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package jalview.structure; |
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import java.awt.Color; |
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import java.util.ArrayList; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.Map.Entry; |
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import jalview.bin.Console; |
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@author |
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| 75.6% |
Uncovered Elements: 20 (82) |
Complexity: 24 |
Complexity Density: 0.48 |
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public abstract class StructureCommandsBase implements StructureCommandsI |
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{ |
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public static final String NAMESPACE_PREFIX = "jv_"; |
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private static final String CMD_SEPARATOR = ";"; |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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2589 |
protected String getCommandSeparator()... |
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{ |
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return CMD_SEPARATOR; |
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} |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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2 |
@Override... |
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public int getModelStartNo() |
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{ |
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return 0; |
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} |
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@param |
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@param |
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@param |
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@param |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
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public static final void addAtomSpecRange(Map<Object, AtomSpecModel> map,... |
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Object value, String model, int startPos, int endPos, |
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String chain) |
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{ |
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AtomSpecModel atomSpec = map.get(value); |
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if (atomSpec == null) |
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{ |
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atomSpec = new AtomSpecModel(); |
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map.put(value, atomSpec); |
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} |
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atomSpec.addRange(model, startPos, endPos, chain); |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
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protected String makeAttributeName(String featureType)... |
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{ |
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StringBuilder sb = new StringBuilder(); |
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if (featureType != null) |
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{ |
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for (char c : featureType.toCharArray()) |
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{ |
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sb.append(Character.isLetterOrDigit(c) ? c : '_'); |
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} |
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} |
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String attName = NAMESPACE_PREFIX + sb.toString(); |
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return attName; |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (15) |
Complexity: 2 |
Complexity Density: 0.15 |
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270 |
@Override... |
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public List<StructureCommandI> colourBySequence( |
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Map<Object, AtomSpecModel> colourMap) |
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{ |
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List<StructureCommandI> commands = new ArrayList<>(); |
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StringBuilder sb = new StringBuilder(colourMap.size() * 20); |
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boolean first = true; |
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for (Object key : colourMap.keySet()) |
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{ |
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Color colour = (Color) key; |
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final AtomSpecModel colourData = colourMap.get(colour); |
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StructureCommandI command = getColourCommand(colourData, colour); |
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if (!first) |
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{ |
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1178 |
sb.append(getCommandSeparator()); |
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} |
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first = false; |
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sb.append(command.getCommand()); |
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} |
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commands.add(new StructureCommand(sb.toString())); |
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return commands; |
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} |
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@param |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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1416 |
protected StructureCommandI getColourCommand(AtomSpecModel atomSpecModel,... |
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Color colour) |
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{ |
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1416 |
String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY); |
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return colourResidues(atomSpec, colour); |
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} |
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@param |
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@param |
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@return |
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protected abstract StructureCommandI colourResidues(String atomSpec, |
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Color colour); |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
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0 |
@Override... |
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public List<StructureCommandI> colourByResidues( |
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Map<String, Color> colours) |
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{ |
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List<StructureCommandI> commands = new ArrayList<>(); |
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for (Entry<String, Color> entry : colours.entrySet()) |
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{ |
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commands.add(colourResidue(entry.getKey(), entry.getValue())); |
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} |
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return commands; |
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} |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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0 |
private StructureCommandI colourResidue(String resName, Color col)... |
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{ |
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String atomSpec = getResidueSpec(resName); |
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return colourResidues(atomSpec, col); |
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} |
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@param |
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@param |
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@param |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (17) |
Complexity: 5 |
Complexity Density: 0.56 |
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protected void appendRange(StringBuilder sb, int start, int end,... |
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String chain, boolean firstPositionForModel, boolean isChimeraX) |
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{ |
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if (!firstPositionForModel) |
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{ |
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59 |
sb.append(","); |
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} |
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if (end == start) |
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{ |
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sb.append(start); |
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} |
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else |
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{ |
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sb.append(start).append("-").append(end); |
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} |
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if (!isChimeraX) |
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{ |
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sb.append("."); |
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if (!" ".equals(chain)) |
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{ |
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sb.append(chain); |
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} |
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} |
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} |
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@param |
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@return |
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protected abstract String getResidueSpec(String residue); |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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0 |
@Override... |
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public List<StructureCommandI> setAttributes( |
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Map<String, Map<Object, AtomSpecModel>> featureValues) |
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{ |
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0 |
return null; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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0 |
@Override... |
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public List<StructureCommandI> startNotifications(String uri) |
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{ |
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return null; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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23 |
@Override... |
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public List<StructureCommandI> stopNotifications() |
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{ |
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return null; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
@Override... |
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public StructureCommandI getSelectedResidues() |
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{ |
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0 |
return null; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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0 |
@Override... |
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public StructureCommandI listResidueAttributes() |
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{ |
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0 |
return null; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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0 |
@Override... |
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public StructureCommandI getResidueAttributes(String attName) |
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{ |
278 |
0 |
return null; |
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} |
280 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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281 |
0 |
@Override... |
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public StructureCommandI restoreSession(String filePath) |
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{ |
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return loadFile(filePath); |
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} |
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} |