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package ext.edu.ucsf.rbvi.strucviz2; |
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import java.awt.Color; |
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import java.util.ArrayList; |
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import java.util.Collection; |
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import java.util.HashSet; |
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import java.util.List; |
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import java.util.Set; |
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import java.util.TreeMap; |
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import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType; |
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@author |
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| 0% |
Uncovered Elements: 213 (213) |
Complexity: 59 |
Complexity Density: 0.45 |
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public class ChimeraModel implements ChimeraStructuralObject |
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{ |
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private String name; |
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private ModelType type; |
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private int modelNumber; |
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private int subModelNumber; |
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private Color modelColor = null; |
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private Object userData = null; |
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private boolean selected = false; |
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private TreeMap<String, ChimeraChain> chainMap; |
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private HashSet<ChimeraResidue> funcResidues; |
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@param |
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@param |
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@param |
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@param |
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| 0% |
Uncovered Elements: 6 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
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public ChimeraModel(String name, ModelType type, int modelNumber,... |
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int subModelNumber) |
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{ |
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this.name = name; |
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this.type = type; |
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this.modelNumber = modelNumber; |
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this.subModelNumber = subModelNumber; |
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this.chainMap = new TreeMap<String, ChimeraChain>(); |
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this.funcResidues = new HashSet<ChimeraResidue>(); |
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} |
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@param |
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| 0% |
Uncovered Elements: 10 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
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public ChimeraModel(String inputLine)... |
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{ |
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this.name = ChimUtils.parseModelName(inputLine); |
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if (name.startsWith("smiles")) |
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{ |
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this.type = ModelType.SMILES; |
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} |
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else |
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{ |
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this.type = ModelType.PDB_MODEL; |
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} |
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this.modelNumber = ChimUtils.parseModelNumber(inputLine)[0]; |
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this.subModelNumber = ChimUtils.parseModelNumber(inputLine)[1]; |
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this.chainMap = new TreeMap<String, ChimeraChain>(); |
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this.funcResidues = new HashSet<ChimeraResidue>(); |
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} |
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@param |
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| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
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public void addResidue(ChimeraResidue residue)... |
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{ |
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residue.setChimeraModel(this); |
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String chainId = residue.getChainId(); |
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if (chainId != null) |
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{ |
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addResidue(chainId, residue); |
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} |
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else |
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{ |
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addResidue("_", residue); |
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} |
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} |
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@param |
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@param |
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| 0% |
Uncovered Elements: 9 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
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public void addResidue(String chainId, ChimeraResidue residue)... |
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{ |
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ChimeraChain chain = null; |
161 |
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if (!chainMap.containsKey(chainId)) |
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{ |
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chain = new ChimeraChain(this.modelNumber, this.subModelNumber, |
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chainId); |
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chain.setChimeraModel(this); |
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chainMap.put(chainId, chain); |
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} |
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else |
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{ |
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chain = chainMap.get(chainId); |
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} |
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chain.addResidue(residue); |
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} |
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@return |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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@Override... |
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public ChimeraModel getChimeraModel() |
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{ |
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return this; |
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} |
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@return |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public Color getModelColor()... |
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{ |
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return this.modelColor; |
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} |
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@param |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void setModelColor(Color color)... |
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{ |
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this.modelColor = color; |
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} |
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@return |
211 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public String getModelName()... |
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{ |
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return name; |
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} |
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218 |
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@param |
221 |
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222 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void setModelName(String name)... |
224 |
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{ |
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this.name = name; |
226 |
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} |
227 |
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228 |
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229 |
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230 |
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231 |
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@return |
232 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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233 |
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public int getModelNumber()... |
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{ |
235 |
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return modelNumber; |
236 |
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} |
237 |
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239 |
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240 |
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241 |
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@param |
242 |
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243 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
244 |
0 |
public void setModelNumber(int modelNumber)... |
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{ |
246 |
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this.modelNumber = modelNumber; |
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} |
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249 |
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250 |
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251 |
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252 |
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@return |
253 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
254 |
0 |
public int getSubModelNumber()... |
255 |
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{ |
256 |
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return subModelNumber; |
257 |
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} |
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259 |
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260 |
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261 |
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|
262 |
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@param |
263 |
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|
264 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
265 |
0 |
public void setSubModelNumber(int subModelNumber)... |
266 |
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{ |
267 |
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this.subModelNumber = subModelNumber; |
268 |
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} |
269 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
270 |
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public ModelType getModelType()... |
271 |
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{ |
272 |
0 |
return type; |
273 |
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} |
274 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
275 |
0 |
public void setModelType(ModelType type)... |
276 |
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{ |
277 |
0 |
this.type = type; |
278 |
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} |
279 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
280 |
0 |
public HashSet<ChimeraResidue> getFuncResidues()... |
281 |
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{ |
282 |
0 |
return funcResidues; |
283 |
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} |
284 |
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| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
285 |
0 |
public void setFuncResidues(List<String> residues)... |
286 |
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{ |
287 |
0 |
for (String residue : residues) |
288 |
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{ |
289 |
0 |
for (ChimeraChain chain : getChains()) |
290 |
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{ |
291 |
0 |
if (residue.indexOf("-") > 0) |
292 |
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{ |
293 |
0 |
funcResidues.addAll(chain.getResidueRange(residue)); |
294 |
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} |
295 |
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else |
296 |
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{ |
297 |
0 |
funcResidues.add(chain.getResidue(residue)); |
298 |
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} |
299 |
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} |
300 |
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} |
301 |
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} |
302 |
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303 |
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304 |
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305 |
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|
306 |
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@return |
307 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
308 |
0 |
@Override... |
309 |
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public Object getUserData() |
310 |
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{ |
311 |
0 |
return userData; |
312 |
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} |
313 |
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314 |
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315 |
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316 |
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317 |
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@param |
318 |
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|
319 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
320 |
0 |
@Override... |
321 |
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public void setUserData(Object data) |
322 |
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{ |
323 |
0 |
this.userData = data; |
324 |
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} |
325 |
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326 |
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|
327 |
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|
328 |
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|
329 |
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@return |
330 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
331 |
0 |
@Override... |
332 |
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public boolean isSelected() |
333 |
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{ |
334 |
0 |
return selected; |
335 |
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} |
336 |
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337 |
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|
338 |
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|
339 |
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|
340 |
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@param |
341 |
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|
342 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
343 |
0 |
@Override... |
344 |
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public void setSelected(boolean selected) |
345 |
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{ |
346 |
0 |
this.selected = selected; |
347 |
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} |
348 |
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349 |
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|
350 |
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351 |
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|
352 |
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@return |
353 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
354 |
0 |
@Override... |
355 |
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public List<ChimeraStructuralObject> getChildren() |
356 |
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{ |
357 |
0 |
return new ArrayList<ChimeraStructuralObject>(chainMap.values()); |
358 |
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} |
359 |
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|
360 |
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|
361 |
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|
362 |
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|
363 |
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@return |
364 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
365 |
0 |
public Collection<ChimeraChain> getChains()... |
366 |
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{ |
367 |
0 |
return chainMap.values(); |
368 |
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} |
369 |
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370 |
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|
371 |
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|
372 |
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|
373 |
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@return |
374 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
375 |
0 |
public int getChainCount()... |
376 |
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{ |
377 |
0 |
return chainMap.size(); |
378 |
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} |
379 |
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|
380 |
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|
381 |
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|
382 |
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|
383 |
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@return |
384 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
385 |
0 |
public Collection<String> getChainNames()... |
386 |
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{ |
387 |
0 |
return chainMap.keySet(); |
388 |
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} |
389 |
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|
390 |
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|
391 |
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|
392 |
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|
393 |
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@return |
394 |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
395 |
0 |
public Collection<ChimeraResidue> getResidues()... |
396 |
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{ |
397 |
0 |
Collection<ChimeraResidue> residues = new ArrayList<ChimeraResidue>(); |
398 |
0 |
for (ChimeraChain chain : getChains()) |
399 |
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{ |
400 |
0 |
residues.addAll(chain.getResidues()); |
401 |
|
} |
402 |
0 |
return residues; |
403 |
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} |
404 |
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|
405 |
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|
406 |
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|
407 |
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|
408 |
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@return |
409 |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
410 |
0 |
public int getResidueCount()... |
411 |
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{ |
412 |
0 |
int count = 0; |
413 |
0 |
for (ChimeraChain chain : getChains()) |
414 |
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{ |
415 |
0 |
count += chain.getResidueCount(); |
416 |
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} |
417 |
0 |
return count; |
418 |
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} |
419 |
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420 |
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421 |
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|
422 |
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|
423 |
|
@param |
424 |
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|
425 |
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@return |
426 |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
427 |
0 |
public ChimeraChain getChain(String chain)... |
428 |
|
{ |
429 |
0 |
if (chainMap.containsKey(chain)) |
430 |
|
{ |
431 |
0 |
return chainMap.get(chain); |
432 |
|
} |
433 |
0 |
return null; |
434 |
|
} |
435 |
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|
436 |
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|
437 |
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|
438 |
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|
439 |
|
@param |
440 |
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|
441 |
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@return |
442 |
|
|
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|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
443 |
0 |
public ChimeraResidue getResidue(String chainId, String index)... |
444 |
|
{ |
445 |
0 |
if (chainMap.containsKey(chainId)) |
446 |
|
{ |
447 |
0 |
return chainMap.get(chainId).getResidue(index); |
448 |
|
} |
449 |
0 |
return null; |
450 |
|
} |
451 |
|
|
452 |
|
|
453 |
|
|
454 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
455 |
0 |
@Override... |
456 |
|
public boolean hasSelectedChildren() |
457 |
|
{ |
458 |
0 |
if (selected) |
459 |
|
{ |
460 |
0 |
return true; |
461 |
|
} |
462 |
|
else |
463 |
|
{ |
464 |
0 |
for (ChimeraChain chain : getChains()) |
465 |
|
{ |
466 |
0 |
if (chain.hasSelectedChildren()) |
467 |
|
{ |
468 |
0 |
return true; |
469 |
|
} |
470 |
|
} |
471 |
|
} |
472 |
0 |
return false; |
473 |
|
} |
474 |
|
|
475 |
|
|
476 |
|
|
477 |
|
|
478 |
|
@return |
479 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
480 |
0 |
public List<ChimeraResidue> getSelectedResidues()... |
481 |
|
{ |
482 |
0 |
List<ChimeraResidue> residueList = new ArrayList<ChimeraResidue>(); |
483 |
0 |
for (ChimeraChain chain : getChains()) |
484 |
|
{ |
485 |
0 |
if (selected) |
486 |
|
{ |
487 |
0 |
residueList.addAll(chain.getSelectedResidues()); |
488 |
|
} |
489 |
|
else |
490 |
|
{ |
491 |
0 |
residueList.addAll(getResidues()); |
492 |
|
} |
493 |
|
} |
494 |
0 |
return residueList; |
495 |
|
} |
496 |
|
|
497 |
|
|
498 |
|
|
499 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
500 |
0 |
@Override... |
501 |
|
public String toSpec() |
502 |
|
{ |
503 |
0 |
if (subModelNumber == 0) |
504 |
|
{ |
505 |
0 |
return ("#" + modelNumber); |
506 |
|
} |
507 |
0 |
return ("#" + modelNumber + "." + subModelNumber); |
508 |
|
} |
509 |
|
|
510 |
|
|
511 |
|
|
512 |
|
|
513 |
|
|
|
|
| 0% |
Uncovered Elements: 67 (67) |
Complexity: 14 |
Complexity Density: 0.34 |
|
514 |
0 |
@Override... |
515 |
|
public String toString() |
516 |
|
{ |
517 |
0 |
String modelName = ""; |
518 |
|
|
519 |
|
|
520 |
0 |
if (getChainCount() > 0) |
521 |
|
{ |
522 |
0 |
modelName = "Model " + toSpec() + " " + name + " (" + getChainCount() |
523 |
|
+ " chains, " + getResidueCount() + " residues)"; |
524 |
|
} |
525 |
0 |
else if (getResidueCount() > 0) |
526 |
|
{ |
527 |
0 |
modelName = "Model " + toSpec() + " " + name + " (" |
528 |
|
+ getResidueCount() + " residues)"; |
529 |
|
} |
530 |
|
else |
531 |
|
{ |
532 |
0 |
modelName = "Model " + toSpec() + " " + name + ""; |
533 |
|
} |
534 |
|
|
535 |
0 |
Set<String> networkNames = new HashSet<String>(); |
536 |
0 |
Set<String> nodeNames = new HashSet<String>(); |
537 |
0 |
Set<String> edgeNames = new HashSet<String>(); |
538 |
|
|
539 |
0 |
String cytoName = " ["; |
540 |
0 |
if (networkNames.size() > 0) |
541 |
|
{ |
542 |
0 |
if (networkNames.size() == 1) |
543 |
|
{ |
544 |
0 |
cytoName += "Network {"; |
545 |
|
} |
546 |
0 |
else if (networkNames.size() > 1) |
547 |
|
{ |
548 |
0 |
cytoName += "Networks {"; |
549 |
|
} |
550 |
0 |
for (String cName : networkNames) |
551 |
|
{ |
552 |
0 |
cytoName += cName + ","; |
553 |
|
} |
554 |
0 |
cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, "; |
555 |
|
} |
556 |
0 |
if (nodeNames.size() > 0) |
557 |
|
{ |
558 |
0 |
if (nodeNames.size() == 1) |
559 |
|
{ |
560 |
0 |
cytoName += "Node {"; |
561 |
|
} |
562 |
0 |
else if (nodeNames.size() > 1) |
563 |
|
{ |
564 |
0 |
cytoName += "Nodes {"; |
565 |
|
} |
566 |
0 |
for (String cName : nodeNames) |
567 |
|
{ |
568 |
0 |
cytoName += cName + ","; |
569 |
|
} |
570 |
0 |
cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, "; |
571 |
|
} |
572 |
0 |
if (edgeNames.size() > 0) |
573 |
|
{ |
574 |
0 |
if (edgeNames.size() == 1) |
575 |
|
{ |
576 |
0 |
cytoName += "Edge {"; |
577 |
|
} |
578 |
0 |
else if (edgeNames.size() > 1) |
579 |
|
{ |
580 |
0 |
cytoName += "Edges {"; |
581 |
|
} |
582 |
0 |
for (String cName : edgeNames) |
583 |
|
{ |
584 |
0 |
cytoName += cName + ","; |
585 |
|
} |
586 |
0 |
cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, "; |
587 |
|
} |
588 |
0 |
if (cytoName.endsWith(", ")) |
589 |
|
{ |
590 |
0 |
cytoName = cytoName.substring(0, cytoName.length() - 2); |
591 |
|
} |
592 |
0 |
cytoName += "]"; |
593 |
0 |
String nodeName = modelName + cytoName; |
594 |
0 |
if (nodeName.length() > 100) |
595 |
|
{ |
596 |
0 |
nodeName = nodeName.substring(0, 100) + "..."; |
597 |
|
} |
598 |
0 |
return nodeName; |
599 |
|
} |
600 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
601 |
0 |
@Override... |
602 |
|
public boolean equals(Object otherChimeraModel) |
603 |
|
{ |
604 |
0 |
if (!(otherChimeraModel instanceof ChimeraModel)) |
605 |
|
{ |
606 |
0 |
return false; |
607 |
|
} |
608 |
0 |
ChimeraModel otherCM = ((ChimeraModel) otherChimeraModel); |
609 |
0 |
return this.name.equals(otherCM.name) |
610 |
|
&& this.modelNumber == otherCM.modelNumber |
611 |
|
&& this.type == otherCM.type; |
612 |
|
} |
613 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
614 |
0 |
@Override... |
615 |
|
public int hashCode() |
616 |
|
{ |
617 |
0 |
int hashCode = 1; |
618 |
0 |
hashCode = hashCode * 37 + this.name.hashCode(); |
619 |
0 |
hashCode = hashCode * 37 + this.type.hashCode(); |
620 |
0 |
hashCode = (hashCode * 37) + modelNumber; |
621 |
0 |
return hashCode; |
622 |
|
} |
623 |
|
} |