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package jalview.structure; |
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import java.io.PrintStream; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.Collections; |
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import java.util.Enumeration; |
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import java.util.HashMap; |
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import java.util.IdentityHashMap; |
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import java.util.List; |
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import java.util.Locale; |
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import java.util.Map; |
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import java.util.Vector; |
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import jalview.analysis.AlignSeq; |
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import jalview.api.StructureSelectionManagerProvider; |
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import jalview.bin.Cache; |
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import jalview.bin.Console; |
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import jalview.commands.CommandI; |
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import jalview.commands.EditCommand; |
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import jalview.commands.OrderCommand; |
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import jalview.datamodel.AlignedCodonFrame; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.Annotation; |
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import jalview.datamodel.ContiguousI; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.SearchResults; |
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import jalview.datamodel.SearchResultsI; |
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import jalview.datamodel.SequenceI; |
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import jalview.ext.jmol.JmolParser; |
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import jalview.gui.IProgressIndicator; |
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import jalview.gui.Preferences; |
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import jalview.io.AppletFormatAdapter; |
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import jalview.io.DataSourceType; |
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import jalview.io.StructureFile; |
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import jalview.structure.StructureImportSettings.TFType; |
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import jalview.util.Constants; |
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import jalview.util.MappingUtils; |
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import jalview.util.MessageManager; |
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import jalview.util.Platform; |
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import jalview.ws.sifts.SiftsClient; |
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import jalview.ws.sifts.SiftsException; |
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import jalview.ws.sifts.SiftsSettings; |
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import mc_view.Atom; |
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import mc_view.PDBChain; |
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import mc_view.PDBfile; |
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| 56.1% |
Uncovered Elements: 344 (783) |
Complexity: 226 |
Complexity Density: 0.48 |
|
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public class StructureSelectionManager |
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{ |
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public final static String NEWLINE = System.lineSeparator(); |
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static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances; |
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private List<StructureMapping> mappings = new ArrayList<>(); |
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private boolean processSecondaryStructure = false; |
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private boolean secStructServices = false; |
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private boolean addTempFacAnnot = false; |
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private List<AlignedCodonFrame> seqmappings = new ArrayList<>(); |
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private List<CommandListener> commandListeners = new ArrayList<>(); |
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private List<SelectionListener> sel_listeners = new ArrayList<>(); |
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@return |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
public boolean isSecStructServices()... |
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{ |
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0 |
return secStructServices; |
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} |
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@param |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public void setSecStructServices(boolean secStructServices)... |
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{ |
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this.secStructServices = secStructServices; |
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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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0 |
public boolean isAddTempFacAnnot()... |
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{ |
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return addTempFacAnnot; |
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} |
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@param |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public void setAddTempFacAnnot(boolean addTempFacAnnot)... |
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{ |
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this.addTempFacAnnot = addTempFacAnnot; |
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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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0 |
public boolean isProcessSecondaryStructure()... |
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{ |
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return processSecondaryStructure; |
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} |
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@param |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
149 |
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public void setProcessSecondaryStructure(boolean enable)... |
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{ |
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processSecondaryStructure = enable; |
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} |
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156 |
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| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
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0 |
public void reportMapping()... |
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{ |
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if (mappings.isEmpty()) |
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{ |
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jalview.bin.Console |
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.errPrintln("reportMapping: No PDB/Sequence mappings."); |
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} |
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else |
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{ |
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jalview.bin.Console.errPrintln( |
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"reportMapping: There are " + mappings.size() + " mappings."); |
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int i = 0; |
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for (StructureMapping sm : mappings) |
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{ |
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jalview.bin.Console |
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.errPrintln("mapping " + i++ + " : " + sm.pdbfile); |
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} |
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} |
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} |
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Map<String, String> pdbIdFileName = new HashMap<>(); |
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Map<String, String> pdbFileNameId = new HashMap<>(); |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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public void registerPDBFile(String idForFile, String absoluteFile)... |
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{ |
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pdbIdFileName.put(idForFile, absoluteFile); |
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pdbFileNameId.put(absoluteFile, idForFile); |
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} |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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public String findIdForPDBFile(String idOrFile)... |
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{ |
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String id = pdbFileNameId.get(idOrFile); |
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254 |
return id; |
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} |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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1 |
public String findFileForPDBId(String idOrFile)... |
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{ |
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1 |
String id = pdbIdFileName.get(idOrFile); |
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1 |
return id; |
201 |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
203 |
135 |
public boolean isPDBFileRegistered(String idOrFile)... |
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{ |
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return pdbFileNameId.containsKey(idOrFile) |
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|| pdbIdFileName.containsKey(idOrFile); |
207 |
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} |
208 |
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private static StructureSelectionManager nullProvider = null; |
210 |
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|
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| 92.6% |
Uncovered Elements: 2 (27) |
Complexity: 7 |
Complexity Density: 0.47 |
|
211 |
6087 |
public static StructureSelectionManager getStructureSelectionManager(... |
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StructureSelectionManagerProvider context) |
213 |
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{ |
214 |
6087 |
if (context == null) |
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{ |
216 |
615 |
if (nullProvider == null) |
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{ |
218 |
47 |
if (instances != null) |
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{ |
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throw new Error(MessageManager.getString( |
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"error.implementation_error_structure_selection_manager_null"), |
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new NullPointerException(MessageManager |
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.getString("exception.ssm_context_is_null"))); |
224 |
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} |
225 |
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else |
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{ |
227 |
47 |
nullProvider = new StructureSelectionManager(); |
228 |
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} |
229 |
47 |
return nullProvider; |
230 |
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} |
231 |
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} |
232 |
6040 |
if (instances == null) |
233 |
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{ |
234 |
54 |
instances = new java.util.IdentityHashMap<>(); |
235 |
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} |
236 |
6040 |
StructureSelectionManager instance = instances.get(context); |
237 |
6040 |
if (instance == null) |
238 |
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{ |
239 |
122 |
if (nullProvider != null) |
240 |
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{ |
241 |
115 |
instance = nullProvider; |
242 |
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} |
243 |
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else |
244 |
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{ |
245 |
7 |
instance = new StructureSelectionManager(); |
246 |
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} |
247 |
122 |
instances.put(context, instance); |
248 |
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} |
249 |
6040 |
return instance; |
250 |
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} |
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252 |
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253 |
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254 |
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255 |
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256 |
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boolean relaySeqMappings = true; |
257 |
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258 |
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259 |
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260 |
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261 |
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262 |
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263 |
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@param |
264 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
265 |
0 |
public void setRelaySeqMappings(boolean relay)... |
266 |
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{ |
267 |
0 |
relaySeqMappings = relay; |
268 |
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} |
269 |
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270 |
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271 |
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272 |
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|
273 |
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@return |
274 |
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275 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
276 |
0 |
public boolean isRelaySeqMappingsEnabled()... |
277 |
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{ |
278 |
0 |
return relaySeqMappings; |
279 |
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} |
280 |
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281 |
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Vector listeners = new Vector(); |
282 |
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|
283 |
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|
284 |
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|
285 |
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|
286 |
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@param |
287 |
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| 100% |
Uncovered Elements: 0 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
288 |
526 |
public void addStructureViewerListener(Object svl)... |
289 |
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{ |
290 |
526 |
if (!listeners.contains(svl)) |
291 |
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{ |
292 |
524 |
listeners.addElement(svl); |
293 |
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} |
294 |
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} |
295 |
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296 |
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297 |
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298 |
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|
299 |
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|
300 |
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@param |
301 |
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@return |
302 |
|
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| 66.7% |
Uncovered Elements: 2 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
303 |
1 |
public String alreadyMappedToFile(String pdbid)... |
304 |
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{ |
305 |
1 |
for (StructureMapping sm : mappings) |
306 |
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{ |
307 |
1 |
if (sm.getPdbId().equalsIgnoreCase(pdbid)) |
308 |
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{ |
309 |
0 |
return sm.pdbfile; |
310 |
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} |
311 |
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} |
312 |
1 |
return null; |
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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318 |
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319 |
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@param |
320 |
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321 |
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@param |
322 |
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323 |
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324 |
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@param |
325 |
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326 |
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@param |
327 |
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328 |
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@return |
329 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
330 |
90 |
synchronized public StructureFile setMapping(SequenceI[] sequence,... |
331 |
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String[] targetChains, String pdbFile, DataSourceType protocol, |
332 |
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IProgressIndicator progress) |
333 |
|
{ |
334 |
90 |
return computeMapping(true, sequence, targetChains, pdbFile, protocol, |
335 |
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progress, null, null, true); |
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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341 |
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342 |
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343 |
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@param |
344 |
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345 |
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@param |
346 |
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347 |
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@param |
348 |
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349 |
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350 |
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@param |
351 |
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352 |
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@param |
353 |
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|
354 |
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@return |
355 |
|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
356 |
3 |
synchronized public StructureFile setMapping(boolean forStructureView,... |
357 |
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SequenceI[] sequenceArray, String[] targetChainIds, |
358 |
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String pdbFile, DataSourceType sourceType, TFType tft, |
359 |
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String paeFilename) |
360 |
|
{ |
361 |
3 |
return setMapping(forStructureView, sequenceArray, targetChainIds, |
362 |
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pdbFile, sourceType, tft, paeFilename, true); |
363 |
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} |
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 |
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@param |
371 |
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372 |
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373 |
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@param |
374 |
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375 |
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@param |
376 |
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377 |
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378 |
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379 |
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380 |
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@param |
381 |
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382 |
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@param |
383 |
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384 |
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@param |
385 |
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386 |
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387 |
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@param |
388 |
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389 |
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390 |
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@param |
391 |
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392 |
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393 |
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@return |
394 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
395 |
58 |
synchronized public StructureFile setMapping(boolean forStructureView,... |
396 |
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SequenceI[] sequenceArray, String[] targetChainIds, |
397 |
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String pdbFile, DataSourceType sourceType, TFType tft, |
398 |
|
String paeFilename, boolean doXferSettings) |
399 |
|
{ |
400 |
58 |
return computeMapping(forStructureView, sequenceArray, targetChainIds, |
401 |
|
pdbFile, sourceType, null, tft, paeFilename, doXferSettings); |
402 |
|
} |
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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409 |
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@param |
410 |
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411 |
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412 |
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@param |
413 |
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414 |
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@param |
415 |
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416 |
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417 |
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418 |
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419 |
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@param |
420 |
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421 |
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@param |
422 |
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423 |
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@param |
424 |
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425 |
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426 |
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@param |
427 |
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428 |
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429 |
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@param |
430 |
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|
431 |
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|
432 |
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@param |
433 |
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|
434 |
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|
435 |
|
@return |
436 |
|
|
|
|
| 62.3% |
Uncovered Elements: 75 (199) |
Complexity: 49 |
Complexity Density: 0.35 |
|
437 |
150 |
synchronized public StructureFile computeMapping(boolean forStructureView,... |
438 |
|
SequenceI[] sequenceArray, String[] targetChainIds, |
439 |
|
String pdbFile, DataSourceType sourceType, |
440 |
|
IProgressIndicator progress, TFType tft, String paeFilename, |
441 |
|
boolean doXferSettings) |
442 |
|
{ |
443 |
150 |
long progressSessionId = System.currentTimeMillis() * 3; |
444 |
|
|
445 |
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|
446 |
|
|
447 |
|
|
448 |
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|
449 |
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|
450 |
150 |
boolean parseSecStr = processSecondaryStructure |
451 |
|
&& !isStructureFileProcessed(pdbFile, sequenceArray); |
452 |
|
|
453 |
150 |
StructureFile pdb = null; |
454 |
150 |
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts(); |
455 |
150 |
try |
456 |
|
{ |
457 |
|
|
458 |
150 |
sourceType = AppletFormatAdapter.checkProtocol(pdbFile); |
459 |
150 |
pdb = new JmolParser(false, pdbFile, sourceType); |
460 |
150 |
if (paeFilename != null) |
461 |
|
{ |
462 |
36 |
pdb.setPAEMatrix(paeFilename); |
463 |
|
} |
464 |
150 |
pdb.setTemperatureFactorType(tft); |
465 |
150 |
pdb.addSettings(parseSecStr && processSecondaryStructure, |
466 |
|
parseSecStr && addTempFacAnnot, |
467 |
|
parseSecStr && secStructServices); |
468 |
|
|
469 |
150 |
boolean temp = pdb.getDoXferSettings(); |
470 |
150 |
pdb.setDoXferSettings(doXferSettings); |
471 |
150 |
pdb.doParse(); |
472 |
150 |
pdb.setDoXferSettings(temp); |
473 |
150 |
if (pdb.getId() != null && pdb.getId().trim().length() > 0 |
474 |
|
&& DataSourceType.FILE == sourceType) |
475 |
|
{ |
476 |
138 |
registerPDBFile(pdb.getId().trim(), pdbFile); |
477 |
|
} |
478 |
|
|
479 |
|
|
480 |
|
|
481 |
|
|
482 |
150 |
boolean isProtein = false; |
483 |
150 |
for (SequenceI s : sequenceArray) |
484 |
|
{ |
485 |
150 |
if (s.isProtein()) |
486 |
|
{ |
487 |
150 |
isProtein = true; |
488 |
150 |
break; |
489 |
|
} |
490 |
|
} |
491 |
150 |
isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable() |
492 |
|
&& !pdb.getId().startsWith("AF-") && isProtein; |
493 |
|
|
494 |
|
} catch (Exception ex) |
495 |
|
{ |
496 |
0 |
ex.printStackTrace(); |
497 |
0 |
return null; |
498 |
|
} |
499 |
|
|
500 |
|
|
501 |
|
|
502 |
150 |
SiftsClient siftsClient = null; |
503 |
150 |
try |
504 |
|
{ |
505 |
150 |
if (isMapUsingSIFTs) |
506 |
|
{ |
507 |
0 |
siftsClient = new SiftsClient(pdb); |
508 |
|
} |
509 |
|
} catch (SiftsException e) |
510 |
|
{ |
511 |
0 |
isMapUsingSIFTs = false; |
512 |
0 |
Console.error("SIFTS mapping failed", e); |
513 |
0 |
Console.error("Falling back on Needleman & Wunsch alignment"); |
514 |
0 |
siftsClient = null; |
515 |
|
} |
516 |
|
|
517 |
150 |
String targetChainId; |
518 |
345 |
for (int s = 0; s < sequenceArray.length; s++) |
519 |
|
{ |
520 |
195 |
boolean infChain = true; |
521 |
195 |
final SequenceI seq = sequenceArray[s]; |
522 |
195 |
SequenceI ds = seq; |
523 |
388 |
while (ds.getDatasetSequence() != null) |
524 |
|
{ |
525 |
193 |
ds = ds.getDatasetSequence(); |
526 |
|
} |
527 |
|
|
528 |
195 |
if (targetChainIds != null && targetChainIds[s] != null) |
529 |
|
{ |
530 |
40 |
infChain = false; |
531 |
40 |
targetChainId = targetChainIds[s]; |
532 |
|
} |
533 |
155 |
else if (seq.getName().indexOf("|") > -1) |
534 |
|
{ |
535 |
59 |
targetChainId = seq.getName() |
536 |
|
.substring(seq.getName().lastIndexOf("|") + 1); |
537 |
59 |
if (targetChainId.length() > 1) |
538 |
|
{ |
539 |
1 |
if (targetChainId.trim().length() == 0) |
540 |
|
{ |
541 |
0 |
targetChainId = " "; |
542 |
|
} |
543 |
|
else |
544 |
|
{ |
545 |
|
|
546 |
1 |
targetChainId = ""; |
547 |
|
} |
548 |
|
} |
549 |
|
} |
550 |
|
else |
551 |
|
{ |
552 |
96 |
targetChainId = ""; |
553 |
|
} |
554 |
|
|
555 |
|
|
556 |
|
|
557 |
|
|
558 |
|
|
559 |
195 |
float max = -10; |
560 |
195 |
AlignSeq maxAlignseq = null; |
561 |
195 |
String maxChainId = " "; |
562 |
195 |
PDBChain maxChain = null; |
563 |
195 |
boolean first = true; |
564 |
195 |
for (PDBChain chain : pdb.getChains()) |
565 |
|
{ |
566 |
247 |
if (targetChainId.length() > 0 && !targetChainId.equals(chain.id) |
567 |
|
&& !infChain) |
568 |
|
{ |
569 |
16 |
continue; |
570 |
|
} |
571 |
|
|
572 |
|
|
573 |
231 |
final String type = chain.isNa ? AlignSeq.DNA : AlignSeq.PEP; |
574 |
231 |
AlignSeq as = AlignSeq.doGlobalNWAlignment(seq, chain.sequence, |
575 |
|
type); |
576 |
|
|
577 |
|
|
578 |
|
|
579 |
|
|
580 |
|
|
581 |
231 |
if (first || as.maxscore > max |
582 |
|
|| (as.maxscore == max && chain.id.equals(targetChainId))) |
583 |
|
{ |
584 |
203 |
first = false; |
585 |
203 |
maxChain = chain; |
586 |
203 |
max = as.maxscore; |
587 |
203 |
maxAlignseq = as; |
588 |
203 |
maxChainId = chain.id; |
589 |
|
} |
590 |
|
} |
591 |
195 |
if (maxChain == null) |
592 |
|
{ |
593 |
0 |
continue; |
594 |
|
} |
595 |
|
|
596 |
195 |
if (sourceType == DataSourceType.PASTE) |
597 |
|
{ |
598 |
16 |
pdbFile = "INLINE" + pdb.getId(); |
599 |
|
} |
600 |
|
|
601 |
195 |
List<StructureMapping> seqToStrucMapping = new ArrayList<>(); |
602 |
195 |
String provider = null; |
603 |
195 |
if (isMapUsingSIFTs && seq.isProtein()) |
604 |
|
{ |
605 |
0 |
if (progress != null) |
606 |
|
{ |
607 |
0 |
progress.setProgressBar( |
608 |
|
MessageManager |
609 |
|
.getString("status.obtaining_mapping_with_sifts"), |
610 |
|
progressSessionId); |
611 |
|
} |
612 |
0 |
jalview.datamodel.Mapping sqmpping = maxAlignseq |
613 |
|
.getMappingFromS1(false); |
614 |
0 |
if (targetChainId != null && !targetChainId.trim().isEmpty()) |
615 |
|
{ |
616 |
0 |
StructureMapping siftsMapping; |
617 |
0 |
try |
618 |
|
{ |
619 |
0 |
siftsMapping = getStructureMapping(seq, pdbFile, targetChainId, |
620 |
|
pdb, maxChain, sqmpping, maxAlignseq, siftsClient); |
621 |
0 |
seqToStrucMapping.add(siftsMapping); |
622 |
0 |
maxChain.makeExactMapping(siftsMapping, seq); |
623 |
0 |
maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS", |
624 |
|
pdb.getId().toLowerCase(Locale.ROOT)); |
625 |
0 |
maxChain.transferResidueAnnotation(siftsMapping, null); |
626 |
0 |
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); |
627 |
|
|
628 |
|
} catch (SiftsException e) |
629 |
|
{ |
630 |
|
|
631 |
0 |
Console.error(e.getMessage()); |
632 |
0 |
StructureMapping nwMapping = getNWMappings(seq, pdbFile, |
633 |
|
targetChainId, maxChain, pdb, maxAlignseq); |
634 |
0 |
seqToStrucMapping.add(nwMapping); |
635 |
0 |
maxChain.makeExactMapping(maxAlignseq, seq); |
636 |
0 |
maxChain.transferRESNUMFeatures(seq, "IEA:Jalview", |
637 |
|
pdb.getId().toLowerCase(Locale.ROOT)); |
638 |
|
|
639 |
0 |
maxChain.transferResidueAnnotation(nwMapping, sqmpping); |
640 |
0 |
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); |
641 |
|
} |
642 |
|
} |
643 |
|
else |
644 |
|
{ |
645 |
0 |
List<StructureMapping> foundSiftsMappings = new ArrayList<>(); |
646 |
0 |
for (PDBChain chain : pdb.getChains()) |
647 |
|
{ |
648 |
0 |
StructureMapping siftsMapping = null; |
649 |
0 |
try |
650 |
|
{ |
651 |
0 |
siftsMapping = getStructureMapping(seq, pdbFile, chain.id, |
652 |
|
pdb, chain, sqmpping, maxAlignseq, siftsClient); |
653 |
0 |
foundSiftsMappings.add(siftsMapping); |
654 |
0 |
chain.makeExactMapping(siftsMapping, seq); |
655 |
0 |
chain.transferRESNUMFeatures(seq, "IEA: SIFTS", |
656 |
|
pdb.getId().toLowerCase(Locale.ROOT)); |
657 |
|
|
658 |
0 |
chain.transferResidueAnnotation(siftsMapping, null); |
659 |
|
} catch (SiftsException e) |
660 |
|
{ |
661 |
0 |
jalview.bin.Console.errPrintln(e.getMessage()); |
662 |
|
} catch (Exception e) |
663 |
|
{ |
664 |
0 |
jalview.bin.Console.errPrintln( |
665 |
|
"Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair"); |
666 |
0 |
jalview.bin.Console.errPrintln(e.getMessage()); |
667 |
|
} |
668 |
|
} |
669 |
0 |
if (!foundSiftsMappings.isEmpty()) |
670 |
|
{ |
671 |
0 |
seqToStrucMapping.addAll(foundSiftsMappings); |
672 |
0 |
ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0)); |
673 |
|
} |
674 |
|
else |
675 |
|
{ |
676 |
0 |
StructureMapping nwMapping = getNWMappings(seq, pdbFile, |
677 |
|
maxChainId, maxChain, pdb, maxAlignseq); |
678 |
0 |
seqToStrucMapping.add(nwMapping); |
679 |
0 |
maxChain.transferRESNUMFeatures(seq, null, |
680 |
|
pdb.getId().toLowerCase(Locale.ROOT)); |
681 |
|
|
682 |
0 |
maxChain.transferResidueAnnotation(nwMapping, sqmpping); |
683 |
0 |
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); |
684 |
|
} |
685 |
|
} |
686 |
|
} |
687 |
|
else |
688 |
|
{ |
689 |
195 |
if (progress != null) |
690 |
|
{ |
691 |
0 |
progress.setProgressBar( |
692 |
|
MessageManager.getString( |
693 |
|
"status.obtaining_mapping_with_nw_alignment"), |
694 |
|
progressSessionId); |
695 |
|
} |
696 |
195 |
StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId, |
697 |
|
maxChain, pdb, maxAlignseq); |
698 |
195 |
seqToStrucMapping.add(nwMapping); |
699 |
195 |
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); |
700 |
|
} |
701 |
|
|
702 |
|
|
703 |
|
|
704 |
195 |
String ssAnnotDescriptionInPDB = null; |
705 |
195 |
String ssStructFilePathNameInPDB = pdb.getInFile(); |
706 |
|
|
707 |
|
|
708 |
195 |
AlignmentAnnotation[] ssAnnotationsInPDB = pdb.getSeqs().get(0) |
709 |
|
.getAnnotation(Constants.SS_ANNOTATION_LABEL); |
710 |
195 |
if (ssAnnotationsInPDB != null && ssAnnotationsInPDB.length > 0) |
711 |
|
{ |
712 |
149 |
ssAnnotDescriptionInPDB = ssAnnotationsInPDB[0].description; |
713 |
|
} |
714 |
|
|
715 |
|
|
716 |
|
|
717 |
195 |
if (ssStructFilePathNameInPDB != null |
718 |
|
&& seq.getDatasetSequence() != null) |
719 |
|
{ |
720 |
193 |
Vector<PDBEntry> pdbEntries = seq.getDatasetSequence() |
721 |
|
.getAllPDBEntries(); |
722 |
193 |
if (pdbEntries != null) |
723 |
|
{ |
724 |
193 |
for (PDBEntry pdbEntry : pdbEntries) |
725 |
|
{ |
726 |
236 |
if (pdbEntry.getFile() != null && ssStructFilePathNameInPDB |
727 |
|
.startsWith(pdbEntry.getFile())) |
728 |
|
{ |
729 |
177 |
provider = pdbEntry.getProvider(); |
730 |
177 |
break; |
731 |
|
} |
732 |
|
} |
733 |
|
|
734 |
193 |
if (provider != null) |
735 |
|
{ |
736 |
|
|
737 |
|
|
738 |
0 |
AlignmentAnnotation[] ssAnnotList = ds |
739 |
|
.getAnnotation(Constants.SS_ANNOTATION_LABEL); |
740 |
0 |
if (ssAnnotList != null) |
741 |
|
{ |
742 |
0 |
for (AlignmentAnnotation ssAnnot : ssAnnotList) |
743 |
|
{ |
744 |
|
|
745 |
|
|
746 |
0 |
if (ssAnnot |
747 |
|
.getProperty(Constants.SS_PROVIDER_PROPERTY) == null |
748 |
|
&& ssAnnot.description |
749 |
|
.equals(ssAnnotDescriptionInPDB)) |
750 |
|
{ |
751 |
0 |
ssAnnot.setProperty(Constants.SS_PROVIDER_PROPERTY, |
752 |
|
provider); |
753 |
|
} |
754 |
|
} |
755 |
|
} |
756 |
|
} |
757 |
|
} |
758 |
|
} |
759 |
|
|
760 |
195 |
if (forStructureView) |
761 |
|
{ |
762 |
138 |
for (StructureMapping sm : seqToStrucMapping) |
763 |
|
{ |
764 |
138 |
addStructureMapping(sm); |
765 |
|
} |
766 |
|
} |
767 |
195 |
if (progress != null) |
768 |
|
{ |
769 |
0 |
progress.setProgressBar(null, progressSessionId); |
770 |
|
} |
771 |
|
} |
772 |
150 |
return pdb; |
773 |
|
} |
774 |
|
|
775 |
|
|
776 |
|
|
777 |
|
|
778 |
|
|
779 |
|
@param |
780 |
|
@param |
781 |
|
@return |
782 |
|
|
|
|
| 90% |
Uncovered Elements: 2 (20) |
Complexity: 5 |
Complexity Density: 0.42 |
|
783 |
135 |
private boolean isStructureFileProcessed(String pdbFile,... |
784 |
|
SequenceI[] sequenceArray) |
785 |
|
{ |
786 |
135 |
boolean processed = false; |
787 |
135 |
if (isPDBFileRegistered(pdbFile)) |
788 |
|
{ |
789 |
84 |
for (SequenceI sq : sequenceArray) |
790 |
|
{ |
791 |
125 |
SequenceI ds = sq; |
792 |
250 |
while (ds.getDatasetSequence() != null) |
793 |
|
{ |
794 |
125 |
ds = ds.getDatasetSequence(); |
795 |
|
} |
796 |
125 |
; |
797 |
125 |
if (ds.getAnnotation() != null) |
798 |
|
{ |
799 |
103 |
for (AlignmentAnnotation ala : ds.getAnnotation()) |
800 |
|
{ |
801 |
|
|
802 |
|
|
803 |
|
|
804 |
254 |
if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile))) |
805 |
|
{ |
806 |
0 |
processed = true; |
807 |
|
} |
808 |
|
} |
809 |
|
} |
810 |
|
} |
811 |
|
} |
812 |
135 |
return processed; |
813 |
|
} |
814 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
815 |
145 |
public void addStructureMapping(StructureMapping sm)... |
816 |
|
{ |
817 |
145 |
if (!mappings.contains(sm)) |
818 |
|
{ |
819 |
78 |
mappings.add(sm); |
820 |
|
} |
821 |
|
} |
822 |
|
|
823 |
|
|
824 |
|
|
825 |
|
|
826 |
|
|
827 |
|
@param |
828 |
|
@param |
829 |
|
@param |
830 |
|
@param |
831 |
|
@param |
832 |
|
@param |
833 |
|
@param |
834 |
|
@param |
835 |
|
|
836 |
|
@return |
837 |
|
@throws |
838 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 3 |
Complexity Density: 0.43 |
|
839 |
0 |
private StructureMapping getStructureMapping(SequenceI seq,... |
840 |
|
String pdbFile, String targetChainId, StructureFile pdb, |
841 |
|
PDBChain maxChain, jalview.datamodel.Mapping sqmpping, |
842 |
|
AlignSeq maxAlignseq, SiftsClient siftsClient) |
843 |
|
throws SiftsException |
844 |
|
{ |
845 |
0 |
StructureMapping curChainMapping = siftsClient |
846 |
|
.getSiftsStructureMapping(seq, pdbFile, targetChainId); |
847 |
0 |
try |
848 |
|
{ |
849 |
0 |
PDBChain chain = pdb.findChain(targetChainId); |
850 |
0 |
if (chain != null) |
851 |
|
{ |
852 |
0 |
chain.transferResidueAnnotation(curChainMapping, null); |
853 |
|
} |
854 |
|
} catch (Exception e) |
855 |
|
{ |
856 |
0 |
e.printStackTrace(); |
857 |
|
} |
858 |
0 |
return curChainMapping; |
859 |
|
} |
860 |
|
|
|
|
| 97.4% |
Uncovered Elements: 1 (39) |
Complexity: 6 |
Complexity Density: 0.18 |
|
861 |
195 |
private StructureMapping getNWMappings(SequenceI seq, String pdbFile,... |
862 |
|
String maxChainId, PDBChain maxChain, StructureFile pdb, |
863 |
|
AlignSeq maxAlignseq) |
864 |
|
{ |
865 |
195 |
final StringBuilder mappingDetails = new StringBuilder(128); |
866 |
195 |
mappingDetails.append(NEWLINE) |
867 |
|
.append("Sequence \u27f7 Structure mapping details"); |
868 |
195 |
mappingDetails.append(NEWLINE); |
869 |
195 |
mappingDetails |
870 |
|
.append("Method: inferred with Needleman & Wunsch alignment"); |
871 |
195 |
mappingDetails.append(NEWLINE).append("PDB Sequence is :") |
872 |
|
.append(NEWLINE).append("Sequence = ") |
873 |
|
.append(maxChain.sequence.getSequenceAsString()); |
874 |
195 |
mappingDetails.append(NEWLINE).append("No of residues = ") |
875 |
|
.append(maxChain.residues.size()).append(NEWLINE) |
876 |
|
.append(NEWLINE); |
877 |
195 |
PrintStream ps = new PrintStream(System.out) |
878 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
879 |
195 |
@Override... |
880 |
|
public void print(String x) |
881 |
|
{ |
882 |
195 |
mappingDetails.append(x); |
883 |
|
} |
884 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
885 |
0 |
@Override... |
886 |
|
public void println() |
887 |
|
{ |
888 |
0 |
mappingDetails.append(NEWLINE); |
889 |
|
} |
890 |
|
}; |
891 |
|
|
892 |
195 |
maxAlignseq.printAlignment(ps); |
893 |
|
|
894 |
195 |
mappingDetails.append(NEWLINE).append("PDB start/end "); |
895 |
195 |
mappingDetails.append(String.valueOf(maxAlignseq.seq2start)) |
896 |
|
.append(" "); |
897 |
195 |
mappingDetails.append(String.valueOf(maxAlignseq.seq2end)); |
898 |
195 |
mappingDetails.append(NEWLINE).append("SEQ start/end "); |
899 |
195 |
mappingDetails |
900 |
|
.append(String |
901 |
|
.valueOf(maxAlignseq.seq1start + (seq.getStart() - 1))) |
902 |
|
.append(" "); |
903 |
195 |
mappingDetails.append( |
904 |
|
String.valueOf(maxAlignseq.seq1end + (seq.getStart() - 1))); |
905 |
195 |
mappingDetails.append(NEWLINE); |
906 |
195 |
maxChain.makeExactMapping(maxAlignseq, seq); |
907 |
195 |
jalview.datamodel.Mapping sqmpping = maxAlignseq |
908 |
|
.getMappingFromS1(false); |
909 |
195 |
maxChain.transferRESNUMFeatures(seq, null, |
910 |
|
pdb.getId().toLowerCase(Locale.ROOT)); |
911 |
|
|
912 |
195 |
HashMap<Integer, int[]> mapping = new HashMap<>(); |
913 |
195 |
int resNum = -10000; |
914 |
195 |
int index = 0; |
915 |
195 |
char insCode = ' '; |
916 |
|
|
917 |
195 |
do |
918 |
|
{ |
919 |
21404 |
Atom tmp = maxChain.atoms.elementAt(index); |
920 |
21404 |
if ((resNum != tmp.resNumber || insCode != tmp.insCode) |
921 |
|
&& tmp.alignmentMapping != -1) |
922 |
|
{ |
923 |
21354 |
resNum = tmp.resNumber; |
924 |
21354 |
insCode = tmp.insCode; |
925 |
21354 |
if (tmp.alignmentMapping >= -1) |
926 |
|
{ |
927 |
21354 |
mapping.put(tmp.alignmentMapping + 1, |
928 |
|
new int[] |
929 |
|
{ tmp.resNumber, tmp.atomIndex }); |
930 |
|
} |
931 |
|
} |
932 |
|
|
933 |
21404 |
index++; |
934 |
21404 |
} while (index < maxChain.atoms.size()); |
935 |
|
|
936 |
195 |
StructureMapping nwMapping = new StructureMapping(seq, pdbFile, |
937 |
|
pdb.getId(), maxChainId, mapping, mappingDetails.toString()); |
938 |
195 |
maxChain.transferResidueAnnotation(nwMapping, sqmpping); |
939 |
195 |
return nwMapping; |
940 |
|
} |
941 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (36) |
Complexity: 9 |
Complexity Density: 0.45 |
|
942 |
529 |
public void removeStructureViewerListener(Object svl, String[] pdbfiles)... |
943 |
|
{ |
944 |
529 |
listeners.removeElement(svl); |
945 |
529 |
if (svl instanceof SequenceListener) |
946 |
|
{ |
947 |
1316 |
for (int i = 0; i < listeners.size(); i++) |
948 |
|
{ |
949 |
810 |
if (listeners.elementAt(i) instanceof StructureListener) |
950 |
|
{ |
951 |
34 |
((StructureListener) listeners.elementAt(i)) |
952 |
|
.releaseReferences(svl); |
953 |
|
} |
954 |
|
} |
955 |
|
} |
956 |
|
|
957 |
529 |
if (pdbfiles == null) |
958 |
|
{ |
959 |
506 |
return; |
960 |
|
} |
961 |
|
|
962 |
|
|
963 |
|
|
964 |
|
|
965 |
|
|
966 |
23 |
List<String> pdbs = new ArrayList<>(Arrays.asList(pdbfiles)); |
967 |
|
|
968 |
23 |
StructureListener sl; |
969 |
76 |
for (int i = 0; i < listeners.size(); i++) |
970 |
|
{ |
971 |
53 |
if (listeners.elementAt(i) instanceof StructureListener) |
972 |
|
{ |
973 |
6 |
sl = (StructureListener) listeners.elementAt(i); |
974 |
6 |
for (String pdbfile : sl.getStructureFiles()) |
975 |
|
{ |
976 |
7 |
pdbs.remove(pdbfile); |
977 |
|
} |
978 |
|
} |
979 |
|
} |
980 |
|
|
981 |
|
|
982 |
|
|
983 |
|
|
984 |
|
|
985 |
23 |
if (pdbs.size() > 0) |
986 |
|
{ |
987 |
22 |
List<StructureMapping> tmp = new ArrayList<>(); |
988 |
22 |
for (StructureMapping sm : mappings) |
989 |
|
{ |
990 |
37 |
if (!pdbs.contains(sm.pdbfile)) |
991 |
|
{ |
992 |
7 |
tmp.add(sm); |
993 |
|
} |
994 |
|
} |
995 |
|
|
996 |
22 |
mappings = tmp; |
997 |
|
} |
998 |
|
} |
999 |
|
|
1000 |
|
|
1001 |
|
|
1002 |
|
|
1003 |
|
@param |
1004 |
|
@param |
1005 |
|
|
1006 |
|
@param |
1007 |
|
@param |
1008 |
|
|
|
|
| 0% |
Uncovered Elements: 24 (24) |
Complexity: 5 |
Complexity Density: 0.31 |
|
1009 |
0 |
public void highlightPositionsOn(SequenceI sequenceRef, int[][] is,... |
1010 |
|
Object source) |
1011 |
|
{ |
1012 |
0 |
boolean hasSequenceListeners = handlingVamsasMo |
1013 |
|
|| !seqmappings.isEmpty(); |
1014 |
0 |
SearchResultsI results = null; |
1015 |
0 |
ArrayList<Integer> listOfPositions = new ArrayList<Integer>(); |
1016 |
0 |
for (int[] s_e : is) |
1017 |
|
{ |
1018 |
0 |
for (int p = s_e[0]; p <= s_e[1]; listOfPositions.add(p++)) |
1019 |
0 |
; |
1020 |
|
} |
1021 |
0 |
int seqpos[] = new int[listOfPositions.size()]; |
1022 |
0 |
int i = 0; |
1023 |
0 |
for (Integer p : listOfPositions) |
1024 |
|
{ |
1025 |
0 |
seqpos[i++] = p; |
1026 |
|
} |
1027 |
|
|
1028 |
0 |
for (i = 0; i < listeners.size(); i++) |
1029 |
|
{ |
1030 |
0 |
Object listener = listeners.elementAt(i); |
1031 |
0 |
if (listener == source) |
1032 |
|
{ |
1033 |
|
|
1034 |
|
|
1035 |
0 |
continue; |
1036 |
|
} |
1037 |
0 |
if (listener instanceof StructureListener) |
1038 |
|
{ |
1039 |
0 |
highlightStructure((StructureListener) listener, sequenceRef, |
1040 |
|
seqpos); |
1041 |
|
} |
1042 |
|
|
1043 |
|
} |
1044 |
|
} |
1045 |
|
|
1046 |
|
|
1047 |
|
|
1048 |
|
|
1049 |
|
@param |
1050 |
|
@param |
1051 |
|
@param |
1052 |
|
@return |
1053 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
1054 |
1 |
public String mouseOverStructure(int pdbResNum, String chain,... |
1055 |
|
String pdbfile) |
1056 |
|
{ |
1057 |
1 |
AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0); |
1058 |
1 |
List<AtomSpec> atoms = Collections.singletonList(atomSpec); |
1059 |
1 |
return mouseOverStructure(atoms); |
1060 |
|
} |
1061 |
|
|
1062 |
|
|
1063 |
|
|
1064 |
|
|
1065 |
|
@param |
1066 |
|
|
|
|
| 78.6% |
Uncovered Elements: 6 (28) |
Complexity: 7 |
Complexity Density: 0.44 |
|
1067 |
1 |
public String mouseOverStructure(List<AtomSpec> atoms)... |
1068 |
|
{ |
1069 |
1 |
if (listeners == null) |
1070 |
|
{ |
1071 |
|
|
1072 |
0 |
return null; |
1073 |
|
} |
1074 |
1 |
boolean hasSequenceListener = false; |
1075 |
3 |
for (int i = 0; i < listeners.size(); i++) |
1076 |
|
{ |
1077 |
2 |
if (listeners.elementAt(i) instanceof SequenceListener) |
1078 |
|
{ |
1079 |
1 |
hasSequenceListener = true; |
1080 |
|
} |
1081 |
|
} |
1082 |
1 |
if (!hasSequenceListener) |
1083 |
|
{ |
1084 |
0 |
return null; |
1085 |
|
} |
1086 |
|
|
1087 |
1 |
SearchResultsI results = findAlignmentPositionsForStructurePositions( |
1088 |
|
atoms); |
1089 |
1 |
String result = null; |
1090 |
1 |
for (Object li : listeners) |
1091 |
|
{ |
1092 |
2 |
if (li instanceof SequenceListener) |
1093 |
|
{ |
1094 |
1 |
String s = ((SequenceListener) li).highlightSequence(results); |
1095 |
1 |
if (s != null) |
1096 |
|
{ |
1097 |
0 |
result = s; |
1098 |
|
} |
1099 |
|
} |
1100 |
|
} |
1101 |
1 |
return result; |
1102 |
|
} |
1103 |
|
|
1104 |
|
|
1105 |
|
|
1106 |
|
|
1107 |
|
|
1108 |
|
|
1109 |
|
@param |
1110 |
|
@return |
1111 |
|
|
|
|
| 88.9% |
Uncovered Elements: 2 (18) |
Complexity: 5 |
Complexity Density: 0.36 |
|
1112 |
1 |
public SearchResultsI findAlignmentPositionsForStructurePositions(... |
1113 |
|
List<AtomSpec> atoms) |
1114 |
|
{ |
1115 |
1 |
SearchResultsI results = new SearchResults(); |
1116 |
1 |
for (AtomSpec atom : atoms) |
1117 |
|
{ |
1118 |
1 |
SequenceI lastseq = null; |
1119 |
1 |
int lastipos = -1; |
1120 |
1 |
for (StructureMapping sm : mappings) |
1121 |
|
{ |
1122 |
2 |
if (sm.pdbfile.equals(atom.getPdbFile()) |
1123 |
|
&& sm.pdbchain.equals(atom.getChain())) |
1124 |
|
{ |
1125 |
1 |
int indexpos = sm.getSeqPos(atom.getPdbResNum()); |
1126 |
1 |
if (lastipos != indexpos || lastseq != sm.sequence) |
1127 |
|
{ |
1128 |
1 |
results.appendResult(sm.sequence, indexpos, indexpos); |
1129 |
1 |
lastipos = indexpos; |
1130 |
1 |
lastseq = sm.sequence; |
1131 |
|
|
1132 |
1 |
for (AlignedCodonFrame acf : seqmappings) |
1133 |
|
{ |
1134 |
0 |
acf.markMappedRegion(sm.sequence, indexpos, results); |
1135 |
|
} |
1136 |
|
} |
1137 |
|
} |
1138 |
|
} |
1139 |
|
} |
1140 |
1 |
return results; |
1141 |
|
} |
1142 |
|
|
1143 |
|
|
1144 |
|
|
1145 |
|
|
1146 |
|
@param |
1147 |
|
|
1148 |
|
@param |
1149 |
|
|
1150 |
|
@param |
1151 |
|
|
1152 |
|
|
1153 |
|
|
|
|
| 0% |
Uncovered Elements: 48 (48) |
Complexity: 15 |
Complexity Density: 0.62 |
|
1154 |
0 |
public void mouseOverSequence(SequenceI seq, int indexpos, int seqPos,... |
1155 |
|
VamsasSource source) |
1156 |
|
{ |
1157 |
0 |
boolean hasSequenceListeners = handlingVamsasMo |
1158 |
|
|| !seqmappings.isEmpty(); |
1159 |
0 |
SearchResultsI results = null; |
1160 |
0 |
if (seqPos == -1) |
1161 |
|
{ |
1162 |
0 |
seqPos = seq.findPosition(indexpos); |
1163 |
|
} |
1164 |
0 |
for (int i = 0; i < listeners.size(); i++) |
1165 |
|
{ |
1166 |
0 |
Object listener = listeners.elementAt(i); |
1167 |
0 |
if (listener == source) |
1168 |
|
{ |
1169 |
|
|
1170 |
|
|
1171 |
0 |
continue; |
1172 |
|
} |
1173 |
0 |
if (listener instanceof StructureListener) |
1174 |
|
{ |
1175 |
0 |
highlightStructure((StructureListener) listener, seq, seqPos); |
1176 |
|
} |
1177 |
|
else |
1178 |
|
{ |
1179 |
0 |
if (listener instanceof SequenceListener) |
1180 |
|
{ |
1181 |
0 |
final SequenceListener seqListener = (SequenceListener) listener; |
1182 |
0 |
if (hasSequenceListeners |
1183 |
|
&& seqListener.getVamsasSource() != source) |
1184 |
|
{ |
1185 |
0 |
if (relaySeqMappings) |
1186 |
|
{ |
1187 |
0 |
if (results == null) |
1188 |
|
{ |
1189 |
0 |
results = MappingUtils.buildSearchResults(seq, seqPos, |
1190 |
|
seqmappings); |
1191 |
|
} |
1192 |
0 |
if (handlingVamsasMo) |
1193 |
|
{ |
1194 |
0 |
results.addResult(seq, seqPos, seqPos); |
1195 |
|
|
1196 |
|
} |
1197 |
0 |
if (!results.isEmpty()) |
1198 |
|
{ |
1199 |
0 |
seqListener.highlightSequence(results); |
1200 |
|
} |
1201 |
|
} |
1202 |
|
} |
1203 |
|
} |
1204 |
0 |
else if (listener instanceof VamsasListener && !handlingVamsasMo) |
1205 |
|
{ |
1206 |
0 |
((VamsasListener) listener).mouseOverSequence(seq, indexpos, |
1207 |
|
source); |
1208 |
|
} |
1209 |
0 |
else if (listener instanceof SecondaryStructureListener) |
1210 |
|
{ |
1211 |
0 |
((SecondaryStructureListener) listener).mouseOverSequence(seq, |
1212 |
|
indexpos, seqPos); |
1213 |
|
} |
1214 |
|
} |
1215 |
|
} |
1216 |
|
} |
1217 |
|
|
1218 |
|
|
1219 |
|
|
1220 |
|
|
1221 |
|
|
1222 |
|
@param |
1223 |
|
@param |
1224 |
|
@param |
1225 |
|
|
|
|
| 0% |
Uncovered Elements: 17 (17) |
Complexity: 7 |
Complexity Density: 0.64 |
|
1226 |
0 |
public void highlightStructure(StructureListener sl, SequenceI seq,... |
1227 |
|
int... positions) |
1228 |
|
{ |
1229 |
0 |
if (!sl.isListeningFor(seq)) |
1230 |
|
{ |
1231 |
0 |
return; |
1232 |
|
} |
1233 |
0 |
int atomNo; |
1234 |
0 |
List<AtomSpec> atoms = new ArrayList<>(); |
1235 |
0 |
for (StructureMapping sm : mappings) |
1236 |
|
{ |
1237 |
0 |
if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence() |
1238 |
|
|| (sm.sequence.getDatasetSequence() != null && sm.sequence |
1239 |
|
.getDatasetSequence() == seq.getDatasetSequence())) |
1240 |
|
{ |
1241 |
0 |
for (int index : positions) |
1242 |
|
{ |
1243 |
0 |
atomNo = sm.getAtomNum(index); |
1244 |
|
|
1245 |
0 |
if (atomNo > 0) |
1246 |
|
{ |
1247 |
0 |
atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, |
1248 |
|
sm.getPDBResNum(index), atomNo)); |
1249 |
|
} |
1250 |
|
} |
1251 |
|
} |
1252 |
|
} |
1253 |
0 |
sl.highlightAtoms(atoms); |
1254 |
|
} |
1255 |
|
|
|
|
| 0% |
Uncovered Elements: 37 (37) |
Complexity: 12 |
Complexity Density: 0.57 |
|
1256 |
0 |
public void highlightStructureRegionsFor(StructureListener sl,... |
1257 |
|
SequenceI[] seqs, int... columns) |
1258 |
|
{ |
1259 |
0 |
List<SequenceI> to_highlight = new ArrayList<SequenceI>(); |
1260 |
0 |
for (SequenceI seq : seqs) |
1261 |
|
{ |
1262 |
0 |
if (sl.isListeningFor(seq)) |
1263 |
|
{ |
1264 |
0 |
to_highlight.add(seq); |
1265 |
|
} |
1266 |
|
} |
1267 |
0 |
if (to_highlight.size() == 0) |
1268 |
|
{ |
1269 |
0 |
return; |
1270 |
|
} |
1271 |
0 |
List<AtomSpec> atoms = new ArrayList<>(); |
1272 |
0 |
for (SequenceI seq : to_highlight) |
1273 |
|
{ |
1274 |
0 |
int atomNo; |
1275 |
0 |
for (StructureMapping sm : mappings) |
1276 |
|
{ |
1277 |
0 |
if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence() |
1278 |
|
|| (sm.sequence.getDatasetSequence() != null && sm.sequence |
1279 |
|
.getDatasetSequence() == seq.getDatasetSequence())) |
1280 |
|
{ |
1281 |
|
|
1282 |
0 |
for (int i = 0; i < columns.length; i += 2) |
1283 |
|
{ |
1284 |
0 |
ContiguousI positions = seq.findPositions(columns[i] + 1, |
1285 |
|
columns[i + 1] + 1); |
1286 |
0 |
if (positions == null) |
1287 |
|
{ |
1288 |
0 |
continue; |
1289 |
|
} |
1290 |
0 |
for (int index = positions.getBegin(); index <= positions |
1291 |
|
.getEnd(); index++) |
1292 |
|
{ |
1293 |
|
|
1294 |
0 |
atomNo = sm.getAtomNum(index); |
1295 |
|
|
1296 |
0 |
if (atomNo > 0) |
1297 |
|
{ |
1298 |
0 |
atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, |
1299 |
|
sm.getPDBResNum(index), atomNo)); |
1300 |
|
} |
1301 |
|
} |
1302 |
|
} |
1303 |
|
} |
1304 |
|
} |
1305 |
0 |
if (atoms.size() > 0) |
1306 |
|
{ |
1307 |
0 |
sl.highlightAtoms(atoms); |
1308 |
|
} |
1309 |
|
} |
1310 |
|
} |
1311 |
|
|
1312 |
|
|
1313 |
|
|
1314 |
|
|
1315 |
|
|
1316 |
|
boolean handlingVamsasMo = false; |
1317 |
|
|
1318 |
|
long lastmsg = 0; |
1319 |
|
|
1320 |
|
|
1321 |
|
|
1322 |
|
|
1323 |
|
@param |
1324 |
|
@param |
1325 |
|
|
1326 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
1327 |
0 |
public void mouseOverVamsasSequence(SequenceI sequenceI, int position,... |
1328 |
|
VamsasSource source) |
1329 |
|
{ |
1330 |
0 |
handlingVamsasMo = true; |
1331 |
0 |
long msg = sequenceI.hashCode() * (1 + position); |
1332 |
0 |
if (lastmsg != msg) |
1333 |
|
{ |
1334 |
0 |
lastmsg = msg; |
1335 |
0 |
mouseOverSequence(sequenceI, position, -1, source); |
1336 |
|
} |
1337 |
0 |
handlingVamsasMo = false; |
1338 |
|
} |
1339 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1340 |
0 |
public Annotation[] colourSequenceFromStructure(SequenceI seq,... |
1341 |
|
String pdbid) |
1342 |
|
{ |
1343 |
0 |
return null; |
1344 |
|
|
1345 |
|
|
1346 |
|
|
1347 |
|
|
1348 |
|
|
1349 |
|
|
1350 |
|
|
1351 |
|
|
1352 |
|
|
1353 |
|
|
1354 |
|
|
1355 |
|
|
1356 |
|
|
1357 |
|
|
1358 |
|
|
1359 |
|
|
1360 |
|
|
1361 |
|
|
1362 |
|
|
1363 |
|
|
1364 |
|
|
1365 |
|
|
1366 |
|
|
1367 |
|
|
1368 |
|
|
1369 |
|
|
1370 |
|
|
1371 |
|
|
1372 |
|
|
1373 |
|
} |
1374 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1375 |
0 |
public void structureSelectionChanged()... |
1376 |
|
{ |
1377 |
|
} |
1378 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1379 |
0 |
public void sequenceSelectionChanged()... |
1380 |
|
{ |
1381 |
|
} |
1382 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
1383 |
3672 |
public void sequenceColoursChanged(Object source)... |
1384 |
|
{ |
1385 |
3672 |
StructureListener sl; |
1386 |
17138 |
for (int i = 0; i < listeners.size(); i++) |
1387 |
|
{ |
1388 |
13467 |
if (listeners.elementAt(i) instanceof StructureListener) |
1389 |
|
{ |
1390 |
1129 |
sl = (StructureListener) listeners.elementAt(i); |
1391 |
1129 |
sl.updateColours(source); |
1392 |
|
} |
1393 |
|
} |
1394 |
|
} |
1395 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
1396 |
667 |
public StructureMapping[] getMapping(String pdbfile)... |
1397 |
|
{ |
1398 |
667 |
List<StructureMapping> tmp = new ArrayList<>(); |
1399 |
667 |
for (StructureMapping sm : mappings) |
1400 |
|
{ |
1401 |
711 |
if (sm.pdbfile.equals(pdbfile)) |
1402 |
|
{ |
1403 |
506 |
tmp.add(sm); |
1404 |
|
} |
1405 |
|
} |
1406 |
667 |
return tmp.toArray(new StructureMapping[tmp.size()]); |
1407 |
|
} |
1408 |
|
|
1409 |
|
|
1410 |
|
|
1411 |
|
|
1412 |
|
|
1413 |
|
@param |
1414 |
|
@param |
1415 |
|
@return |
1416 |
|
|
|
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 6 |
Complexity Density: 0.55 |
|
1417 |
0 |
public String printMappings(String pdbfile, List<SequenceI> seqs)... |
1418 |
|
{ |
1419 |
0 |
if (pdbfile == null || seqs == null || seqs.isEmpty()) |
1420 |
|
{ |
1421 |
0 |
return ""; |
1422 |
|
} |
1423 |
|
|
1424 |
0 |
StringBuilder sb = new StringBuilder(64); |
1425 |
0 |
for (StructureMapping sm : mappings) |
1426 |
|
{ |
1427 |
0 |
if (Platform.pathEquals(sm.pdbfile, pdbfile) |
1428 |
|
&& seqs.contains(sm.sequence)) |
1429 |
|
{ |
1430 |
0 |
sb.append(sm.mappingDetails); |
1431 |
0 |
sb.append(NEWLINE); |
1432 |
|
|
1433 |
0 |
sb.append("====================="); |
1434 |
0 |
sb.append(NEWLINE); |
1435 |
|
} |
1436 |
|
} |
1437 |
0 |
sb.append(NEWLINE); |
1438 |
|
|
1439 |
0 |
return sb.toString(); |
1440 |
|
} |
1441 |
|
|
1442 |
|
|
1443 |
|
|
1444 |
|
|
1445 |
|
@param |
1446 |
|
|
|
|
| 87.5% |
Uncovered Elements: 1 (8) |
Complexity: 4 |
Complexity Density: 1 |
|
1447 |
27 |
public void deregisterMapping(AlignedCodonFrame acf)... |
1448 |
|
{ |
1449 |
27 |
if (acf != null) |
1450 |
|
{ |
1451 |
27 |
boolean removed = seqmappings.remove(acf); |
1452 |
27 |
if (removed && seqmappings.isEmpty()) |
1453 |
|
{ |
1454 |
2 |
jalview.bin.Console.outPrintln("All mappings removed"); |
1455 |
|
} |
1456 |
|
} |
1457 |
|
} |
1458 |
|
|
1459 |
|
|
1460 |
|
|
1461 |
|
|
1462 |
|
@param |
1463 |
|
|
|
|
| 80% |
Uncovered Elements: 1 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1464 |
555 |
public void registerMappings(List<AlignedCodonFrame> mappings)... |
1465 |
|
{ |
1466 |
555 |
if (mappings != null) |
1467 |
|
{ |
1468 |
555 |
for (AlignedCodonFrame acf : mappings) |
1469 |
|
{ |
1470 |
152 |
registerMapping(acf); |
1471 |
|
} |
1472 |
|
} |
1473 |
|
} |
1474 |
|
|
1475 |
|
|
1476 |
|
|
1477 |
|
|
|
|
| 85.7% |
Uncovered Elements: 1 (7) |
Complexity: 3 |
Complexity Density: 1 |
|
1478 |
161 |
public void registerMapping(AlignedCodonFrame acf)... |
1479 |
|
{ |
1480 |
161 |
if (acf != null) |
1481 |
|
{ |
1482 |
161 |
if (!seqmappings.contains(acf)) |
1483 |
|
{ |
1484 |
38 |
seqmappings.add(acf); |
1485 |
|
} |
1486 |
|
} |
1487 |
|
} |
1488 |
|
|
1489 |
|
|
1490 |
|
|
1491 |
|
|
1492 |
|
|
|
|
| 75% |
Uncovered Elements: 8 (32) |
Complexity: 9 |
Complexity Density: 0.56 |
|
1493 |
237 |
public void resetAll()... |
1494 |
|
{ |
1495 |
237 |
if (mappings != null) |
1496 |
|
{ |
1497 |
237 |
mappings.clear(); |
1498 |
|
} |
1499 |
237 |
if (seqmappings != null) |
1500 |
|
{ |
1501 |
237 |
seqmappings.clear(); |
1502 |
|
} |
1503 |
237 |
if (sel_listeners != null) |
1504 |
|
{ |
1505 |
237 |
sel_listeners.clear(); |
1506 |
|
} |
1507 |
237 |
if (listeners != null) |
1508 |
|
{ |
1509 |
237 |
listeners.clear(); |
1510 |
|
} |
1511 |
237 |
if (commandListeners != null) |
1512 |
|
{ |
1513 |
237 |
commandListeners.clear(); |
1514 |
|
} |
1515 |
237 |
if (view_listeners != null) |
1516 |
|
{ |
1517 |
237 |
view_listeners.clear(); |
1518 |
|
} |
1519 |
237 |
if (pdbFileNameId != null) |
1520 |
|
{ |
1521 |
237 |
pdbFileNameId.clear(); |
1522 |
|
} |
1523 |
237 |
if (pdbIdFileName != null) |
1524 |
|
{ |
1525 |
237 |
pdbIdFileName.clear(); |
1526 |
|
} |
1527 |
|
} |
1528 |
|
|
|
|
| 75% |
Uncovered Elements: 1 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
1529 |
479 |
public void addSelectionListener(SelectionListener selecter)... |
1530 |
|
{ |
1531 |
479 |
if (!sel_listeners.contains(selecter)) |
1532 |
|
{ |
1533 |
479 |
sel_listeners.add(selecter); |
1534 |
|
} |
1535 |
|
} |
1536 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
1537 |
506 |
public void removeSelectionListener(SelectionListener toremove)... |
1538 |
|
{ |
1539 |
506 |
if (sel_listeners.contains(toremove)) |
1540 |
|
{ |
1541 |
253 |
sel_listeners.remove(toremove); |
1542 |
|
} |
1543 |
|
} |
1544 |
|
|
|
|
| 80% |
Uncovered Elements: 1 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1545 |
23 |
public synchronized void sendSelection(... |
1546 |
|
jalview.datamodel.SequenceGroup selection, |
1547 |
|
jalview.datamodel.ColumnSelection colsel, HiddenColumns hidden, |
1548 |
|
SelectionSource source) |
1549 |
|
{ |
1550 |
23 |
for (SelectionListener slis : sel_listeners) |
1551 |
|
{ |
1552 |
100 |
if (slis != source) |
1553 |
|
{ |
1554 |
100 |
slis.selection(selection, colsel, hidden, source); |
1555 |
|
} |
1556 |
|
} |
1557 |
|
} |
1558 |
|
|
1559 |
|
Vector<AlignmentViewPanelListener> view_listeners = new Vector<>(); |
1560 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 5 |
Complexity Density: 0.71 |
|
1561 |
0 |
public synchronized void sendViewPosition(... |
1562 |
|
jalview.api.AlignmentViewPanel source, int startRes, int endRes, |
1563 |
|
int startSeq, int endSeq) |
1564 |
|
{ |
1565 |
|
|
1566 |
0 |
if (view_listeners != null && view_listeners.size() > 0) |
1567 |
|
{ |
1568 |
0 |
Enumeration<AlignmentViewPanelListener> listeners = view_listeners |
1569 |
|
.elements(); |
1570 |
0 |
while (listeners.hasMoreElements()) |
1571 |
|
{ |
1572 |
0 |
AlignmentViewPanelListener slis = listeners.nextElement(); |
1573 |
0 |
if (slis != source) |
1574 |
|
{ |
1575 |
0 |
slis.viewPosition(startRes, endRes, startSeq, endSeq, source); |
1576 |
|
} |
1577 |
0 |
; |
1578 |
|
} |
1579 |
|
} |
1580 |
|
} |
1581 |
|
|
1582 |
|
|
1583 |
|
|
1584 |
|
|
1585 |
|
@param |
1586 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 4 |
Complexity Density: 0.67 |
|
1587 |
0 |
public static void release(StructureSelectionManagerProvider jalviewLite)... |
1588 |
|
{ |
1589 |
|
|
1590 |
|
{ |
1591 |
0 |
if (instances == null) |
1592 |
|
{ |
1593 |
0 |
return; |
1594 |
|
} |
1595 |
0 |
StructureSelectionManager mnger = (instances.get(jalviewLite)); |
1596 |
0 |
if (mnger != null) |
1597 |
|
{ |
1598 |
0 |
instances.remove(jalviewLite); |
1599 |
0 |
try |
1600 |
|
{ |
1601 |
|
|
1602 |
|
|
1603 |
|
|
1604 |
|
|
1605 |
|
} catch (Throwable x) |
1606 |
|
{ |
1607 |
|
} |
1608 |
|
} |
1609 |
|
} |
1610 |
|
} |
1611 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 3 |
Complexity Density: 1.5 |
|
1612 |
359 |
public void registerPDBEntry(PDBEntry pdbentry)... |
1613 |
|
{ |
1614 |
359 |
if (pdbentry.getFile() != null |
1615 |
|
&& pdbentry.getFile().trim().length() > 0) |
1616 |
|
{ |
1617 |
139 |
registerPDBFile(pdbentry.getId(), pdbentry.getFile()); |
1618 |
|
} |
1619 |
|
} |
1620 |
|
|
|
|
| 75% |
Uncovered Elements: 1 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
1621 |
6 |
public void addCommandListener(CommandListener cl)... |
1622 |
|
{ |
1623 |
6 |
if (!commandListeners.contains(cl)) |
1624 |
|
{ |
1625 |
6 |
commandListeners.add(cl); |
1626 |
|
} |
1627 |
|
} |
1628 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1629 |
0 |
public boolean hasCommandListener(CommandListener cl)... |
1630 |
|
{ |
1631 |
0 |
return this.commandListeners.contains(cl); |
1632 |
|
} |
1633 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1634 |
253 |
public boolean removeCommandListener(CommandListener l)... |
1635 |
|
{ |
1636 |
253 |
return commandListeners.remove(l); |
1637 |
|
} |
1638 |
|
|
1639 |
|
|
1640 |
|
|
1641 |
|
|
1642 |
|
|
1643 |
|
@param |
1644 |
|
|
1645 |
|
@param |
1646 |
|
|
1647 |
|
@param |
1648 |
|
|
|
|
| 50% |
Uncovered Elements: 1 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1649 |
1 |
public void commandPerformed(CommandI command, boolean undo,... |
1650 |
|
VamsasSource source) |
1651 |
|
{ |
1652 |
1 |
for (CommandListener listener : commandListeners) |
1653 |
|
{ |
1654 |
0 |
listener.mirrorCommand(command, undo, this, source); |
1655 |
|
} |
1656 |
|
} |
1657 |
|
|
1658 |
|
|
1659 |
|
|
1660 |
|
|
1661 |
|
|
1662 |
|
|
1663 |
|
@param |
1664 |
|
@param |
1665 |
|
@param |
1666 |
|
@param |
1667 |
|
@return |
1668 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
1669 |
0 |
public CommandI mapCommand(CommandI command, boolean undo,... |
1670 |
|
final AlignmentI mapTo, char gapChar) |
1671 |
|
{ |
1672 |
0 |
if (command instanceof EditCommand) |
1673 |
|
{ |
1674 |
0 |
return MappingUtils.mapEditCommand((EditCommand) command, undo, mapTo, |
1675 |
|
gapChar, seqmappings); |
1676 |
|
} |
1677 |
0 |
else if (command instanceof OrderCommand) |
1678 |
|
{ |
1679 |
0 |
return MappingUtils.mapOrderCommand((OrderCommand) command, undo, |
1680 |
|
mapTo, seqmappings); |
1681 |
|
} |
1682 |
0 |
return null; |
1683 |
|
} |
1684 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1685 |
15 |
public List<AlignedCodonFrame> getSequenceMappings()... |
1686 |
|
{ |
1687 |
15 |
return seqmappings; |
1688 |
|
} |
1689 |
|
|
1690 |
|
|
1691 |
|
|
1692 |
|
|
1693 |
|
|
1694 |
|
@param |
1695 |
|
@param |
1696 |
|
|
1697 |
|
@param |
1698 |
|
|
1699 |
|
|
|
|
| 66.7% |
Uncovered Elements: 4 (12) |
Complexity: 4 |
Complexity Density: 0.67 |
|
1700 |
8 |
public void highlightPositionsOnMany(SequenceI[] sequencesArray, int[] is,... |
1701 |
|
Object source) |
1702 |
|
{ |
1703 |
16 |
for (int i = 0; i < listeners.size(); i++) |
1704 |
|
{ |
1705 |
8 |
Object listener = listeners.elementAt(i); |
1706 |
8 |
if (listener == source) |
1707 |
|
{ |
1708 |
|
|
1709 |
|
|
1710 |
0 |
continue; |
1711 |
|
} |
1712 |
8 |
if (listener instanceof StructureListener) |
1713 |
|
{ |
1714 |
0 |
highlightStructureRegionsFor((StructureListener) listener, |
1715 |
|
sequencesArray, is); |
1716 |
|
} |
1717 |
|
} |
1718 |
|
} |
1719 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1720 |
0 |
public Map<String, String> getPdbFileNameIdMap()... |
1721 |
|
{ |
1722 |
0 |
return pdbFileNameId; |
1723 |
|
} |
1724 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1725 |
0 |
public Map<String, String> getPdbIdFileNameMap()... |
1726 |
|
{ |
1727 |
0 |
return pdbIdFileName; |
1728 |
|
} |
1729 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1730 |
127 |
public static void doConfigureStructurePrefs(... |
1731 |
|
StructureSelectionManager ssm) |
1732 |
|
{ |
1733 |
127 |
doConfigureStructurePrefs(ssm, |
1734 |
|
Cache.getDefault(Preferences.ADD_SS_ANN, true), |
1735 |
|
Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true), |
1736 |
|
Cache.getDefault(Preferences.STRUCT_FROM_PDB, true), |
1737 |
|
Cache.getDefault(Preferences.USE_RNAVIEW, false)); |
1738 |
|
} |
1739 |
|
|
|
|
| 55.6% |
Uncovered Elements: 4 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
1740 |
127 |
public static void doConfigureStructurePrefs(... |
1741 |
|
StructureSelectionManager ssm, boolean add_ss_ann, |
1742 |
|
boolean add_tempfact_ann, boolean struct_from_pdb, |
1743 |
|
boolean use_rnaview) |
1744 |
|
{ |
1745 |
127 |
if (add_ss_ann) |
1746 |
|
{ |
1747 |
127 |
ssm.setAddTempFacAnnot(add_tempfact_ann); |
1748 |
127 |
ssm.setProcessSecondaryStructure(struct_from_pdb); |
1749 |
|
|
1750 |
127 |
ssm.setSecStructServices(use_rnaview); |
1751 |
|
} |
1752 |
|
else |
1753 |
|
{ |
1754 |
0 |
ssm.setAddTempFacAnnot(false); |
1755 |
0 |
ssm.setProcessSecondaryStructure(false); |
1756 |
0 |
ssm.setSecStructServices(false); |
1757 |
|
} |
1758 |
|
} |
1759 |
|
|
1760 |
|
} |