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package jalview.ext.rbvi.chimera; |
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import jalview.api.AlignmentViewPanel; |
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import jalview.api.SequenceRenderer; |
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import jalview.api.structures.JalviewStructureDisplayI; |
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import jalview.bin.Cache; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.SearchResultMatchI; |
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import jalview.datamodel.SearchResultsI; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import jalview.httpserver.AbstractRequestHandler; |
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import jalview.io.DataSourceType; |
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import jalview.schemes.ColourSchemeI; |
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import jalview.schemes.ResidueProperties; |
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import jalview.structure.AtomSpec; |
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import jalview.structure.StructureMappingcommandSet; |
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import jalview.structure.StructureSelectionManager; |
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import jalview.structures.models.AAStructureBindingModel; |
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import jalview.util.MessageManager; |
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import java.awt.Color; |
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import java.io.File; |
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import java.io.FileOutputStream; |
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import java.io.IOException; |
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import java.io.PrintWriter; |
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import java.net.BindException; |
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import java.util.ArrayList; |
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import java.util.BitSet; |
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import java.util.Collections; |
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import java.util.Hashtable; |
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import java.util.LinkedHashMap; |
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import java.util.List; |
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import java.util.Map; |
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import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager; |
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import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel; |
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import ext.edu.ucsf.rbvi.strucviz2.StructureManager; |
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import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType; |
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| 0% |
Uncovered Elements: 515 (515) |
Complexity: 125 |
Complexity Density: 0.36 |
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public abstract class JalviewChimeraBinding extends AAStructureBindingModel |
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{ |
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public static final String CHIMERA_FEATURE_GROUP = "Chimera"; |
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private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9"; |
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private static final String COLOURING_CHIMERA = MessageManager |
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.getString("status.colouring_chimera"); |
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private static final boolean debug = false; |
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private static final String PHOSPHORUS = "P"; |
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private static final String ALPHACARBON = "CA"; |
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private List<String> chainNames = new ArrayList<String>(); |
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private Hashtable<String, String> chainFile = new Hashtable<String, String>(); |
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private ChimeraManager viewer; |
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private AbstractRequestHandler chimeraListener; |
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private boolean loadingFromArchive = false; |
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private boolean loadingFinished = true; |
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private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>(); |
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String lastHighlightCommand; |
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private long loadNotifiesHandled = 0; |
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private Thread chimeraMonitor; |
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@param |
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@return |
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| 0% |
Uncovered Elements: 30 (30) |
Complexity: 6 |
Complexity Density: 0.27 |
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public boolean openFile(PDBEntry pe)... |
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{ |
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String file = pe.getFile(); |
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try |
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{ |
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List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>(); |
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List<ChimeraModel> oldList = viewer.getModelList(); |
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boolean alreadyOpen = false; |
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for (ChimeraModel open : oldList) |
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{ |
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if (open.getModelName().equals(pe.getId())) |
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{ |
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alreadyOpen = true; |
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modelsToMap.add(open); |
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} |
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} |
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if (!alreadyOpen) |
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{ |
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viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL); |
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List<ChimeraModel> newList = viewer.getModelList(); |
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for (ChimeraModel cm : newList) |
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{ |
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if (cm.getModelName().equals(pe.getId())) |
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{ |
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modelsToMap.add(cm); |
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} |
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} |
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} |
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chimeraMaps.put(file, modelsToMap); |
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if (getSsm() != null) |
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{ |
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getSsm().addStructureViewerListener(this); |
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} |
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return true; |
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} catch (Exception q) |
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{ |
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log("Exception when trying to open model " + file + "\n" |
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+ q.toString()); |
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q.printStackTrace(); |
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} |
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return false; |
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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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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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public JalviewChimeraBinding(StructureSelectionManager ssm,... |
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PDBEntry[] pdbentry, SequenceI[][] sequenceIs, |
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DataSourceType protocol) |
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{ |
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super(ssm, pdbentry, sequenceIs, protocol); |
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viewer = new ChimeraManager(new StructureManager(true)); |
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} |
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| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
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protected void startChimeraProcessMonitor()... |
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{ |
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final Process p = viewer.getChimeraProcess(); |
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chimeraMonitor = new Thread(new Runnable() |
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{ |
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| 0% |
Uncovered Elements: 7 (7) |
Complexity: 3 |
Complexity Density: 0.6 |
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@Override... |
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public void run() |
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{ |
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try |
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{ |
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p.waitFor(); |
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JalviewStructureDisplayI display = getViewer(); |
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if (display != null) |
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{ |
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display.closeViewer(false); |
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} |
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} catch (InterruptedException e) |
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{ |
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} |
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} |
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}); |
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chimeraMonitor.start(); |
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} |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
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public void startChimeraListener()... |
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{ |
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try |
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{ |
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chimeraListener = new ChimeraListener(this); |
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viewer.startListening(chimeraListener.getUri()); |
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} catch (BindException e) |
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{ |
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System.err.println( |
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"Failed to start Chimera listener: " + e.getMessage()); |
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} |
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} |
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253 |
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@param |
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| 0% |
Uncovered Elements: 15 (15) |
Complexity: 3 |
Complexity Density: 0.27 |
|
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public void showChains(List<String> toshow)... |
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{ |
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StringBuilder cmd = new StringBuilder(64); |
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boolean first = true; |
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for (String chain : toshow) |
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{ |
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int modelNumber = getModelNoForChain(chain); |
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String showChainCmd = modelNumber == -1 ? "" |
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: modelNumber + ":." + chain.split(":")[1]; |
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0 |
if (!first) |
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{ |
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cmd.append(","); |
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} |
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cmd.append(showChainCmd); |
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first = false; |
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} |
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277 |
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278 |
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279 |
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280 |
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281 |
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282 |
0 |
final String command = "~display #*; ~ribbon #*; ribbon :" |
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+ cmd.toString(); |
284 |
0 |
sendChimeraCommand(command, false); |
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} |
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290 |
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| 0% |
Uncovered Elements: 16 (16) |
Complexity: 4 |
Complexity Density: 0.4 |
|
291 |
0 |
public void closeViewer(boolean closeChimera)... |
292 |
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{ |
293 |
0 |
getSsm().removeStructureViewerListener(this, this.getStructureFiles()); |
294 |
0 |
if (closeChimera) |
295 |
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{ |
296 |
0 |
viewer.exitChimera(); |
297 |
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} |
298 |
0 |
if (this.chimeraListener != null) |
299 |
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{ |
300 |
0 |
chimeraListener.shutdown(); |
301 |
0 |
chimeraListener = null; |
302 |
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} |
303 |
0 |
viewer = null; |
304 |
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305 |
0 |
if (chimeraMonitor != null) |
306 |
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{ |
307 |
0 |
chimeraMonitor.interrupt(); |
308 |
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} |
309 |
0 |
releaseUIResources(); |
310 |
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} |
311 |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
312 |
0 |
@Override... |
313 |
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public void colourByChain() |
314 |
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{ |
315 |
0 |
colourBySequence = false; |
316 |
0 |
sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA); |
317 |
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} |
318 |
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327 |
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| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
328 |
0 |
@Override... |
329 |
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public void colourByCharge() |
330 |
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{ |
331 |
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colourBySequence = false; |
332 |
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String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS"; |
333 |
0 |
sendAsynchronousCommand(command, COLOURING_CHIMERA); |
334 |
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} |
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336 |
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337 |
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@inheritDoc |
338 |
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| 0% |
Uncovered Elements: 143 (143) |
Complexity: 31 |
Complexity Density: 0.35 |
|
339 |
0 |
@Override... |
340 |
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public String superposeStructures(AlignmentI[] _alignment, |
341 |
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int[] _refStructure, HiddenColumns[] _hiddenCols) |
342 |
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{ |
343 |
0 |
StringBuilder allComs = new StringBuilder(128); |
344 |
0 |
String[] files = getStructureFiles(); |
345 |
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346 |
0 |
if (!waitForFileLoad(files)) |
347 |
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{ |
348 |
0 |
return null; |
349 |
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} |
350 |
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351 |
0 |
refreshPdbEntries(); |
352 |
0 |
StringBuilder selectioncom = new StringBuilder(256); |
353 |
0 |
for (int a = 0; a < _alignment.length; a++) |
354 |
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{ |
355 |
0 |
int refStructure = _refStructure[a]; |
356 |
0 |
AlignmentI alignment = _alignment[a]; |
357 |
0 |
HiddenColumns hiddenCols = _hiddenCols[a]; |
358 |
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359 |
0 |
if (refStructure >= files.length) |
360 |
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{ |
361 |
0 |
System.err.println("Ignoring invalid reference structure value " |
362 |
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+ refStructure); |
363 |
0 |
refStructure = -1; |
364 |
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} |
365 |
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366 |
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367 |
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368 |
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369 |
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370 |
0 |
BitSet matched = new BitSet(); |
371 |
0 |
for (int m = 0; m < alignment.getWidth(); m++) |
372 |
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{ |
373 |
0 |
if (hiddenCols == null || hiddenCols.isVisible(m)) |
374 |
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{ |
375 |
0 |
matched.set(m); |
376 |
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} |
377 |
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} |
378 |
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379 |
0 |
SuperposeData[] structures = new SuperposeData[files.length]; |
380 |
0 |
for (int f = 0; f < files.length; f++) |
381 |
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{ |
382 |
0 |
structures[f] = new SuperposeData(alignment.getWidth()); |
383 |
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} |
384 |
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385 |
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386 |
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387 |
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388 |
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389 |
0 |
int candidateRefStructure = findSuperposableResidues(alignment, |
390 |
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matched, structures); |
391 |
0 |
if (refStructure < 0) |
392 |
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{ |
393 |
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394 |
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395 |
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396 |
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397 |
0 |
refStructure = candidateRefStructure; |
398 |
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} |
399 |
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|
400 |
0 |
int nmatched = matched.cardinality(); |
401 |
0 |
if (nmatched < 4) |
402 |
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{ |
403 |
0 |
return MessageManager.formatMessage("label.insufficient_residues", |
404 |
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nmatched); |
405 |
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} |
406 |
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407 |
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408 |
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409 |
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|
410 |
0 |
String[] selcom = new String[files.length]; |
411 |
0 |
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) |
412 |
|
{ |
413 |
0 |
String chainCd = "." + structures[pdbfnum].chain; |
414 |
0 |
int lpos = -1; |
415 |
0 |
boolean run = false; |
416 |
0 |
StringBuilder molsel = new StringBuilder(); |
417 |
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|
418 |
0 |
int nextColumnMatch = matched.nextSetBit(0); |
419 |
0 |
while (nextColumnMatch != -1) |
420 |
|
{ |
421 |
0 |
int pdbResNum = structures[pdbfnum].pdbResNo[nextColumnMatch]; |
422 |
0 |
if (lpos != pdbResNum - 1) |
423 |
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{ |
424 |
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425 |
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426 |
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|
427 |
0 |
if (lpos != -1) |
428 |
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{ |
429 |
0 |
molsel.append(String.valueOf(lpos)); |
430 |
0 |
molsel.append(chainCd); |
431 |
0 |
molsel.append(","); |
432 |
|
} |
433 |
0 |
run = false; |
434 |
|
} |
435 |
|
else |
436 |
|
{ |
437 |
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438 |
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439 |
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|
440 |
0 |
if (!run) |
441 |
|
{ |
442 |
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443 |
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444 |
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|
445 |
0 |
molsel.append(String.valueOf(lpos)); |
446 |
0 |
molsel.append("-"); |
447 |
|
} |
448 |
0 |
run = true; |
449 |
|
} |
450 |
0 |
lpos = pdbResNum; |
451 |
0 |
nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1); |
452 |
|
} |
453 |
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|
454 |
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|
455 |
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|
456 |
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|
457 |
0 |
if (lpos != -1) |
458 |
|
{ |
459 |
0 |
molsel.append(String.valueOf(lpos)); |
460 |
0 |
molsel.append(chainCd); |
461 |
|
} |
462 |
0 |
if (molsel.length() > 1) |
463 |
|
{ |
464 |
0 |
selcom[pdbfnum] = molsel.toString(); |
465 |
0 |
selectioncom.append("#").append(String.valueOf(pdbfnum)) |
466 |
|
.append(":"); |
467 |
0 |
selectioncom.append(selcom[pdbfnum]); |
468 |
0 |
selectioncom.append(" "); |
469 |
0 |
if (pdbfnum < files.length - 1) |
470 |
|
{ |
471 |
0 |
selectioncom.append("| "); |
472 |
|
} |
473 |
|
} |
474 |
|
else |
475 |
|
{ |
476 |
0 |
selcom[pdbfnum] = null; |
477 |
|
} |
478 |
|
} |
479 |
|
|
480 |
0 |
StringBuilder command = new StringBuilder(256); |
481 |
0 |
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) |
482 |
|
{ |
483 |
0 |
if (pdbfnum == refStructure || selcom[pdbfnum] == null |
484 |
|
|| selcom[refStructure] == null) |
485 |
|
{ |
486 |
0 |
continue; |
487 |
|
} |
488 |
0 |
if (command.length() > 0) |
489 |
|
{ |
490 |
0 |
command.append(";"); |
491 |
|
} |
492 |
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493 |
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494 |
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|
495 |
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496 |
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|
497 |
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|
498 |
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|
499 |
|
@see |
500 |
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|
501 |
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|
502 |
0 |
command.append("match ").append(getModelSpec(pdbfnum)).append(":"); |
503 |
0 |
command.append(selcom[pdbfnum]); |
504 |
0 |
command.append("@").append( |
505 |
0 |
structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON); |
506 |
|
|
507 |
0 |
command.append(NO_ALTLOCS); |
508 |
0 |
command.append(" ").append(getModelSpec(refStructure)).append(":"); |
509 |
0 |
command.append(selcom[refStructure]); |
510 |
0 |
command.append("@").append( |
511 |
0 |
structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON); |
512 |
0 |
command.append(NO_ALTLOCS); |
513 |
|
} |
514 |
0 |
if (selectioncom.length() > 0) |
515 |
|
{ |
516 |
0 |
if (debug) |
517 |
|
{ |
518 |
0 |
System.out.println("Select regions:\n" + selectioncom.toString()); |
519 |
0 |
System.out.println( |
520 |
|
"Superimpose command(s):\n" + command.toString()); |
521 |
|
} |
522 |
0 |
allComs.append("~display all; chain @CA|P; ribbon ") |
523 |
|
.append(selectioncom.toString()) |
524 |
|
.append(";" + command.toString()); |
525 |
|
} |
526 |
|
} |
527 |
|
|
528 |
0 |
String error = null; |
529 |
0 |
if (selectioncom.length() > 0) |
530 |
|
{ |
531 |
|
|
532 |
0 |
if (selectioncom.substring(selectioncom.length() - 1).equals("|")) |
533 |
|
{ |
534 |
0 |
selectioncom.setLength(selectioncom.length() - 1); |
535 |
|
} |
536 |
0 |
if (debug) |
537 |
|
{ |
538 |
0 |
System.out.println("Select regions:\n" + selectioncom.toString()); |
539 |
|
} |
540 |
0 |
allComs.append("; ~display all; chain @CA|P; ribbon ") |
541 |
|
.append(selectioncom.toString()).append("; focus"); |
542 |
0 |
List<String> chimeraReplies = sendChimeraCommand(allComs.toString(), |
543 |
|
true); |
544 |
0 |
for (String reply : chimeraReplies) |
545 |
|
{ |
546 |
0 |
if (reply.toLowerCase().contains("unequal numbers of atoms")) |
547 |
|
{ |
548 |
0 |
error = reply; |
549 |
|
} |
550 |
|
} |
551 |
|
} |
552 |
0 |
return error; |
553 |
|
} |
554 |
|
|
555 |
|
|
556 |
|
|
557 |
|
|
558 |
|
|
559 |
|
|
560 |
|
|
561 |
|
|
562 |
|
|
563 |
|
|
564 |
|
|
565 |
|
@param |
566 |
|
@return |
567 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 4 |
Complexity Density: 0.8 |
|
568 |
0 |
protected String getModelSpec(int pdbfnum)... |
569 |
|
{ |
570 |
0 |
if (pdbfnum < 0 || pdbfnum >= getPdbCount()) |
571 |
|
{ |
572 |
0 |
return ""; |
573 |
|
} |
574 |
|
|
575 |
|
|
576 |
|
|
577 |
|
|
578 |
|
|
579 |
|
|
580 |
|
|
581 |
0 |
List<ChimeraModel> maps = chimeraMaps.get(getStructureFiles()[pdbfnum]); |
582 |
0 |
boolean hasSubModels = maps != null && maps.size() > 1; |
583 |
0 |
return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : ""); |
584 |
|
} |
585 |
|
|
586 |
|
|
587 |
|
|
588 |
|
|
589 |
|
|
590 |
|
|
591 |
|
@return |
592 |
|
|
|
|
| 0% |
Uncovered Elements: 11 (11) |
Complexity: 3 |
Complexity Density: 0.43 |
|
593 |
0 |
public boolean launchChimera()... |
594 |
|
{ |
595 |
0 |
if (viewer.isChimeraLaunched()) |
596 |
|
{ |
597 |
0 |
return true; |
598 |
|
} |
599 |
|
|
600 |
0 |
boolean launched = viewer |
601 |
|
.launchChimera(StructureManager.getChimeraPaths()); |
602 |
0 |
if (launched) |
603 |
|
{ |
604 |
0 |
startChimeraProcessMonitor(); |
605 |
|
} |
606 |
|
else |
607 |
|
{ |
608 |
0 |
log("Failed to launch Chimera!"); |
609 |
|
} |
610 |
0 |
return launched; |
611 |
|
} |
612 |
|
|
613 |
|
|
614 |
|
|
615 |
|
|
616 |
|
|
617 |
|
@return |
618 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
619 |
0 |
public boolean isChimeraRunning()... |
620 |
|
{ |
621 |
0 |
return viewer.isChimeraLaunched(); |
622 |
|
} |
623 |
|
|
624 |
|
|
625 |
|
|
626 |
|
|
627 |
|
|
628 |
|
|
629 |
|
|
630 |
|
@param |
631 |
|
@param |
632 |
|
|
|
|
| 0% |
Uncovered Elements: 18 (18) |
Complexity: 4 |
Complexity Density: 0.33 |
|
633 |
0 |
public List<String> sendChimeraCommand(final String command,... |
634 |
|
boolean getResponse) |
635 |
|
{ |
636 |
0 |
if (viewer == null) |
637 |
|
{ |
638 |
|
|
639 |
0 |
return null; |
640 |
|
} |
641 |
0 |
List<String> reply = null; |
642 |
0 |
viewerCommandHistory(false); |
643 |
0 |
if (true ) |
644 |
|
{ |
645 |
|
|
646 |
0 |
List<String> lastReply = viewer.sendChimeraCommand(command.trim(), |
647 |
|
getResponse); |
648 |
0 |
if (getResponse) |
649 |
|
{ |
650 |
0 |
reply = lastReply; |
651 |
0 |
if (debug) |
652 |
|
{ |
653 |
0 |
log("Response from command ('" + command + "') was:\n" |
654 |
|
+ lastReply); |
655 |
|
} |
656 |
|
} |
657 |
|
} |
658 |
0 |
viewerCommandHistory(true); |
659 |
|
|
660 |
0 |
return reply; |
661 |
|
} |
662 |
|
|
663 |
|
|
664 |
|
|
665 |
|
|
666 |
|
|
667 |
|
@param |
668 |
|
@param |
669 |
|
|
670 |
|
protected abstract void sendAsynchronousCommand(String command, |
671 |
|
String progressMsg); |
672 |
|
|
673 |
|
|
674 |
|
|
675 |
|
|
676 |
|
@param |
677 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
678 |
0 |
@Override... |
679 |
|
protected void colourBySequence( |
680 |
|
StructureMappingcommandSet[] colourBySequenceCommands) |
681 |
|
{ |
682 |
0 |
for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands) |
683 |
|
{ |
684 |
0 |
for (String command : cpdbbyseq.commands) |
685 |
|
{ |
686 |
0 |
sendAsynchronousCommand(command, COLOURING_CHIMERA); |
687 |
|
} |
688 |
|
} |
689 |
|
} |
690 |
|
|
691 |
|
|
692 |
|
@param |
693 |
|
@param |
694 |
|
@param |
695 |
|
@return |
696 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
697 |
0 |
@Override... |
698 |
|
protected StructureMappingcommandSet[] getColourBySequenceCommands( |
699 |
|
String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel) |
700 |
|
{ |
701 |
0 |
return ChimeraCommands.getColourBySequenceCommand(getSsm(), files, |
702 |
|
getSequence(), sr, viewPanel); |
703 |
|
} |
704 |
|
|
705 |
|
|
706 |
|
@param |
707 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
708 |
0 |
protected void executeWhenReady(String command)... |
709 |
|
{ |
710 |
0 |
waitForChimera(); |
711 |
0 |
sendChimeraCommand(command, false); |
712 |
0 |
waitForChimera(); |
713 |
|
} |
714 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 4 |
Complexity Density: 1.33 |
|
715 |
0 |
private void waitForChimera()... |
716 |
|
{ |
717 |
0 |
while (viewer != null && viewer.isBusy()) |
718 |
|
{ |
719 |
0 |
try |
720 |
|
{ |
721 |
0 |
Thread.sleep(15); |
722 |
|
} catch (InterruptedException q) |
723 |
|
{ |
724 |
|
} |
725 |
|
} |
726 |
|
} |
727 |
|
|
728 |
|
|
729 |
|
|
730 |
|
|
731 |
|
|
732 |
|
|
733 |
|
|
734 |
|
|
735 |
|
|
736 |
|
public abstract void refreshPdbEntries(); |
737 |
|
|
738 |
|
|
739 |
|
|
740 |
|
|
741 |
|
|
742 |
|
|
743 |
|
private int _modelFileNameMap[]; |
744 |
|
|
745 |
|
|
746 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
747 |
0 |
@Override... |
748 |
|
public synchronized String[] getStructureFiles() |
749 |
|
{ |
750 |
0 |
if (viewer == null) |
751 |
|
{ |
752 |
0 |
return new String[0]; |
753 |
|
} |
754 |
|
|
755 |
0 |
return chimeraMaps.keySet() |
756 |
|
.toArray(modelFileNames = new String[chimeraMaps.size()]); |
757 |
|
} |
758 |
|
|
759 |
|
|
760 |
|
|
761 |
|
|
762 |
|
|
763 |
|
|
|
|
| 0% |
Uncovered Elements: 41 (41) |
Complexity: 10 |
Complexity Density: 0.37 |
|
764 |
0 |
@Override... |
765 |
|
public void highlightAtoms(List<AtomSpec> atoms) |
766 |
|
{ |
767 |
0 |
if (atoms == null || atoms.size() == 0) |
768 |
|
{ |
769 |
0 |
return; |
770 |
|
} |
771 |
|
|
772 |
0 |
StringBuilder cmd = new StringBuilder(128); |
773 |
0 |
boolean first = true; |
774 |
0 |
boolean found = false; |
775 |
|
|
776 |
0 |
for (AtomSpec atom : atoms) |
777 |
|
{ |
778 |
0 |
int pdbResNum = atom.getPdbResNum(); |
779 |
0 |
String chain = atom.getChain(); |
780 |
0 |
String pdbfile = atom.getPdbFile(); |
781 |
0 |
List<ChimeraModel> cms = chimeraMaps.get(pdbfile); |
782 |
0 |
if (cms != null && !cms.isEmpty()) |
783 |
|
{ |
784 |
0 |
if (first) |
785 |
|
{ |
786 |
0 |
cmd.append("rlabel #").append(cms.get(0).getModelNumber()) |
787 |
|
.append(":"); |
788 |
|
} |
789 |
|
else |
790 |
|
{ |
791 |
0 |
cmd.append(","); |
792 |
|
} |
793 |
0 |
first = false; |
794 |
0 |
cmd.append(pdbResNum); |
795 |
0 |
if (!chain.equals(" ")) |
796 |
|
{ |
797 |
0 |
cmd.append(".").append(chain); |
798 |
|
} |
799 |
0 |
found = true; |
800 |
|
} |
801 |
|
} |
802 |
0 |
String command = cmd.toString(); |
803 |
|
|
804 |
|
|
805 |
|
|
806 |
|
|
807 |
0 |
if (command.equals(lastHighlightCommand)) |
808 |
|
{ |
809 |
0 |
return; |
810 |
|
} |
811 |
|
|
812 |
|
|
813 |
|
|
814 |
|
|
815 |
0 |
if (lastHighlightCommand != null) |
816 |
|
{ |
817 |
0 |
viewer.sendChimeraCommand("~" + lastHighlightCommand, false); |
818 |
|
} |
819 |
0 |
if (found) |
820 |
|
{ |
821 |
0 |
viewer.sendChimeraCommand(command, false); |
822 |
|
} |
823 |
0 |
this.lastHighlightCommand = command; |
824 |
|
} |
825 |
|
|
826 |
|
|
827 |
|
|
828 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
829 |
0 |
public void highlightChimeraSelection()... |
830 |
|
{ |
831 |
|
|
832 |
|
|
833 |
|
|
834 |
0 |
List<String> selection = viewer.getSelectedResidueSpecs(); |
835 |
|
|
836 |
|
|
837 |
|
|
838 |
|
|
839 |
|
|
840 |
0 |
List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment( |
841 |
|
selection); |
842 |
|
|
843 |
|
|
844 |
|
|
845 |
|
|
846 |
|
|
847 |
0 |
getSsm().mouseOverStructure(atomSpecs); |
848 |
|
} |
849 |
|
|
850 |
|
|
851 |
|
|
852 |
|
|
853 |
|
|
854 |
|
@param |
855 |
|
@return |
856 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 2 |
Complexity Density: 0.22 |
|
857 |
0 |
protected List<AtomSpec> convertStructureResiduesToAlignment(... |
858 |
|
List<String> structureSelection) |
859 |
|
{ |
860 |
0 |
List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>(); |
861 |
0 |
for (String atomSpec : structureSelection) |
862 |
|
{ |
863 |
0 |
try |
864 |
|
{ |
865 |
0 |
AtomSpec spec = AtomSpec.fromChimeraAtomspec(atomSpec); |
866 |
0 |
String pdbfilename = getPdbFileForModel(spec.getModelNumber()); |
867 |
0 |
spec.setPdbFile(pdbfilename); |
868 |
0 |
atomSpecs.add(spec); |
869 |
|
} catch (IllegalArgumentException e) |
870 |
|
{ |
871 |
0 |
System.err.println("Failed to parse atomspec: " + atomSpec); |
872 |
|
} |
873 |
|
} |
874 |
0 |
return atomSpecs; |
875 |
|
} |
876 |
|
|
877 |
|
|
878 |
|
@param |
879 |
|
@return |
880 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
881 |
0 |
protected String getPdbFileForModel(int modelId)... |
882 |
|
{ |
883 |
|
|
884 |
|
|
885 |
|
|
886 |
0 |
String pdbfilename = modelFileNames[0]; |
887 |
0 |
findfileloop: for (String pdbfile : this.chimeraMaps.keySet()) |
888 |
|
{ |
889 |
0 |
for (ChimeraModel cm : chimeraMaps.get(pdbfile)) |
890 |
|
{ |
891 |
0 |
if (cm.getModelNumber() == modelId) |
892 |
|
{ |
893 |
0 |
pdbfilename = pdbfile; |
894 |
0 |
break findfileloop; |
895 |
|
} |
896 |
|
} |
897 |
|
} |
898 |
0 |
return pdbfilename; |
899 |
|
} |
900 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
901 |
0 |
private void log(String message)... |
902 |
|
{ |
903 |
0 |
System.err.println("## Chimera log: " + message); |
904 |
|
} |
905 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
906 |
0 |
private void viewerCommandHistory(boolean enable)... |
907 |
|
{ |
908 |
|
|
909 |
|
|
910 |
|
} |
911 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
912 |
0 |
public long getLoadNotifiesHandled()... |
913 |
|
{ |
914 |
0 |
return loadNotifiesHandled; |
915 |
|
} |
916 |
|
|
|
|
| 0% |
Uncovered Elements: 17 (17) |
Complexity: 3 |
Complexity Density: 0.23 |
|
917 |
0 |
@Override... |
918 |
|
public void setJalviewColourScheme(ColourSchemeI cs) |
919 |
|
{ |
920 |
0 |
colourBySequence = false; |
921 |
|
|
922 |
0 |
if (cs == null) |
923 |
|
{ |
924 |
0 |
return; |
925 |
|
} |
926 |
|
|
927 |
|
|
928 |
0 |
final double normalise = 255D; |
929 |
0 |
viewerCommandHistory(false); |
930 |
0 |
StringBuilder command = new StringBuilder(128); |
931 |
|
|
932 |
0 |
List<String> residueSet = ResidueProperties.getResidues(isNucleotide(), |
933 |
|
false); |
934 |
0 |
for (String resName : residueSet) |
935 |
|
{ |
936 |
0 |
char res = resName.length() == 3 |
937 |
|
? ResidueProperties.getSingleCharacterCode(resName) |
938 |
|
: resName.charAt(0); |
939 |
0 |
Color col = cs.findColour(res, 0, null, null, 0f); |
940 |
0 |
command.append("color " + col.getRed() / normalise + "," |
941 |
|
+ col.getGreen() / normalise + "," + col.getBlue() / normalise |
942 |
|
+ " ::" + resName + ";"); |
943 |
|
} |
944 |
|
|
945 |
0 |
sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA); |
946 |
0 |
viewerCommandHistory(true); |
947 |
|
} |
948 |
|
|
949 |
|
|
950 |
|
|
951 |
|
|
952 |
|
|
953 |
|
|
954 |
|
public abstract void refreshGUI(); |
955 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
956 |
0 |
@Override... |
957 |
|
public void setLoadingFromArchive(boolean loadingFromArchive) |
958 |
|
{ |
959 |
0 |
this.loadingFromArchive = loadingFromArchive; |
960 |
|
} |
961 |
|
|
962 |
|
|
963 |
|
|
964 |
|
@return |
965 |
|
|
966 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
967 |
0 |
@Override... |
968 |
|
public boolean isLoadingFromArchive() |
969 |
|
{ |
970 |
0 |
return loadingFromArchive && !loadingFinished; |
971 |
|
} |
972 |
|
|
973 |
|
|
974 |
|
|
975 |
|
|
976 |
|
|
977 |
|
@param |
978 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
979 |
0 |
@Override... |
980 |
|
public void setFinishedLoadingFromArchive(boolean finishedLoading) |
981 |
|
{ |
982 |
0 |
loadingFinished = finishedLoading; |
983 |
|
} |
984 |
|
|
985 |
|
|
986 |
|
|
987 |
|
|
988 |
|
@see |
989 |
|
|
990 |
|
|
991 |
|
@param |
992 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
993 |
0 |
@Override... |
994 |
|
public void setBackgroundColour(Color col) |
995 |
|
{ |
996 |
0 |
viewerCommandHistory(false); |
997 |
0 |
double normalise = 255D; |
998 |
0 |
final String command = "background solid " + col.getRed() / normalise |
999 |
|
+ "," + col.getGreen() / normalise + "," |
1000 |
|
+ col.getBlue() / normalise + ";"; |
1001 |
0 |
viewer.sendChimeraCommand(command, false); |
1002 |
0 |
viewerCommandHistory(true); |
1003 |
|
} |
1004 |
|
|
1005 |
|
|
1006 |
|
|
1007 |
|
|
1008 |
|
|
1009 |
|
@param |
1010 |
|
@return |
1011 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
1012 |
0 |
public boolean saveSession(String filepath)... |
1013 |
|
{ |
1014 |
0 |
if (isChimeraRunning()) |
1015 |
|
{ |
1016 |
0 |
List<String> reply = viewer.sendChimeraCommand("save " + filepath, |
1017 |
|
true); |
1018 |
0 |
if (reply.contains("Session written")) |
1019 |
|
{ |
1020 |
0 |
return true; |
1021 |
|
} |
1022 |
|
else |
1023 |
|
{ |
1024 |
0 |
Cache.log |
1025 |
|
.error("Error saving Chimera session: " + reply.toString()); |
1026 |
|
} |
1027 |
|
} |
1028 |
0 |
return false; |
1029 |
|
} |
1030 |
|
|
1031 |
|
|
1032 |
|
|
1033 |
|
|
1034 |
|
|
1035 |
|
@param |
1036 |
|
@return |
1037 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1038 |
0 |
public boolean openSession(String filepath)... |
1039 |
|
{ |
1040 |
0 |
sendChimeraCommand("open " + filepath, true); |
1041 |
|
|
1042 |
0 |
return true; |
1043 |
|
} |
1044 |
|
|
1045 |
|
|
1046 |
|
|
1047 |
|
|
1048 |
|
|
1049 |
|
@return |
1050 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1051 |
0 |
@Override... |
1052 |
|
public List<String> getChainNames() |
1053 |
|
{ |
1054 |
0 |
return chainNames; |
1055 |
|
} |
1056 |
|
|
1057 |
|
|
1058 |
|
|
1059 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1060 |
0 |
public void focusView()... |
1061 |
|
{ |
1062 |
0 |
sendChimeraCommand("focus", false); |
1063 |
|
} |
1064 |
|
|
1065 |
|
|
1066 |
|
|
1067 |
|
|
1068 |
|
|
1069 |
|
|
1070 |
|
@param |
1071 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
|
1072 |
0 |
public void highlightSelection(AlignmentViewPanel vp)... |
1073 |
|
{ |
1074 |
0 |
List<Integer> cols = vp.getAlignViewport().getColumnSelection() |
1075 |
|
.getSelected(); |
1076 |
0 |
AlignmentI alignment = vp.getAlignment(); |
1077 |
0 |
StructureSelectionManager sm = getSsm(); |
1078 |
0 |
for (SequenceI seq : alignment.getSequences()) |
1079 |
|
{ |
1080 |
|
|
1081 |
|
|
1082 |
|
|
1083 |
0 |
int[] positions = new int[cols.size()]; |
1084 |
0 |
int i = 0; |
1085 |
0 |
for (Integer col : cols) |
1086 |
|
{ |
1087 |
0 |
positions[i++] = seq.findPosition(col); |
1088 |
|
} |
1089 |
0 |
sm.highlightStructure(this, seq, positions); |
1090 |
|
} |
1091 |
|
} |
1092 |
|
|
1093 |
|
|
1094 |
|
|
1095 |
|
|
1096 |
|
|
1097 |
|
@param |
1098 |
|
@return |
1099 |
|
|
|
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 3 |
Complexity Density: 0.27 |
|
1100 |
0 |
public int sendFeaturesToViewer(AlignmentViewPanel avp)... |
1101 |
|
{ |
1102 |
|
|
1103 |
0 |
AlignmentI alignment = avp.getAlignment(); |
1104 |
|
|
1105 |
0 |
String[] files = getStructureFiles(); |
1106 |
0 |
if (files == null) |
1107 |
|
{ |
1108 |
0 |
return 0; |
1109 |
|
} |
1110 |
|
|
1111 |
0 |
StructureMappingcommandSet commandSet = ChimeraCommands |
1112 |
|
.getSetAttributeCommandsForFeatures(getSsm(), files, |
1113 |
|
getSequence(), avp); |
1114 |
0 |
String[] commands = commandSet.commands; |
1115 |
0 |
if (commands.length > 10) |
1116 |
|
{ |
1117 |
0 |
sendCommandsByFile(commands); |
1118 |
|
} |
1119 |
|
else |
1120 |
|
{ |
1121 |
0 |
for (String command : commands) |
1122 |
|
{ |
1123 |
0 |
sendAsynchronousCommand(command, null); |
1124 |
|
} |
1125 |
|
} |
1126 |
0 |
return commands.length; |
1127 |
|
} |
1128 |
|
|
1129 |
|
|
1130 |
|
|
1131 |
|
|
1132 |
|
|
1133 |
|
|
1134 |
|
@param |
1135 |
|
|
|
|
| 0% |
Uncovered Elements: 11 (11) |
Complexity: 2 |
Complexity Density: 0.18 |
|
1136 |
0 |
protected void sendCommandsByFile(String[] commands)... |
1137 |
|
{ |
1138 |
0 |
try |
1139 |
|
{ |
1140 |
0 |
File tmp = File.createTempFile("chim", ".com"); |
1141 |
0 |
tmp.deleteOnExit(); |
1142 |
0 |
PrintWriter out = new PrintWriter(new FileOutputStream(tmp)); |
1143 |
0 |
for (String command : commands) |
1144 |
|
{ |
1145 |
0 |
out.println(command); |
1146 |
|
} |
1147 |
0 |
out.flush(); |
1148 |
0 |
out.close(); |
1149 |
0 |
String path = tmp.getAbsolutePath(); |
1150 |
0 |
sendAsynchronousCommand("open cmd:" + path, null); |
1151 |
|
} catch (IOException e) |
1152 |
|
{ |
1153 |
0 |
System.err.println("Sending commands to Chimera via file failed with " |
1154 |
|
+ e.getMessage()); |
1155 |
|
} |
1156 |
|
} |
1157 |
|
|
1158 |
|
|
1159 |
|
|
1160 |
|
|
1161 |
|
|
1162 |
|
@param |
1163 |
|
@param |
1164 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
1165 |
0 |
public void copyStructureAttributesToFeatures(String attName,... |
1166 |
|
AlignmentViewPanel alignmentPanel) |
1167 |
|
{ |
1168 |
|
|
1169 |
|
|
1170 |
|
|
1171 |
|
|
1172 |
|
|
1173 |
|
|
1174 |
|
|
1175 |
|
|
1176 |
|
|
1177 |
|
|
1178 |
0 |
String cmd = "list residues attr '" + attName + "'"; |
1179 |
0 |
List<String> residues = sendChimeraCommand(cmd, true); |
1180 |
|
|
1181 |
0 |
boolean featureAdded = createFeaturesForAttributes(attName, residues); |
1182 |
0 |
if (featureAdded) |
1183 |
|
{ |
1184 |
0 |
alignmentPanel.getFeatureRenderer().featuresAdded(); |
1185 |
|
} |
1186 |
|
} |
1187 |
|
|
1188 |
|
|
1189 |
|
|
1190 |
|
|
1191 |
|
|
1192 |
|
|
1193 |
|
|
1194 |
|
|
1195 |
|
|
1196 |
|
|
1197 |
|
|
1198 |
|
|
1199 |
|
@param |
1200 |
|
@param |
1201 |
|
@return |
1202 |
|
|
|
|
| 0% |
Uncovered Elements: 36 (36) |
Complexity: 6 |
Complexity Density: 0.19 |
|
1203 |
0 |
protected boolean createFeaturesForAttributes(String attName,... |
1204 |
|
List<String> residues) |
1205 |
|
{ |
1206 |
0 |
boolean featureAdded = false; |
1207 |
0 |
String featureGroup = getViewerFeatureGroup(); |
1208 |
|
|
1209 |
0 |
for (String residue : residues) |
1210 |
|
{ |
1211 |
0 |
AtomSpec spec = null; |
1212 |
0 |
String[] tokens = residue.split(" "); |
1213 |
0 |
if (tokens.length < 5) |
1214 |
|
{ |
1215 |
0 |
continue; |
1216 |
|
} |
1217 |
0 |
String atomSpec = tokens[2]; |
1218 |
0 |
String attValue = tokens[4]; |
1219 |
|
|
1220 |
|
|
1221 |
|
|
1222 |
|
|
1223 |
0 |
if ("None".equalsIgnoreCase(attValue) |
1224 |
|
|| "False".equalsIgnoreCase(attValue)) |
1225 |
|
{ |
1226 |
0 |
continue; |
1227 |
|
} |
1228 |
|
|
1229 |
0 |
try |
1230 |
|
{ |
1231 |
0 |
spec = AtomSpec.fromChimeraAtomspec(atomSpec); |
1232 |
|
} catch (IllegalArgumentException e) |
1233 |
|
{ |
1234 |
0 |
System.err.println("Problem parsing atomspec " + atomSpec); |
1235 |
0 |
continue; |
1236 |
|
} |
1237 |
|
|
1238 |
0 |
String chainId = spec.getChain(); |
1239 |
0 |
String description = attValue; |
1240 |
0 |
float score = Float.NaN; |
1241 |
0 |
try |
1242 |
|
{ |
1243 |
0 |
score = Float.valueOf(attValue); |
1244 |
0 |
description = chainId; |
1245 |
|
} catch (NumberFormatException e) |
1246 |
|
{ |
1247 |
|
|
1248 |
|
} |
1249 |
|
|
1250 |
0 |
String pdbFile = getPdbFileForModel(spec.getModelNumber()); |
1251 |
0 |
spec.setPdbFile(pdbFile); |
1252 |
|
|
1253 |
0 |
List<AtomSpec> atoms = Collections.singletonList(spec); |
1254 |
|
|
1255 |
|
|
1256 |
|
|
1257 |
|
|
1258 |
0 |
SearchResultsI sr = getSsm() |
1259 |
|
.findAlignmentPositionsForStructurePositions(atoms); |
1260 |
|
|
1261 |
|
|
1262 |
|
|
1263 |
|
|
1264 |
|
|
1265 |
0 |
for (SearchResultMatchI m : sr.getResults()) |
1266 |
|
{ |
1267 |
0 |
SequenceI seq = m.getSequence(); |
1268 |
0 |
int start = m.getStart(); |
1269 |
0 |
int end = m.getEnd(); |
1270 |
0 |
SequenceFeature sf = new SequenceFeature(attName, description, |
1271 |
|
start, end, score, featureGroup); |
1272 |
|
|
1273 |
|
|
1274 |
0 |
featureAdded |= seq.addSequenceFeature(sf); |
1275 |
|
} |
1276 |
|
} |
1277 |
0 |
return featureAdded; |
1278 |
|
} |
1279 |
|
|
1280 |
|
|
1281 |
|
|
1282 |
|
|
1283 |
|
|
1284 |
|
@return |
1285 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1286 |
0 |
protected String getViewerFeatureGroup()... |
1287 |
|
{ |
1288 |
|
|
1289 |
0 |
return CHIMERA_FEATURE_GROUP; |
1290 |
|
} |
1291 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1292 |
0 |
public Hashtable<String, String> getChainFile()... |
1293 |
|
{ |
1294 |
0 |
return chainFile; |
1295 |
|
} |
1296 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1297 |
0 |
public List<ChimeraModel> getChimeraModelByChain(String chain)... |
1298 |
|
{ |
1299 |
0 |
return chimeraMaps.get(chainFile.get(chain)); |
1300 |
|
} |
1301 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
|
1302 |
0 |
public int getModelNoForChain(String chain)... |
1303 |
|
{ |
1304 |
0 |
List<ChimeraModel> foundModels = getChimeraModelByChain(chain); |
1305 |
0 |
if (foundModels != null && !foundModels.isEmpty()) |
1306 |
|
{ |
1307 |
0 |
return foundModels.get(0).getModelNumber(); |
1308 |
|
} |
1309 |
0 |
return -1; |
1310 |
|
} |
1311 |
|
} |