((curAtom.getResno() |
315 |
|
- chainTerMap.get(curAtomChId).getResno()) < 5) |
316 |
|
{ |
317 |
0 |
chainTerMap.put(curAtomChId, curAtom); |
318 |
0 |
return true; |
319 |
|
} |
320 |
0 |
return false; |
321 |
|
} |
322 |
|
|
323 |
19022 |
return !(curAtom.isHetero() |
324 |
|
&& ((curAtom.getResno() - prevAtom.getResno()) > 2)); |
325 |
|
} |
326 |
|
|
|
|
| 84.6% |
Uncovered Elements: 2 (13) |
Complexity: 2 |
Complexity Density: 0.18 |
|
327 |
125 |
private void createAnnotation(SequenceI sequence, PDBChain chain,... |
328 |
|
org.jmol.modelset.Atom[] jmolAtoms) |
329 |
|
{ |
330 |
125 |
char[] secstr = new char[sequence.getLength()]; |
331 |
125 |
char[] secstrcode = new char[sequence.getLength()]; |
332 |
|
|
333 |
|
|
334 |
125 |
if (chain.residues.size() != sequence.getLength()) |
335 |
|
{ |
336 |
0 |
return; |
337 |
|
} |
338 |
125 |
int annotIndex = 0; |
339 |
125 |
for (Residue residue : chain.residues) |
340 |
|
{ |
341 |
19051 |
Atom repAtom = residue.getAtoms().get(0); |
342 |
19051 |
STR proteinStructureSubType = jmolAtoms[repAtom.atomIndex].group |
343 |
|
.getProteinStructureSubType(); |
344 |
19051 |
setSecondaryStructure(proteinStructureSubType, annotIndex, secstr, |
345 |
|
secstrcode); |
346 |
19051 |
++annotIndex; |
347 |
|
} |
348 |
125 |
addSecondaryStructureAnnotation(chain.pdbid, sequence, secstr, |
349 |
|
secstrcode, chain.id, sequence.getStart()); |
350 |
|
} |
351 |
|
|
352 |
|
|
353 |
|
|
354 |
|
|
355 |
|
|
356 |
|
|
357 |
|
@param |
358 |
|
@param |
359 |
|
@param |
360 |
|
@param |
361 |
|
@param |
362 |
|
@param |
363 |
|
@return |
364 |
|
|
|
|
| 96.4% |
Uncovered Elements: 1 (28) |
Complexity: 7 |
Complexity Density: 0.35 |
|
365 |
125 |
protected void addSecondaryStructureAnnotation(String modelTitle,... |
366 |
|
SequenceI sq, char[] secstr, char[] secstrcode, String chainId, |
367 |
|
int firstResNum) |
368 |
|
{ |
369 |
125 |
int length = sq.getLength(); |
370 |
125 |
boolean ssFound = false; |
371 |
125 |
Annotation asecstr[] = new Annotation[length + firstResNum - 1]; |
372 |
19176 |
for (int p = 0; p < length; p++) |
373 |
|
{ |
374 |
19051 |
if (secstr[p] >= 'A' && secstr[p] <= 'z') |
375 |
|
{ |
376 |
7446 |
try |
377 |
|
{ |
378 |
7446 |
asecstr[p] = new Annotation(String.valueOf(secstr[p]), null, |
379 |
|
secstrcode[p], Float.NaN); |
380 |
7446 |
ssFound = true; |
381 |
|
} catch (Exception e) |
382 |
|
{ |
383 |
|
|
384 |
|
} |
385 |
|
} |
386 |
|
} |
387 |
|
|
388 |
125 |
if (ssFound) |
389 |
|
{ |
390 |
119 |
String mt = modelTitle == null ? getDataName() : modelTitle; |
391 |
119 |
mt += chainId; |
392 |
119 |
AlignmentAnnotation ann = new AlignmentAnnotation( |
393 |
|
"Secondary Structure", "Secondary Structure for " + mt, |
394 |
|
asecstr); |
395 |
119 |
ann.belowAlignment = true; |
396 |
119 |
ann.visible = true; |
397 |
119 |
ann.autoCalculated = false; |
398 |
119 |
ann.setCalcId(getClass().getName()); |
399 |
119 |
ann.adjustForAlignment(); |
400 |
119 |
ann.validateRangeAndDisplay(); |
401 |
119 |
annotations.add(ann); |
402 |
119 |
sq.addAlignmentAnnotation(ann); |
403 |
|
} |
404 |
|
} |
405 |
|
|
|
|
| 40% |
Uncovered Elements: 3 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
406 |
92 |
private void waitForScript(Viewer jmd)... |
407 |
|
{ |
408 |
92 |
while (jmd.isScriptExecuting()) |
409 |
|
{ |
410 |
0 |
try |
411 |
|
{ |
412 |
0 |
Thread.sleep(50); |
413 |
|
|
414 |
|
} catch (InterruptedException x) |
415 |
|
{ |
416 |
|
} |
417 |
|
} |
418 |
|
} |
419 |
|
|
420 |
|
|
421 |
|
|
422 |
|
|
423 |
|
|
424 |
|
@param |
425 |
|
@param |
426 |
|
@param |
427 |
|
@param |
428 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (28) |
Complexity: 11 |
Complexity Density: 0.39 |
|
429 |
19057 |
protected void setSecondaryStructure(STR proteinStructureSubType, int pos,... |
430 |
|
char[] secstr, char[] secstrcode) |
431 |
|
{ |
432 |
19057 |
switch (proteinStructureSubType) |
433 |
|
{ |
434 |
449 |
case HELIX310: |
435 |
449 |
secstr[pos] = '3'; |
436 |
449 |
break; |
437 |
1915 |
case HELIX: |
438 |
2247 |
case HELIXALPHA: |
439 |
4162 |
secstr[pos] = 'H'; |
440 |
4162 |
break; |
441 |
1 |
case HELIXPI: |
442 |
1 |
secstr[pos] = 'P'; |
443 |
1 |
break; |
444 |
3287 |
case SHEET: |
445 |
3287 |
secstr[pos] = 'E'; |
446 |
3287 |
break; |
447 |
11158 |
default: |
448 |
11158 |
secstr[pos] = 0; |
449 |
|
} |
450 |
|
|
451 |
19057 |
switch (proteinStructureSubType) |
452 |
|
{ |
453 |
449 |
case HELIX310: |
454 |
2247 |
case HELIXALPHA: |
455 |
1 |
case HELIXPI: |
456 |
1915 |
case HELIX: |
457 |
4612 |
secstrcode[pos] = 'H'; |
458 |
4612 |
break; |
459 |
3287 |
case SHEET: |
460 |
3287 |
secstrcode[pos] = 'E'; |
461 |
3287 |
break; |
462 |
11158 |
default: |
463 |
11158 |
secstrcode[pos] = 0; |
464 |
|
} |
465 |
|
} |
466 |
|
|
467 |
|
|
468 |
|
|
469 |
|
|
470 |
|
|
471 |
|
@param |
472 |
|
@param |
473 |
|
@param |
474 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
475 |
0 |
protected void replaceNonCanonicalResidue(String threeLetterCode,... |
476 |
|
char[] seq, int pos) |
477 |
|
{ |
478 |
0 |
String canonical = ResidueProperties |
479 |
|
.getCanonicalAminoAcid(threeLetterCode); |
480 |
0 |
if (canonical != null && !canonical.equalsIgnoreCase(threeLetterCode)) |
481 |
|
{ |
482 |
0 |
seq[pos] = ResidueProperties.getSingleCharacterCode(canonical); |
483 |
|
} |
484 |
|
} |
485 |
|
|
486 |
|
|
487 |
|
|
488 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
489 |
0 |
@Override... |
490 |
|
public String print(SequenceI[] seqs, boolean jvSuffix) |
491 |
|
{ |
492 |
0 |
return null; |
493 |
|
} |
494 |
|
|
495 |
|
|
496 |
|
|
497 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
498 |
0 |
@Override... |
499 |
|
public void setCallbackFunction(String callbackType, |
500 |
|
String callbackFunction) |
501 |
|
{ |
502 |
|
} |
503 |
|
|
|
|
| 0% |
Uncovered Elements: 31 (31) |
Complexity: 12 |
Complexity Density: 0.52 |
|
504 |
0 |
@Override... |
505 |
|
public void notifyCallback(CBK cbType, Object[] data) |
506 |
|
{ |
507 |
0 |
String strInfo = (data == null || data[1] == null ? null |
508 |
|
: data[1].toString()); |
509 |
0 |
switch (cbType) |
510 |
|
{ |
511 |
0 |
case ECHO: |
512 |
0 |
sendConsoleEcho(strInfo); |
513 |
0 |
break; |
514 |
0 |
case SCRIPT: |
515 |
0 |
notifyScriptTermination((String) data[2], |
516 |
|
((Integer) data[3]).intValue()); |
517 |
0 |
break; |
518 |
0 |
case MEASURE: |
519 |
0 |
String mystatus = (String) data[3]; |
520 |
0 |
if (mystatus.indexOf("Picked") >= 0 |
521 |
|
|| mystatus.indexOf("Sequence") >= 0) |
522 |
|
{ |
523 |
|
|
524 |
0 |
sendConsoleMessage(strInfo); |
525 |
|
} |
526 |
0 |
else if (mystatus.indexOf("Completed") >= 0) |
527 |
|
{ |
528 |
0 |
sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2, |
529 |
|
strInfo.length() - 1)); |
530 |
|
} |
531 |
0 |
break; |
532 |
0 |
case MESSAGE: |
533 |
0 |
sendConsoleMessage(data == null ? null : strInfo); |
534 |
0 |
break; |
535 |
0 |
case PICK: |
536 |
0 |
sendConsoleMessage(strInfo); |
537 |
0 |
break; |
538 |
0 |
default: |
539 |
0 |
break; |
540 |
|
} |
541 |
|
} |
542 |
|
|
543 |
|
String lastConsoleEcho = ""; |
544 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
545 |
0 |
private void sendConsoleEcho(String string)... |
546 |
|
{ |
547 |
0 |
lastConsoleEcho += string; |
548 |
0 |
lastConsoleEcho += "\n"; |
549 |
|
} |
550 |
|
|
551 |
|
String lastConsoleMessage = ""; |
552 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
553 |
0 |
private void sendConsoleMessage(String string)... |
554 |
|
{ |
555 |
0 |
lastConsoleMessage += string; |
556 |
0 |
lastConsoleMessage += "\n"; |
557 |
|
} |
558 |
|
|
559 |
|
int lastScriptTermination = -1; |
560 |
|
|
561 |
|
String lastScriptMessage = ""; |
562 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
563 |
0 |
private void notifyScriptTermination(String string, int intValue)... |
564 |
|
{ |
565 |
0 |
lastScriptMessage += string; |
566 |
0 |
lastScriptMessage += "\n"; |
567 |
0 |
lastScriptTermination = intValue; |
568 |
|
} |
569 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 6 |
Complexity Density: 0.67 |
|
570 |
0 |
@Override... |
571 |
|
public boolean notifyEnabled(CBK callbackPick) |
572 |
|
{ |
573 |
0 |
switch (callbackPick) |
574 |
|
{ |
575 |
0 |
case MESSAGE: |
576 |
0 |
case SCRIPT: |
577 |
0 |
case ECHO: |
578 |
0 |
case LOADSTRUCT: |
579 |
0 |
case ERROR: |
580 |
0 |
return true; |
581 |
0 |
default: |
582 |
0 |
return false; |
583 |
|
} |
584 |
|
} |
585 |
|
|
586 |
|
|
587 |
|
|
588 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
589 |
0 |
@Override... |
590 |
|
public String eval(String strEval) |
591 |
|
{ |
592 |
0 |
return null; |
593 |
|
} |
594 |
|
|
595 |
|
|
596 |
|
|
597 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
598 |
0 |
@Override... |
599 |
|
public float[][] functionXY(String functionName, int x, int y) |
600 |
|
{ |
601 |
0 |
return null; |
602 |
|
} |
603 |
|
|
604 |
|
|
605 |
|
|
606 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
607 |
0 |
@Override... |
608 |
|
public float[][][] functionXYZ(String functionName, int nx, int ny, |
609 |
|
int nz) |
610 |
|
{ |
611 |
0 |
return null; |
612 |
|
} |
613 |
|
|
614 |
|
|
615 |
|
|
616 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
617 |
0 |
@Override... |
618 |
|
public String createImage(String fileName, String imageType, |
619 |
|
Object text_or_bytes, int quality) |
620 |
|
{ |
621 |
0 |
return null; |
622 |
|
} |
623 |
|
|
624 |
|
|
625 |
|
|
626 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
627 |
0 |
@Override... |
628 |
|
public Map<String, Object> getRegistryInfo() |
629 |
|
{ |
630 |
0 |
return null; |
631 |
|
} |
632 |
|
|
633 |
|
|
634 |
|
|
635 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
636 |
0 |
@Override... |
637 |
|
public void showUrl(String url) |
638 |
|
{ |
639 |
|
} |
640 |
|
|
641 |
|
|
642 |
|
|
643 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
644 |
0 |
@Override... |
645 |
|
public int[] resizeInnerPanel(String data) |
646 |
|
{ |
647 |
0 |
return null; |
648 |
|
} |
649 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
650 |
0 |
@Override... |
651 |
|
public Map<String, Object> getJSpecViewProperty(String arg0) |
652 |
|
{ |
653 |
0 |
return null; |
654 |
|
} |
655 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
656 |
0 |
public boolean isPredictSecondaryStructure()... |
657 |
|
{ |
658 |
0 |
return predictSecondaryStructure; |
659 |
|
} |
660 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
661 |
0 |
public void setPredictSecondaryStructure(... |
662 |
|
boolean predictSecondaryStructure) |
663 |
|
{ |
664 |
0 |
this.predictSecondaryStructure = predictSecondaryStructure; |
665 |
|
} |
666 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
667 |
0 |
public boolean isVisibleChainAnnotation()... |
668 |
|
{ |
669 |
0 |
return visibleChainAnnotation; |
670 |
|
} |
671 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
672 |
0 |
public void setVisibleChainAnnotation(boolean visibleChainAnnotation)... |
673 |
|
{ |
674 |
0 |
this.visibleChainAnnotation = visibleChainAnnotation; |
675 |
|
} |
676 |
|
|
677 |
|
} |