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package jalview.structures.models; |
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import java.awt.Color; |
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import java.io.File; |
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import java.io.IOException; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.BitSet; |
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import java.util.Collections; |
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import java.util.HashMap; |
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import java.util.LinkedHashMap; |
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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 javax.swing.SwingUtilities; |
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import jalview.api.AlignViewportI; |
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import jalview.api.AlignmentViewPanel; |
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import jalview.api.FeatureRenderer; |
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import jalview.api.SequenceRenderer; |
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import jalview.api.StructureSelectionManagerProvider; |
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import jalview.api.structures.JalviewStructureDisplayI; |
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import jalview.bin.Console; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.ColumnSelection; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.MappedFeatures; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import jalview.ext.rbvi.chimera.JalviewChimeraBinding; |
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import jalview.gui.AlignmentPanel; |
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import jalview.gui.Desktop; |
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import jalview.gui.StructureViewer.ViewerType; |
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import jalview.io.DataSourceType; |
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import jalview.io.StructureFile; |
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import jalview.renderer.seqfeatures.FeatureColourFinder; |
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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.AtomSpecModel; |
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import jalview.structure.StructureCommandI; |
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import jalview.structure.StructureCommandsI; |
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import jalview.structure.StructureCommandsI.AtomSpecType; |
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import jalview.structure.StructureListener; |
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import jalview.structure.StructureMapping; |
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import jalview.structure.StructureSelectionManager; |
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import jalview.util.Comparison; |
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import jalview.util.MessageManager; |
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@author |
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| 59.9% |
Uncovered Elements: 342 (853) |
Complexity: 252 |
Complexity Density: 0.49 |
|
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public abstract class AAStructureBindingModel |
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extends SequenceStructureBindingModel |
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implements StructureListener, StructureSelectionManagerProvider |
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{ |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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public static class SuperposeData |
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{ |
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public String filename; |
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public String pdbId; |
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public String chain = ""; |
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public boolean isRna; |
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public int[] pdbResNo; |
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public String modelId; |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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public SuperposeData(int width, String model)... |
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{ |
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pdbResNo = new int[width]; |
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modelId = model; |
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} |
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} |
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private static final int MIN_POS_TO_SUPERPOSE = 4; |
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private static final String COLOURING_STRUCTURES = MessageManager |
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.getString("status.colouring_structures"); |
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private JalviewStructureDisplayI viewer; |
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private StructureCommandsI commandGenerator; |
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private StructureSelectionManager ssm; |
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private List<String> chainNames; |
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private Map<String, String> chainFile; |
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private PDBEntry[] pdbEntry; |
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private SequenceI[][] sequence; |
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private String[][] chains; |
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DataSourceType protocol = null; |
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protected boolean colourBySequence = true; |
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private boolean nucleotide; |
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private boolean finishedInit = false; |
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protected String[] modelFileNames = null; |
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public String fileLoadingError; |
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protected Thread externalViewerMonitor; |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
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public AAStructureBindingModel(StructureSelectionManager ssm,... |
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SequenceI[][] seqs) |
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{ |
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this.ssm = ssm; |
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this.sequence = seqs; |
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chainNames = new ArrayList<>(); |
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chainFile = new HashMap<>(); |
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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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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
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public AAStructureBindingModel(StructureSelectionManager ssm,... |
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PDBEntry[] pdbentry, SequenceI[][] sequenceIs, |
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DataSourceType protocol) |
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{ |
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this(ssm, sequenceIs); |
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this.nucleotide = Comparison.isNucleotide(sequenceIs); |
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this.pdbEntry = pdbentry; |
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this.protocol = protocol; |
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resolveChains(); |
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} |
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| 91.7% |
Uncovered Elements: 3 (36) |
Complexity: 11 |
Complexity Density: 0.46 |
|
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private boolean resolveChains()... |
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{ |
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int chainmaps = 0; |
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String[][] newchains = new String[pdbEntry.length][]; |
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int pe = 0; |
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for (PDBEntry pdb : pdbEntry) |
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{ |
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SequenceI[] seqsForPdb = sequence[pe]; |
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if (seqsForPdb != null) |
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{ |
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newchains[pe] = new String[seqsForPdb.length]; |
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int se = 0; |
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for (SequenceI asq : seqsForPdb) |
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{ |
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String chain = (chains != null && chains[pe] != null) |
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? chains[pe][se] |
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: null; |
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SequenceI sq = (asq.getDatasetSequence() == null) ? asq |
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: asq.getDatasetSequence(); |
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if (sq.getAllPDBEntries() != null) |
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{ |
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for (PDBEntry pdbentry : sq.getAllPDBEntries()) |
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{ |
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if (pdb.getFile() != null && pdbentry.getFile() != null |
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&& pdb.getFile().equals(pdbentry.getFile())) |
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{ |
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String chaincode = pdbentry.getChainCode(); |
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if (chaincode != null && chaincode.length() > 0) |
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{ |
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chain = chaincode; |
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chainmaps++; |
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break; |
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} |
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} |
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} |
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} |
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newchains[pe][se] = chain; |
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se++; |
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} |
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pe++; |
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} |
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} |
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chains = newchains; |
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return chainmaps > 0; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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768 |
public StructureSelectionManager getSsm()... |
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{ |
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return ssm; |
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} |
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@param |
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@return |
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| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 3 |
Complexity Density: 3 |
|
288 |
280 |
public PDBEntry getPdbEntry(int i)... |
289 |
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{ |
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280 |
return (pdbEntry != null && pdbEntry.length > i) ? pdbEntry[i] : null; |
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} |
292 |
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295 |
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296 |
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@param |
297 |
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@return |
298 |
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| 66.7% |
Uncovered Elements: 3 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
299 |
1 |
public boolean hasPdbId(String pdbId)... |
300 |
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{ |
301 |
1 |
if (pdbEntry != null) |
302 |
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{ |
303 |
1 |
for (PDBEntry pdb : pdbEntry) |
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{ |
305 |
1 |
if (pdb.getId().equals(pdbId)) |
306 |
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{ |
307 |
0 |
return true; |
308 |
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} |
309 |
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} |
310 |
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} |
311 |
1 |
return false; |
312 |
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} |
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314 |
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315 |
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316 |
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317 |
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@return |
318 |
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| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
319 |
536 |
public int getPdbCount()... |
320 |
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{ |
321 |
536 |
return pdbEntry == null ? 0 : pdbEntry.length; |
322 |
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} |
323 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
324 |
1105 |
public SequenceI[][] getSequence()... |
325 |
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{ |
326 |
1105 |
return sequence; |
327 |
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} |
328 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
329 |
535 |
public String[][] getChains()... |
330 |
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{ |
331 |
535 |
return chains; |
332 |
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} |
333 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
334 |
0 |
public DataSourceType getProtocol()... |
335 |
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{ |
336 |
0 |
return protocol; |
337 |
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} |
338 |
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339 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
340 |
1 |
protected void setPdbentry(PDBEntry[] pdbentry)... |
341 |
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{ |
342 |
1 |
this.pdbEntry = pdbentry; |
343 |
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} |
344 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
345 |
1 |
protected void setSequence(SequenceI[][] sequence)... |
346 |
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{ |
347 |
1 |
this.sequence = sequence; |
348 |
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} |
349 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
350 |
1 |
protected void setChains(String[][] chains)... |
351 |
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{ |
352 |
1 |
this.chains = chains; |
353 |
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} |
354 |
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355 |
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356 |
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357 |
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358 |
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359 |
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@param |
360 |
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361 |
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@param |
362 |
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363 |
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@return |
364 |
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| 66.7% |
Uncovered Elements: 7 (21) |
Complexity: 8 |
Complexity Density: 0.62 |
|
365 |
94 |
public String getViewerTitle(String viewerName, boolean verbose)... |
366 |
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{ |
367 |
94 |
if (getSequence() == null || getSequence().length < 1 |
368 |
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|| getPdbCount() < 1 || getSequence()[0].length < 1) |
369 |
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{ |
370 |
0 |
return ("Jalview " + viewerName + " Window"); |
371 |
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} |
372 |
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373 |
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|
374 |
94 |
StringBuilder title = new StringBuilder(64); |
375 |
94 |
final PDBEntry pdbe = getPdbEntry(0); |
376 |
94 |
title.append(viewerName + " view for " + getSequence()[0][0].getName() |
377 |
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+ ":" + pdbe.getId()); |
378 |
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|
379 |
94 |
if (verbose) |
380 |
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{ |
381 |
94 |
String method = (String) pdbe.getProperty("method"); |
382 |
94 |
if (method != null) |
383 |
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{ |
384 |
0 |
title.append(" Method: ").append(method); |
385 |
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} |
386 |
94 |
String chain = (String) pdbe.getProperty("chains"); |
387 |
94 |
if (chain != null) |
388 |
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{ |
389 |
0 |
title.append(" Chain:").append(chain); |
390 |
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} |
391 |
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} |
392 |
94 |
return title.toString(); |
393 |
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} |
394 |
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395 |
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396 |
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397 |
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398 |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
399 |
0 |
protected void releaseUIResources()... |
400 |
|
{ |
401 |
|
} |
402 |
|
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
403 |
0 |
@Override... |
404 |
|
public void releaseReferences(Object svl) |
405 |
|
{ |
406 |
|
} |
407 |
|
|
|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
408 |
159 |
public boolean isColourBySequence()... |
409 |
|
{ |
410 |
159 |
return colourBySequence; |
411 |
|
} |
412 |
|
|
413 |
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|
414 |
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|
415 |
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|
416 |
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|
417 |
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|
418 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
419 |
0 |
public void refreshGUI()... |
420 |
|
{ |
421 |
|
} |
422 |
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|
423 |
|
|
424 |
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|
425 |
|
|
426 |
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|
427 |
|
|
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|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
428 |
47 |
public void refreshPdbEntries()... |
429 |
|
{ |
430 |
|
} |
431 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
432 |
102 |
public void setColourBySequence(boolean colourBySequence)... |
433 |
|
{ |
434 |
102 |
this.colourBySequence = colourBySequence; |
435 |
|
} |
436 |
|
|
|
|
| 75.9% |
Uncovered Elements: 14 (58) |
Complexity: 18 |
Complexity Density: 0.6 |
|
437 |
78 |
protected void addSequenceAndChain(int pe, SequenceI[] seq,... |
438 |
|
String[] tchain) |
439 |
|
{ |
440 |
78 |
if (pe < 0 || pe >= getPdbCount()) |
441 |
|
{ |
442 |
0 |
throw new Error(MessageManager.formatMessage( |
443 |
|
"error.implementation_error_no_pdbentry_from_index", |
444 |
|
new Object[] |
445 |
|
{ Integer.valueOf(pe).toString() })); |
446 |
|
} |
447 |
78 |
final String nullChain = "TheNullChain"; |
448 |
78 |
List<SequenceI> s = new ArrayList<>(); |
449 |
78 |
List<String> c = new ArrayList<>(); |
450 |
78 |
if (getChains() == null) |
451 |
|
{ |
452 |
0 |
setChains(new String[getPdbCount()][]); |
453 |
|
} |
454 |
78 |
if (getSequence()[pe] != null) |
455 |
|
{ |
456 |
189 |
for (int i = 0; i < getSequence()[pe].length; i++) |
457 |
|
{ |
458 |
112 |
s.add(getSequence()[pe][i]); |
459 |
112 |
if (getChains()[pe] != null) |
460 |
|
{ |
461 |
110 |
if (i < getChains()[pe].length) |
462 |
|
{ |
463 |
110 |
c.add(getChains()[pe][i]); |
464 |
|
} |
465 |
|
else |
466 |
|
{ |
467 |
0 |
c.add(nullChain); |
468 |
|
} |
469 |
|
} |
470 |
|
else |
471 |
|
{ |
472 |
2 |
if (tchain != null && tchain.length > 0) |
473 |
|
{ |
474 |
0 |
c.add(nullChain); |
475 |
|
} |
476 |
|
} |
477 |
|
} |
478 |
|
} |
479 |
191 |
for (int i = 0; i < seq.length; i++) |
480 |
|
{ |
481 |
113 |
if (!s.contains(seq[i])) |
482 |
|
{ |
483 |
1 |
s.add(seq[i]); |
484 |
1 |
if (tchain != null && i < tchain.length) |
485 |
|
{ |
486 |
0 |
c.add(tchain[i] == null ? nullChain : tchain[i]); |
487 |
|
} |
488 |
|
} |
489 |
|
} |
490 |
78 |
SequenceI[] tmp = s.toArray(new SequenceI[s.size()]); |
491 |
78 |
getSequence()[pe] = tmp; |
492 |
78 |
if (c.size() > 0) |
493 |
|
{ |
494 |
75 |
String[] tch = c.toArray(new String[c.size()]); |
495 |
185 |
for (int i = 0; i < tch.length; i++) |
496 |
|
{ |
497 |
110 |
if (tch[i] == nullChain) |
498 |
|
{ |
499 |
0 |
tch[i] = null; |
500 |
|
} |
501 |
|
} |
502 |
75 |
getChains()[pe] = tch; |
503 |
|
} |
504 |
|
else |
505 |
|
{ |
506 |
3 |
getChains()[pe] = null; |
507 |
|
} |
508 |
|
} |
509 |
|
|
510 |
|
|
511 |
|
|
512 |
|
|
513 |
|
|
514 |
|
|
|
|
| 88.9% |
Uncovered Elements: 4 (36) |
Complexity: 7 |
Complexity Density: 0.27 |
|
515 |
1 |
public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,... |
516 |
|
SequenceI[][] seq, String[][] chns) |
517 |
|
{ |
518 |
1 |
List<PDBEntry> v = new ArrayList<>(); |
519 |
1 |
List<int[]> rtn = new ArrayList<>(); |
520 |
2 |
for (int i = 0; i < getPdbCount(); i++) |
521 |
|
{ |
522 |
1 |
v.add(getPdbEntry(i)); |
523 |
|
} |
524 |
2 |
for (int i = 0; i < pdbe.length; i++) |
525 |
|
{ |
526 |
1 |
int r = v.indexOf(pdbe[i]); |
527 |
1 |
if (r == -1 || r >= getPdbCount()) |
528 |
|
{ |
529 |
1 |
rtn.add(new int[] { v.size(), i }); |
530 |
1 |
v.add(pdbe[i]); |
531 |
|
} |
532 |
|
else |
533 |
|
{ |
534 |
|
|
535 |
0 |
addSequenceAndChain(r, seq[i], chns[i]); |
536 |
|
} |
537 |
|
} |
538 |
1 |
pdbe = v.toArray(new PDBEntry[v.size()]); |
539 |
1 |
setPdbentry(pdbe); |
540 |
1 |
if (rtn.size() > 0) |
541 |
|
{ |
542 |
|
|
543 |
1 |
SequenceI[][] sqs = new SequenceI[getPdbCount()][]; |
544 |
1 |
String[][] sch = new String[getPdbCount()][]; |
545 |
1 |
System.arraycopy(getSequence(), 0, sqs, 0, getSequence().length); |
546 |
1 |
System.arraycopy(getChains(), 0, sch, 0, this.getChains().length); |
547 |
1 |
setSequence(sqs); |
548 |
1 |
setChains(sch); |
549 |
1 |
pdbe = new PDBEntry[rtn.size()]; |
550 |
2 |
for (int r = 0; r < pdbe.length; r++) |
551 |
|
{ |
552 |
1 |
int[] stri = (rtn.get(r)); |
553 |
|
|
554 |
1 |
pdbe[r] = getPdbEntry(stri[0]); |
555 |
|
|
556 |
1 |
addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]); |
557 |
|
} |
558 |
|
} |
559 |
|
else |
560 |
|
{ |
561 |
0 |
pdbe = null; |
562 |
|
} |
563 |
1 |
return pdbe; |
564 |
|
} |
565 |
|
|
566 |
|
|
567 |
|
|
568 |
|
|
569 |
|
@param |
570 |
|
@param |
571 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
572 |
77 |
public void addSequence(int pe, SequenceI[] seq)... |
573 |
|
{ |
574 |
77 |
addSequenceAndChain(pe, seq, null); |
575 |
|
} |
576 |
|
|
577 |
|
|
578 |
|
|
579 |
|
|
580 |
|
@param |
581 |
|
|
582 |
|
@param |
583 |
|
|
584 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 3 |
Complexity Density: 1 |
|
585 |
33 |
public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)... |
586 |
|
{ |
587 |
66 |
for (int pe = 0; pe < getPdbCount(); pe++) |
588 |
|
{ |
589 |
33 |
if (getPdbEntry(pe).getFile().equals(pdbFile)) |
590 |
|
{ |
591 |
28 |
addSequence(pe, seq); |
592 |
|
} |
593 |
|
} |
594 |
|
} |
595 |
|
|
596 |
|
@Override |
597 |
|
public abstract void highlightAtoms(List<AtomSpec> atoms); |
598 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
599 |
0 |
protected boolean isNucleotide()... |
600 |
|
{ |
601 |
0 |
return this.nucleotide; |
602 |
|
} |
603 |
|
|
604 |
|
|
605 |
|
|
606 |
|
|
607 |
|
|
608 |
|
@param |
609 |
|
@param |
610 |
|
@return |
611 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
|
612 |
0 |
public String printMappings()... |
613 |
|
{ |
614 |
0 |
if (pdbEntry == null) |
615 |
|
{ |
616 |
0 |
return ""; |
617 |
|
} |
618 |
0 |
StringBuilder sb = new StringBuilder(128); |
619 |
0 |
for (int pdbe = 0; pdbe < getPdbCount(); pdbe++) |
620 |
|
{ |
621 |
0 |
String pdbfile = getPdbEntry(pdbe).getFile(); |
622 |
0 |
List<SequenceI> seqs = Arrays.asList(getSequence()[pdbe]); |
623 |
0 |
sb.append(getSsm().printMappings(pdbfile, seqs)); |
624 |
|
} |
625 |
0 |
return sb.toString(); |
626 |
|
} |
627 |
|
|
628 |
|
|
629 |
|
|
630 |
|
|
631 |
|
|
632 |
|
|
633 |
|
@param |
634 |
|
@param |
635 |
|
@param |
636 |
|
@return |
637 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (11) |
Complexity: 3 |
Complexity Density: 0.43 |
|
638 |
620 |
protected int getMappedPosition(SequenceI seq, int alignedPos,... |
639 |
|
StructureMapping mapping) |
640 |
|
{ |
641 |
620 |
if (alignedPos >= seq.getLength()) |
642 |
|
{ |
643 |
1 |
return -1; |
644 |
|
} |
645 |
|
|
646 |
619 |
if (Comparison.isGap(seq.getCharAt(alignedPos))) |
647 |
|
{ |
648 |
6 |
return -1; |
649 |
|
} |
650 |
613 |
int seqPos = seq.findPosition(alignedPos); |
651 |
613 |
int pos = mapping.getPDBResNum(seqPos); |
652 |
613 |
return pos; |
653 |
|
} |
654 |
|
|
655 |
|
|
656 |
|
|
657 |
|
|
658 |
|
|
659 |
|
|
660 |
|
|
661 |
|
|
662 |
|
@param |
663 |
|
|
664 |
|
|
665 |
|
@param |
666 |
|
|
667 |
|
|
668 |
|
|
669 |
|
@param |
670 |
|
|
671 |
|
@return |
672 |
|
|
|
|
| 91.8% |
Uncovered Elements: 4 (49) |
Complexity: 13 |
Complexity Density: 0.42 |
|
673 |
3 |
protected int findSuperposableResidues(AlignmentI alignment,... |
674 |
|
BitSet matched, |
675 |
|
AAStructureBindingModel.SuperposeData[] structures) |
676 |
|
{ |
677 |
3 |
int refStructure = -1; |
678 |
3 |
String[] files = getStructureFiles(); |
679 |
3 |
if (files == null) |
680 |
|
{ |
681 |
0 |
return -1; |
682 |
|
} |
683 |
11 |
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) |
684 |
|
{ |
685 |
8 |
StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]); |
686 |
8 |
int lastPos = -1; |
687 |
|
|
688 |
|
|
689 |
|
|
690 |
|
|
691 |
|
|
692 |
8 |
final int seqCountForPdbFile = getSequence()[pdbfnum].length; |
693 |
16 |
for (int s = 0; s < seqCountForPdbFile; s++) |
694 |
|
{ |
695 |
8 |
for (StructureMapping mapping : mappings) |
696 |
|
{ |
697 |
8 |
final SequenceI theSequence = getSequence()[pdbfnum][s]; |
698 |
8 |
if (mapping.getSequence() == theSequence |
699 |
|
&& alignment.findIndex(theSequence) > -1) |
700 |
|
{ |
701 |
8 |
if (refStructure < 0) |
702 |
|
{ |
703 |
3 |
refStructure = pdbfnum; |
704 |
|
} |
705 |
638 |
for (int r = 0; r < alignment.getWidth(); r++) |
706 |
|
{ |
707 |
630 |
if (!matched.get(r)) |
708 |
|
{ |
709 |
10 |
continue; |
710 |
|
} |
711 |
620 |
int pos = getMappedPosition(theSequence, r, mapping); |
712 |
620 |
if (pos < 1 || pos == lastPos) |
713 |
|
{ |
714 |
7 |
matched.clear(r); |
715 |
7 |
continue; |
716 |
|
} |
717 |
613 |
lastPos = pos; |
718 |
613 |
structures[pdbfnum].pdbResNo[r] = pos; |
719 |
|
} |
720 |
8 |
String chain = mapping.getChain(); |
721 |
8 |
if (chain != null && chain.trim().length() > 0) |
722 |
|
{ |
723 |
8 |
structures[pdbfnum].chain = chain; |
724 |
|
} |
725 |
8 |
structures[pdbfnum].pdbId = mapping.getPdbId(); |
726 |
8 |
structures[pdbfnum].isRna = !theSequence.isProtein(); |
727 |
|
|
728 |
|
|
729 |
|
|
730 |
|
|
731 |
|
|
732 |
8 |
s = seqCountForPdbFile; |
733 |
8 |
break; |
734 |
|
} |
735 |
|
} |
736 |
|
} |
737 |
|
} |
738 |
3 |
return refStructure; |
739 |
|
} |
740 |
|
|
741 |
|
|
742 |
|
|
743 |
|
|
744 |
|
|
745 |
|
|
746 |
|
@param |
747 |
|
|
|
|
| 70.4% |
Uncovered Elements: 8 (27) |
Complexity: 8 |
Complexity Density: 0.42 |
|
748 |
1 |
protected boolean waitForFileLoad(String[] files)... |
749 |
|
{ |
750 |
|
|
751 |
|
|
752 |
|
|
753 |
1 |
long starttime = System.currentTimeMillis(); |
754 |
1 |
long endTime = 10000 + 1000 * files.length + starttime; |
755 |
1 |
String notLoaded = null; |
756 |
|
|
757 |
1 |
boolean waiting = true; |
758 |
2 |
while (waiting && System.currentTimeMillis() < endTime) |
759 |
|
{ |
760 |
1 |
waiting = false; |
761 |
1 |
for (String file : files) |
762 |
|
{ |
763 |
2 |
notLoaded = file; |
764 |
2 |
if (file == null) |
765 |
|
{ |
766 |
0 |
continue; |
767 |
|
} |
768 |
2 |
try |
769 |
|
{ |
770 |
2 |
StructureMapping[] sm = getSsm().getMapping(file); |
771 |
2 |
if (sm == null || sm.length == 0) |
772 |
|
{ |
773 |
0 |
waiting = true; |
774 |
|
} |
775 |
|
} catch (Throwable x) |
776 |
|
{ |
777 |
0 |
waiting = true; |
778 |
|
} |
779 |
|
} |
780 |
|
} |
781 |
|
|
782 |
1 |
if (waiting) |
783 |
|
{ |
784 |
0 |
jalview.bin.Console.errPrintln( |
785 |
|
"Timed out waiting for structure viewer to load file " |
786 |
|
+ notLoaded); |
787 |
0 |
return false; |
788 |
|
} |
789 |
1 |
return true; |
790 |
|
} |
791 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 6 |
Complexity Density: 0.86 |
|
792 |
0 |
@Override... |
793 |
|
public boolean isListeningFor(SequenceI seq) |
794 |
|
{ |
795 |
0 |
if (sequence != null) |
796 |
|
{ |
797 |
0 |
for (SequenceI[] seqs : sequence) |
798 |
|
{ |
799 |
0 |
if (seqs != null) |
800 |
|
{ |
801 |
0 |
for (SequenceI s : seqs) |
802 |
|
{ |
803 |
0 |
if (s == seq || (s.getDatasetSequence() != null |
804 |
|
&& s.getDatasetSequence() == seq.getDatasetSequence())) |
805 |
|
{ |
806 |
0 |
return true; |
807 |
|
} |
808 |
|
} |
809 |
|
} |
810 |
|
} |
811 |
|
} |
812 |
0 |
return false; |
813 |
|
} |
814 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
815 |
407 |
public boolean isFinishedInit()... |
816 |
|
{ |
817 |
407 |
return finishedInit; |
818 |
|
} |
819 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
820 |
90 |
public void setFinishedInit(boolean fi)... |
821 |
|
{ |
822 |
90 |
this.finishedInit = fi; |
823 |
|
} |
824 |
|
|
825 |
|
|
826 |
|
|
827 |
|
|
828 |
|
|
829 |
|
@return |
830 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
831 |
112 |
public List<String> getChainNames()... |
832 |
|
{ |
833 |
112 |
return chainNames; |
834 |
|
} |
835 |
|
|
836 |
|
|
837 |
|
|
838 |
|
|
839 |
|
@return |
840 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
841 |
2263 |
public JalviewStructureDisplayI getViewer()... |
842 |
|
{ |
843 |
2263 |
return viewer; |
844 |
|
} |
845 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
846 |
67 |
public void setViewer(JalviewStructureDisplayI v)... |
847 |
|
{ |
848 |
67 |
viewer = v; |
849 |
|
} |
850 |
|
|
851 |
|
|
852 |
|
|
853 |
|
|
854 |
|
|
855 |
|
|
856 |
|
@param |
857 |
|
|
858 |
|
@return |
859 |
|
|
|
|
| 75.8% |
Uncovered Elements: 16 (66) |
Complexity: 16 |
Complexity Density: 0.36 |
|
860 |
1 |
public String superposeStructures(List<AlignmentViewPanel> alignWith)... |
861 |
|
{ |
862 |
1 |
String error = ""; |
863 |
1 |
String[] files = getStructureFiles(); |
864 |
|
|
865 |
1 |
if (!waitForFileLoad(files)) |
866 |
|
{ |
867 |
0 |
return null; |
868 |
|
} |
869 |
1 |
refreshPdbEntries(); |
870 |
|
|
871 |
1 |
for (AlignmentViewPanel view : alignWith) |
872 |
|
{ |
873 |
1 |
AlignmentI alignment = view.getAlignment(); |
874 |
1 |
HiddenColumns hiddenCols = alignment.getHiddenColumns(); |
875 |
|
|
876 |
|
|
877 |
|
|
878 |
|
|
879 |
1 |
final int width = alignment.getWidth(); |
880 |
1 |
BitSet matched = new BitSet(); |
881 |
1 |
ColumnSelection cs = view.getAlignViewport().getColumnSelection(); |
882 |
|
|
883 |
1 |
if (cs != null && cs.hasSelectedColumns() |
884 |
|
&& cs.getSelected().size() >= 4) |
885 |
|
{ |
886 |
0 |
for (int s : cs.getSelected()) |
887 |
|
{ |
888 |
0 |
matched.set(s); |
889 |
|
} |
890 |
|
} |
891 |
|
else |
892 |
|
{ |
893 |
298 |
for (int m = 0; m < width; m++) |
894 |
|
{ |
895 |
297 |
if (hiddenCols == null || hiddenCols.isVisible(m)) |
896 |
|
{ |
897 |
297 |
matched.set(m); |
898 |
|
} |
899 |
|
} |
900 |
|
} |
901 |
1 |
AAStructureBindingModel.SuperposeData[] structures = new AAStructureBindingModel.SuperposeData[files.length]; |
902 |
3 |
for (int f = 0; f < files.length; f++) |
903 |
|
{ |
904 |
2 |
structures[f] = new AAStructureBindingModel.SuperposeData(width, |
905 |
|
getModelIdForFile(files[f])); |
906 |
|
} |
907 |
|
|
908 |
|
|
909 |
|
|
910 |
|
|
911 |
|
|
912 |
1 |
int refStructure = findSuperposableResidues(alignment, matched, |
913 |
|
structures); |
914 |
|
|
915 |
|
|
916 |
|
|
917 |
|
|
918 |
1 |
int nmatched = matched.cardinality(); |
919 |
1 |
if (nmatched < MIN_POS_TO_SUPERPOSE) |
920 |
|
{ |
921 |
0 |
String msg = MessageManager |
922 |
|
.formatMessage("label.insufficient_residues", nmatched); |
923 |
0 |
error += view.getViewName() + ": " + msg + "; "; |
924 |
0 |
continue; |
925 |
|
} |
926 |
|
|
927 |
|
|
928 |
|
|
929 |
|
|
930 |
1 |
AtomSpecModel refAtoms = getAtomSpec(structures[refStructure], |
931 |
|
matched); |
932 |
|
|
933 |
|
|
934 |
|
|
935 |
|
|
936 |
|
|
937 |
|
|
938 |
1 |
executeCommands(commandGenerator.showBackbone(), true, null); |
939 |
|
|
940 |
1 |
AtomSpecType backbone = structures[refStructure].isRna |
941 |
|
? AtomSpecType.PHOSPHATE |
942 |
|
: AtomSpecType.ALPHA; |
943 |
1 |
List<AtomSpecModel> models = new ArrayList<AtomSpecModel>(); |
944 |
1 |
models.add(refAtoms); |
945 |
|
|
946 |
|
|
947 |
|
|
948 |
3 |
for (int i = 0; i < structures.length; i++) |
949 |
|
{ |
950 |
2 |
if (i != refStructure) |
951 |
|
{ |
952 |
1 |
AtomSpecModel atomSpec = getAtomSpec(structures[i], matched); |
953 |
1 |
List<StructureCommandI> commands = commandGenerator |
954 |
|
.superposeStructures(refAtoms, atomSpec, backbone); |
955 |
1 |
List<String> replies = executeCommands(commands, true, null); |
956 |
1 |
for (String reply : replies) |
957 |
|
{ |
958 |
|
|
959 |
0 |
if (reply.toLowerCase(Locale.ROOT) |
960 |
|
.contains("unequal numbers of atoms")) |
961 |
|
{ |
962 |
0 |
error += "; " + reply; |
963 |
|
} |
964 |
|
} |
965 |
1 |
models.add(atomSpec); |
966 |
|
} |
967 |
|
} |
968 |
1 |
List<StructureCommandI> finalView = commandGenerator |
969 |
|
.centerViewOn(models); |
970 |
1 |
if (finalView != null && finalView.size() > 0) |
971 |
|
{ |
972 |
1 |
executeCommands(finalView, false, "Centered on Superposition"); |
973 |
|
} |
974 |
|
} |
975 |
1 |
return error; |
976 |
|
} |
977 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
978 |
2 |
private AtomSpecModel getAtomSpec(... |
979 |
|
AAStructureBindingModel.SuperposeData superposeData, |
980 |
|
BitSet matched) |
981 |
|
{ |
982 |
2 |
AtomSpecModel model = new AtomSpecModel(); |
983 |
2 |
int nextColumnMatch = matched.nextSetBit(0); |
984 |
594 |
while (nextColumnMatch != -1) |
985 |
|
{ |
986 |
592 |
int pdbResNum = superposeData.pdbResNo[nextColumnMatch]; |
987 |
592 |
model.addRange(superposeData.modelId, pdbResNum, pdbResNum, |
988 |
|
superposeData.chain); |
989 |
592 |
nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1); |
990 |
|
} |
991 |
|
|
992 |
2 |
return model; |
993 |
|
} |
994 |
|
|
995 |
|
|
996 |
|
|
997 |
|
|
998 |
|
|
999 |
|
@param |
1000 |
|
|
1001 |
|
@return |
1002 |
|
|
1003 |
|
public abstract SequenceRenderer getSequenceRenderer( |
1004 |
|
AlignmentViewPanel alignment); |
1005 |
|
|
1006 |
|
|
1007 |
|
|
1008 |
|
|
1009 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1010 |
0 |
public void colourByChain()... |
1011 |
|
{ |
1012 |
0 |
colourBySequence = false; |
1013 |
|
|
1014 |
|
|
1015 |
|
|
1016 |
0 |
executeCommand(false, COLOURING_STRUCTURES, |
1017 |
|
commandGenerator.colourByChain()); |
1018 |
|
} |
1019 |
|
|
1020 |
|
|
1021 |
|
|
1022 |
|
|
1023 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1024 |
0 |
public void colourByCharge()... |
1025 |
|
{ |
1026 |
0 |
colourBySequence = false; |
1027 |
|
|
1028 |
0 |
executeCommands(commandGenerator.colourByCharge(), false, |
1029 |
|
COLOURING_STRUCTURES); |
1030 |
|
} |
1031 |
|
|
1032 |
|
|
1033 |
|
|
1034 |
|
|
1035 |
|
|
1036 |
|
|
1037 |
|
|
1038 |
|
@param |
1039 |
|
|
|
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 4 |
Complexity Density: 0.36 |
|
1040 |
0 |
public void colourByJalviewColourScheme(ColourSchemeI cs)... |
1041 |
|
{ |
1042 |
0 |
colourBySequence = false; |
1043 |
|
|
1044 |
0 |
if (cs == null || !cs.isSimple()) |
1045 |
|
{ |
1046 |
0 |
return; |
1047 |
|
} |
1048 |
|
|
1049 |
|
|
1050 |
|
|
1051 |
|
|
1052 |
0 |
Map<String, Color> colours = new HashMap<>(); |
1053 |
0 |
List<String> residues = ResidueProperties.getResidues(isNucleotide(), |
1054 |
|
false); |
1055 |
0 |
for (String resName : residues) |
1056 |
|
{ |
1057 |
0 |
char res = resName.length() == 3 |
1058 |
|
? ResidueProperties.getSingleCharacterCode(resName) |
1059 |
|
: resName.charAt(0); |
1060 |
0 |
Color colour = cs.findColour(res, 0, null, null, 0f); |
1061 |
0 |
colours.put(resName, colour); |
1062 |
|
} |
1063 |
|
|
1064 |
|
|
1065 |
|
|
1066 |
|
|
1067 |
0 |
List<StructureCommandI> cmd = commandGenerator |
1068 |
|
.colourByResidues(colours); |
1069 |
0 |
executeCommands(cmd, false, COLOURING_STRUCTURES); |
1070 |
|
} |
1071 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1072 |
0 |
public void setBackgroundColour(Color col)... |
1073 |
|
{ |
1074 |
0 |
StructureCommandI cmd = commandGenerator.setBackgroundColour(col); |
1075 |
0 |
executeCommand(false, null, cmd); |
1076 |
|
} |
1077 |
|
|
1078 |
|
|
1079 |
|
|
1080 |
|
|
1081 |
|
|
1082 |
|
@param |
1083 |
|
@param |
1084 |
|
|
1085 |
|
protected abstract List<String> executeCommand(StructureCommandI cmd, |
1086 |
|
boolean getReply); |
1087 |
|
|
1088 |
|
|
1089 |
|
|
1090 |
|
|
1091 |
|
@param |
1092 |
|
@param |
1093 |
|
@param |
1094 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1095 |
277 |
public List<String> executeCommands(List<StructureCommandI> commands,... |
1096 |
|
boolean getReply, String msg) |
1097 |
|
{ |
1098 |
277 |
return executeCommand(getReply, msg, |
1099 |
|
commands.toArray(new StructureCommandI[commands.size()])); |
1100 |
|
} |
1101 |
|
|
1102 |
|
|
1103 |
|
|
1104 |
|
|
1105 |
|
|
1106 |
|
|
1107 |
|
|
1108 |
|
|
1109 |
|
|
1110 |
|
|
1111 |
|
|
1112 |
|
|
1113 |
|
@param |
1114 |
|
@param |
1115 |
|
@param |
1116 |
|
@return |
1117 |
|
|
|
|
| 80% |
Uncovered Elements: 5 (25) |
Complexity: 6 |
Complexity Density: 0.4 |
|
1118 |
277 |
protected List<String> executeCommand(boolean getReply, String msg,... |
1119 |
|
StructureCommandI... cmds) |
1120 |
|
{ |
1121 |
277 |
JalviewStructureDisplayI theViewer = getViewer(); |
1122 |
277 |
final long handle = msg == null ? 0 : theViewer.startProgressBar(msg); |
1123 |
|
|
1124 |
276 |
if (getReply) |
1125 |
|
{ |
1126 |
|
|
1127 |
|
|
1128 |
|
|
1129 |
2 |
List<String> response = new ArrayList<>(); |
1130 |
2 |
try |
1131 |
|
{ |
1132 |
2 |
for (StructureCommandI cmd : cmds) |
1133 |
|
{ |
1134 |
2 |
List<String> replies = executeCommand(cmd, true); |
1135 |
2 |
if (replies != null) |
1136 |
|
{ |
1137 |
0 |
response.addAll(replies); |
1138 |
|
} |
1139 |
|
} |
1140 |
2 |
return response; |
1141 |
|
} finally |
1142 |
|
{ |
1143 |
2 |
if (msg != null) |
1144 |
|
{ |
1145 |
0 |
theViewer.stopProgressBar(null, handle); |
1146 |
|
} |
1147 |
|
} |
1148 |
|
} |
1149 |
|
|
1150 |
|
|
1151 |
|
|
1152 |
|
|
1153 |
274 |
String threadName = msg == null ? "StructureCommand" : msg; |
1154 |
274 |
new Thread(new Runnable() |
1155 |
|
{ |
|
|
| 85.7% |
Uncovered Elements: 1 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
1156 |
274 |
@Override... |
1157 |
|
public void run() |
1158 |
|
{ |
1159 |
274 |
try |
1160 |
|
{ |
1161 |
274 |
for (StructureCommandI cmd : cmds) |
1162 |
|
{ |
1163 |
264 |
executeCommand(cmd, false); |
1164 |
|
} |
1165 |
|
} finally |
1166 |
|
{ |
1167 |
274 |
if (msg != null) |
1168 |
|
{ |
1169 |
274 |
SwingUtilities.invokeLater(new Runnable() |
1170 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1171 |
273 |
@Override... |
1172 |
|
public void run() |
1173 |
|
{ |
1174 |
273 |
theViewer.stopProgressBar(null, handle); |
1175 |
|
} |
1176 |
|
}); |
1177 |
|
} |
1178 |
|
} |
1179 |
|
} |
1180 |
|
}, threadName).start(); |
1181 |
274 |
return null; |
1182 |
|
} |
1183 |
|
|
1184 |
|
|
1185 |
|
|
1186 |
|
|
1187 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 4 |
Complexity Density: 0.8 |
|
1188 |
286 |
public void colourBySequence(AlignmentViewPanel alignmentv)... |
1189 |
|
{ |
1190 |
286 |
if (!colourBySequence || !isLoadingFinished() || getSsm() == null) |
1191 |
|
{ |
1192 |
13 |
return; |
1193 |
|
} |
1194 |
273 |
Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, sequence, |
1195 |
|
alignmentv); |
1196 |
|
|
1197 |
264 |
List<StructureCommandI> colourBySequenceCommands = commandGenerator |
1198 |
|
.colourBySequence(colourMap); |
1199 |
264 |
executeCommands(colourBySequenceCommands, false, COLOURING_STRUCTURES); |
1200 |
|
} |
1201 |
|
|
1202 |
|
|
1203 |
|
|
1204 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1205 |
0 |
public void focusView()... |
1206 |
|
{ |
1207 |
0 |
executeCommand(false, null, commandGenerator.focusView()); |
1208 |
|
} |
1209 |
|
|
1210 |
|
|
1211 |
|
|
1212 |
|
|
1213 |
|
|
1214 |
|
|
1215 |
|
@param |
1216 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
1217 |
0 |
public void showChains(List<String> toShow)... |
1218 |
|
{ |
1219 |
|
|
1220 |
|
|
1221 |
|
|
1222 |
|
|
1223 |
|
|
1224 |
|
|
1225 |
|
|
1226 |
0 |
List<String> showThese = new ArrayList<>(); |
1227 |
0 |
for (String chainId : toShow) |
1228 |
|
{ |
1229 |
0 |
String[] tokens = chainId.split("\\:"); |
1230 |
0 |
if (tokens.length == 2) |
1231 |
|
{ |
1232 |
0 |
String pdbFile = getFileForChain(chainId); |
1233 |
0 |
String model = getModelIdForFile(pdbFile); |
1234 |
0 |
showThese.add(model + ":" + tokens[1]); |
1235 |
|
} |
1236 |
|
} |
1237 |
0 |
executeCommands(commandGenerator.showChains(showThese), false, null); |
1238 |
|
} |
1239 |
|
|
1240 |
|
|
1241 |
|
|
1242 |
|
|
1243 |
|
|
1244 |
|
@param |
1245 |
|
@return |
1246 |
|
|
1247 |
|
protected abstract String getModelIdForFile(String chainId); |
1248 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1249 |
350 |
public boolean hasFileLoadingError()... |
1250 |
|
{ |
1251 |
350 |
return fileLoadingError != null && fileLoadingError.length() > 0; |
1252 |
|
} |
1253 |
|
|
1254 |
|
|
1255 |
|
|
1256 |
|
|
1257 |
|
@param |
1258 |
|
@return |
1259 |
|
|
|
|
| 62.5% |
Uncovered Elements: 3 (8) |
Complexity: 3 |
Complexity Density: 0.75 |
|
1260 |
43 |
public FeatureRenderer getFeatureRenderer(AlignmentViewPanel avp)... |
1261 |
|
{ |
1262 |
43 |
AlignmentViewPanel ap = (avp == null) ? getViewer().getAlignmentPanel() |
1263 |
|
: avp; |
1264 |
42 |
if (ap == null) |
1265 |
|
{ |
1266 |
0 |
return null; |
1267 |
|
} |
1268 |
42 |
return ap.getFeatureRenderer(); |
1269 |
|
} |
1270 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1271 |
45 |
protected void setStructureCommands(StructureCommandsI cmd)... |
1272 |
|
{ |
1273 |
45 |
commandGenerator = cmd; |
1274 |
|
} |
1275 |
|
|
1276 |
|
|
1277 |
|
|
1278 |
|
|
1279 |
|
|
1280 |
|
@param |
1281 |
|
@param |
1282 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1283 |
63 |
public void addChainFile(String chainId, String fileName)... |
1284 |
|
{ |
1285 |
63 |
chainFile.put(chainId, fileName); |
1286 |
|
} |
1287 |
|
|
1288 |
|
|
1289 |
|
|
1290 |
|
|
1291 |
|
|
1292 |
|
@param |
1293 |
|
@return |
1294 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1295 |
0 |
protected String getFileForChain(String chainId)... |
1296 |
|
{ |
1297 |
0 |
return chainFile.get(chainId); |
1298 |
|
} |
1299 |
|
|
|
|
| 92.3% |
Uncovered Elements: 1 (13) |
Complexity: 4 |
Complexity Density: 0.57 |
|
1300 |
920 |
@Override... |
1301 |
|
public void updateColours(Object source) |
1302 |
|
{ |
1303 |
920 |
if (getViewer() == null) |
1304 |
|
{ |
1305 |
|
|
1306 |
|
|
1307 |
29 |
return; |
1308 |
|
} |
1309 |
891 |
AlignmentViewPanel ap = (AlignmentViewPanel) source; |
1310 |
|
|
1311 |
891 |
if (!getViewer().isUsedForColourBy(ap)) |
1312 |
|
{ |
1313 |
647 |
return; |
1314 |
|
} |
1315 |
244 |
if (!isLoadingFromArchive()) |
1316 |
|
{ |
1317 |
244 |
colourBySequence(ap); |
1318 |
|
} |
1319 |
|
} |
1320 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1321 |
23 |
public StructureCommandsI getCommandGenerator()... |
1322 |
|
{ |
1323 |
23 |
return commandGenerator; |
1324 |
|
} |
1325 |
|
|
1326 |
|
protected abstract ViewerType getViewerType(); |
1327 |
|
|
1328 |
|
|
1329 |
|
|
1330 |
|
|
1331 |
|
|
1332 |
|
|
1333 |
|
|
1334 |
|
|
1335 |
|
|
1336 |
|
|
1337 |
|
|
1338 |
|
|
1339 |
|
|
1340 |
|
|
1341 |
|
|
1342 |
|
|
1343 |
|
@param |
1344 |
|
@param |
1345 |
|
@param |
1346 |
|
@return |
1347 |
|
|
|
|
| 95.6% |
Uncovered Elements: 3 (68) |
Complexity: 18 |
Complexity Density: 0.41 |
|
1348 |
274 |
protected Map<Object, AtomSpecModel> buildColoursMap(... |
1349 |
|
StructureSelectionManager ssm, SequenceI[][] sequence, |
1350 |
|
AlignmentViewPanel viewPanel) |
1351 |
|
{ |
1352 |
274 |
String[] files = getStructureFiles(); |
1353 |
274 |
SequenceRenderer sr = getSequenceRenderer(viewPanel); |
1354 |
274 |
FeatureRenderer fr = viewPanel.getFeatureRenderer(); |
1355 |
274 |
FeatureColourFinder finder = new FeatureColourFinder(fr); |
1356 |
274 |
AlignViewportI viewport = viewPanel.getAlignViewport(); |
1357 |
274 |
HiddenColumns cs = viewport.getAlignment().getHiddenColumns(); |
1358 |
265 |
AlignmentI al = viewport.getAlignment(); |
1359 |
265 |
Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<>(); |
1360 |
265 |
Color lastColour = null; |
1361 |
|
|
1362 |
533 |
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) |
1363 |
|
{ |
1364 |
268 |
final String modelId = getModelIdForFile(files[pdbfnum]); |
1365 |
268 |
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); |
1366 |
|
|
1367 |
268 |
if (mapping == null || mapping.length < 1) |
1368 |
|
{ |
1369 |
31 |
continue; |
1370 |
|
} |
1371 |
|
|
1372 |
237 |
int startPos = -1, lastPos = -1; |
1373 |
237 |
String lastChain = ""; |
1374 |
474 |
for (int s = 0; s < sequence[pdbfnum].length; s++) |
1375 |
|
{ |
1376 |
518 |
for (int sp, m = 0; m < mapping.length; m++) |
1377 |
|
{ |
1378 |
281 |
final SequenceI seq = sequence[pdbfnum][s]; |
1379 |
? |
if (mapping[m].getSequence() == seq |
1380 |
|
&& (sp = al.findIndex(seq)) > -1) |
1381 |
|
{ |
1382 |
232 |
SequenceI asp = al.getSequenceAt(sp); |
1383 |
60462 |
for (int r = 0; r < asp.getLength(); r++) |
1384 |
|
{ |
1385 |
|
|
1386 |
60231 |
if (Comparison.isGap(asp.getCharAt(r))) |
1387 |
|
{ |
1388 |
27980 |
continue; |
1389 |
|
} |
1390 |
32251 |
int pos = mapping[m].getPDBResNum(asp.findPosition(r)); |
1391 |
|
|
1392 |
32251 |
if (pos < 1 || pos == lastPos) |
1393 |
|
{ |
1394 |
14 |
continue; |
1395 |
|
} |
1396 |
|
|
1397 |
32237 |
Color colour = sr.getResidueColour(seq, r, finder); |
1398 |
|
|
1399 |
|
|
1400 |
|
|
1401 |
|
|
1402 |
32237 |
if (!cs.isVisible(r)) |
1403 |
|
{ |
1404 |
6 |
colour = Color.GRAY; |
1405 |
|
} |
1406 |
|
|
1407 |
32237 |
final String chain = mapping[m].getChain(); |
1408 |
|
|
1409 |
|
|
1410 |
|
|
1411 |
|
|
1412 |
|
|
1413 |
|
|
1414 |
32237 |
final boolean newColour = !colour.equals(lastColour); |
1415 |
32237 |
final boolean nonContig = lastPos + 1 != pos; |
1416 |
32237 |
final boolean newChain = !chain.equals(lastChain); |
1417 |
32237 |
if (newColour || nonContig || newChain) |
1418 |
|
{ |
1419 |
6258 |
if (startPos != -1) |
1420 |
|
{ |
1421 |
6026 |
addAtomSpecRange(colourMap, lastColour, modelId, startPos, |
1422 |
|
lastPos, lastChain); |
1423 |
|
} |
1424 |
6258 |
startPos = pos; |
1425 |
|
} |
1426 |
32235 |
lastColour = colour; |
1427 |
32237 |
lastPos = pos; |
1428 |
32235 |
lastChain = chain; |
1429 |
|
} |
1430 |
|
|
1431 |
232 |
if (lastColour != null) |
1432 |
|
{ |
1433 |
232 |
addAtomSpecRange(colourMap, lastColour, modelId, startPos, |
1434 |
|
lastPos, lastChain); |
1435 |
|
} |
1436 |
|
|
1437 |
|
} |
1438 |
|
} |
1439 |
|
} |
1440 |
|
} |
1441 |
265 |
return colourMap; |
1442 |
|
} |
1443 |
|
|
1444 |
|
|
1445 |
|
|
1446 |
|
|
1447 |
|
@param |
1448 |
|
@param |
1449 |
|
@return |
1450 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1451 |
0 |
protected String getModelId(int pdbfnum, String file)... |
1452 |
|
{ |
1453 |
0 |
return String.valueOf(pdbfnum); |
1454 |
|
} |
1455 |
|
|
1456 |
|
|
1457 |
|
|
1458 |
|
|
1459 |
|
|
1460 |
|
@param |
1461 |
|
@param |
1462 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
1463 |
44 |
public void stashFoundChains(StructureFile pdb, String file)... |
1464 |
|
{ |
1465 |
107 |
for (int i = 0; i < pdb.getChains().size(); i++) |
1466 |
|
{ |
1467 |
63 |
String chid = pdb.getId() + ":" + pdb.getChains().elementAt(i).id; |
1468 |
63 |
addChainFile(chid, file); |
1469 |
63 |
getChainNames().add(chid); |
1470 |
|
} |
1471 |
|
} |
1472 |
|
|
1473 |
|
|
1474 |
|
|
1475 |
|
|
1476 |
|
|
1477 |
|
|
1478 |
|
|
1479 |
|
|
1480 |
|
|
1481 |
|
|
1482 |
|
|
1483 |
|
@param |
1484 |
|
@param |
1485 |
|
@param |
1486 |
|
@param |
1487 |
|
@param |
1488 |
|
@param |
1489 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
1490 |
6258 |
public static final void addAtomSpecRange(Map<Object, AtomSpecModel> map,... |
1491 |
|
Object value, String model, int startPos, int endPos, |
1492 |
|
String chain) |
1493 |
|
{ |
1494 |
|
|
1495 |
|
|
1496 |
|
|
1497 |
6258 |
AtomSpecModel atomSpec = map.get(value); |
1498 |
6258 |
if (atomSpec == null) |
1499 |
|
{ |
1500 |
1348 |
atomSpec = new AtomSpecModel(); |
1501 |
1348 |
map.put(value, atomSpec); |
1502 |
|
} |
1503 |
|
|
1504 |
6258 |
atomSpec.addRange(model, startPos, endPos, chain); |
1505 |
|
} |
1506 |
|
|
1507 |
|
|
1508 |
|
|
1509 |
|
|
1510 |
|
|
1511 |
|
|
1512 |
|
@return |
1513 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1514 |
0 |
public String getSessionFileExtension()... |
1515 |
|
{ |
1516 |
0 |
return null; |
1517 |
|
} |
1518 |
|
|
1519 |
|
|
1520 |
|
|
1521 |
|
|
1522 |
|
|
1523 |
|
@return |
1524 |
|
|
|
|
| 87.5% |
Uncovered Elements: 1 (8) |
Complexity: 2 |
Complexity Density: 0.25 |
|
1525 |
2 |
public File saveSession()... |
1526 |
|
{ |
1527 |
2 |
String prefix = getViewerType().toString(); |
1528 |
2 |
String suffix = getSessionFileExtension(); |
1529 |
2 |
File f = null; |
1530 |
2 |
try |
1531 |
|
{ |
1532 |
2 |
f = File.createTempFile(prefix, suffix); |
1533 |
2 |
saveSession(f); |
1534 |
|
} catch (IOException e) |
1535 |
|
{ |
1536 |
0 |
Console.error(String.format("Error saving %s session: %s", prefix, |
1537 |
|
e.toString())); |
1538 |
|
} |
1539 |
|
|
1540 |
2 |
return f; |
1541 |
|
} |
1542 |
|
|
1543 |
|
|
1544 |
|
|
1545 |
|
|
1546 |
|
|
1547 |
|
@param |
1548 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
1549 |
0 |
public void restoreSession(String absolutePath)... |
1550 |
|
{ |
1551 |
0 |
String prefix = getViewerType().toString(); |
1552 |
0 |
try |
1553 |
|
{ |
1554 |
|
|
1555 |
0 |
StructureCommandI cmd = commandGenerator.restoreSession(absolutePath); |
1556 |
0 |
if (cmd != null) |
1557 |
|
{ |
1558 |
0 |
executeCommand(cmd, false); |
1559 |
|
} |
1560 |
|
} catch (Throwable e) |
1561 |
|
{ |
1562 |
0 |
Console.error(String.format("Error restoring %s session: %s", prefix, |
1563 |
|
e.toString())); |
1564 |
|
} |
1565 |
|
|
1566 |
|
} |
1567 |
|
|
1568 |
|
|
1569 |
|
|
1570 |
|
|
1571 |
|
@param |
1572 |
|
|
|
|
| 80% |
Uncovered Elements: 1 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1573 |
2 |
protected void saveSession(File f)... |
1574 |
|
{ |
1575 |
2 |
StructureCommandI cmd = commandGenerator.saveSession(f.getPath()); |
1576 |
2 |
if (cmd != null) |
1577 |
|
{ |
1578 |
2 |
executeCommand(cmd, false); |
1579 |
|
} |
1580 |
|
} |
1581 |
|
|
1582 |
|
|
1583 |
|
|
1584 |
|
|
1585 |
|
|
1586 |
|
|
1587 |
|
@return |
1588 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1589 |
23 |
public boolean isViewerRunning()... |
1590 |
|
{ |
1591 |
23 |
return false; |
1592 |
|
} |
1593 |
|
|
1594 |
|
|
1595 |
|
|
1596 |
|
|
1597 |
|
|
1598 |
|
|
1599 |
|
@param |
1600 |
|
|
|
|
| 68.8% |
Uncovered Elements: 5 (16) |
Complexity: 4 |
Complexity Density: 0.4 |
|
1601 |
23 |
public void closeViewer(boolean forceClose)... |
1602 |
|
{ |
1603 |
23 |
getSsm().removeStructureViewerListener(this, this.getStructureFiles()); |
1604 |
22 |
releaseUIResources(); |
1605 |
|
|
1606 |
|
|
1607 |
|
|
1608 |
|
|
1609 |
22 |
if (externalViewerMonitor != null) |
1610 |
|
{ |
1611 |
0 |
externalViewerMonitor.interrupt(); |
1612 |
0 |
externalViewerMonitor = null; |
1613 |
|
} |
1614 |
|
|
1615 |
22 |
stopListening(); |
1616 |
|
|
1617 |
22 |
if (forceClose) |
1618 |
|
{ |
1619 |
1 |
StructureCommandI cmd = getCommandGenerator().closeViewer(); |
1620 |
1 |
if (cmd != null) |
1621 |
|
{ |
1622 |
0 |
executeCommand(cmd, false); |
1623 |
|
} |
1624 |
|
} |
1625 |
|
} |
1626 |
|
|
1627 |
|
|
1628 |
|
|
1629 |
|
|
1630 |
|
|
1631 |
|
@return |
1632 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1633 |
0 |
public String getHelpURL()... |
1634 |
|
{ |
1635 |
0 |
return null; |
1636 |
|
} |
1637 |
|
|
1638 |
|
|
1639 |
|
|
1640 |
|
|
1641 |
|
|
1642 |
|
|
1643 |
|
|
1644 |
|
@param |
1645 |
|
@return |
1646 |
|
|
|
|
| 0% |
Uncovered Elements: 61 (61) |
Complexity: 16 |
Complexity Density: 0.43 |
|
1647 |
0 |
protected Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(... |
1648 |
|
AlignmentViewPanel viewPanel) |
1649 |
|
{ |
1650 |
0 |
Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<>(); |
1651 |
0 |
String[] files = getStructureFiles(); |
1652 |
0 |
if (files == null) |
1653 |
|
{ |
1654 |
0 |
return theMap; |
1655 |
|
} |
1656 |
|
|
1657 |
0 |
FeatureRenderer fr = viewPanel.getFeatureRenderer(); |
1658 |
0 |
if (fr == null) |
1659 |
|
{ |
1660 |
0 |
return theMap; |
1661 |
|
} |
1662 |
|
|
1663 |
0 |
AlignViewportI viewport = viewPanel.getAlignViewport(); |
1664 |
0 |
List<String> visibleFeatures = fr.getDisplayedFeatureTypes(); |
1665 |
|
|
1666 |
|
|
1667 |
|
|
1668 |
|
|
1669 |
|
|
1670 |
0 |
boolean showLinkedFeatures = viewport.isShowComplementFeatures(); |
1671 |
0 |
List<String> complementFeatures = new ArrayList<>(); |
1672 |
0 |
FeatureRenderer complementRenderer = null; |
1673 |
0 |
if (showLinkedFeatures) |
1674 |
|
{ |
1675 |
0 |
AlignViewportI comp = fr.getViewport().getCodingComplement(); |
1676 |
0 |
if (comp != null) |
1677 |
|
{ |
1678 |
0 |
complementRenderer = Desktop.getAlignFrameFor(comp) |
1679 |
|
.getFeatureRenderer(); |
1680 |
0 |
complementFeatures = complementRenderer.getDisplayedFeatureTypes(); |
1681 |
|
} |
1682 |
|
} |
1683 |
0 |
if (visibleFeatures.isEmpty() && complementFeatures.isEmpty()) |
1684 |
|
{ |
1685 |
0 |
return theMap; |
1686 |
|
} |
1687 |
|
|
1688 |
0 |
AlignmentI alignment = viewPanel.getAlignment(); |
1689 |
0 |
SequenceI[][] seqs = getSequence(); |
1690 |
|
|
1691 |
0 |
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) |
1692 |
|
{ |
1693 |
0 |
String modelId = getModelIdForFile(files[pdbfnum]); |
1694 |
0 |
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); |
1695 |
|
|
1696 |
0 |
if (mapping == null || mapping.length < 1) |
1697 |
|
{ |
1698 |
0 |
continue; |
1699 |
|
} |
1700 |
|
|
1701 |
0 |
for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++) |
1702 |
|
{ |
1703 |
0 |
for (int m = 0; m < mapping.length; m++) |
1704 |
|
{ |
1705 |
0 |
final SequenceI seq = seqs[pdbfnum][seqNo]; |
1706 |
0 |
int sp = alignment.findIndex(seq); |
1707 |
0 |
StructureMapping structureMapping = mapping[m]; |
1708 |
0 |
if (structureMapping.getSequence() == seq && sp > -1) |
1709 |
|
{ |
1710 |
|
|
1711 |
|
|
1712 |
|
|
1713 |
|
|
1714 |
0 |
if (!visibleFeatures.isEmpty()) |
1715 |
|
{ |
1716 |
0 |
scanSequenceFeatures(visibleFeatures, structureMapping, seq, |
1717 |
|
theMap, modelId); |
1718 |
|
} |
1719 |
0 |
if (showLinkedFeatures) |
1720 |
|
{ |
1721 |
0 |
scanComplementFeatures(complementRenderer, structureMapping, |
1722 |
|
seq, theMap, modelId); |
1723 |
|
} |
1724 |
|
} |
1725 |
|
} |
1726 |
|
} |
1727 |
|
} |
1728 |
0 |
return theMap; |
1729 |
|
} |
1730 |
|
|
1731 |
|
|
1732 |
|
|
1733 |
|
|
1734 |
|
|
1735 |
|
@param |
1736 |
|
@return |
1737 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
1738 |
0 |
public boolean openSession(String filepath)... |
1739 |
|
{ |
1740 |
0 |
StructureCommandI cmd = getCommandGenerator().openSession(filepath); |
1741 |
0 |
if (cmd == null) |
1742 |
|
{ |
1743 |
0 |
return false; |
1744 |
|
} |
1745 |
0 |
executeCommand(cmd, true); |
1746 |
|
|
1747 |
0 |
return true; |
1748 |
|
} |
1749 |
|
|
1750 |
|
|
1751 |
|
|
1752 |
|
|
1753 |
|
|
1754 |
|
@param |
1755 |
|
@param |
1756 |
|
@param |
1757 |
|
@param |
1758 |
|
@param |
1759 |
|
|
|
|
| 0% |
Uncovered Elements: 33 (33) |
Complexity: 9 |
Complexity Density: 0.43 |
|
1760 |
0 |
protected static void scanComplementFeatures(... |
1761 |
|
FeatureRenderer complementRenderer, |
1762 |
|
StructureMapping structureMapping, SequenceI seq, |
1763 |
|
Map<String, Map<Object, AtomSpecModel>> theMap, |
1764 |
|
String modelNumber) |
1765 |
|
{ |
1766 |
|
|
1767 |
|
|
1768 |
|
|
1769 |
0 |
for (int seqPos : structureMapping.getMapping().keySet()) |
1770 |
|
{ |
1771 |
|
|
1772 |
|
|
1773 |
|
|
1774 |
0 |
MappedFeatures mf = complementRenderer |
1775 |
|
.findComplementFeaturesAtResidue(seq, seqPos); |
1776 |
0 |
if (mf != null) |
1777 |
|
{ |
1778 |
0 |
for (SequenceFeature sf : mf.features) |
1779 |
|
{ |
1780 |
0 |
String type = sf.getType(); |
1781 |
|
|
1782 |
|
|
1783 |
|
|
1784 |
|
|
1785 |
0 |
if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP |
1786 |
|
.equals(sf.getFeatureGroup())) |
1787 |
|
{ |
1788 |
0 |
continue; |
1789 |
|
} |
1790 |
|
|
1791 |
|
|
1792 |
|
|
1793 |
|
|
1794 |
|
|
1795 |
0 |
List<int[]> mappedRanges = structureMapping |
1796 |
|
.getPDBResNumRanges(seqPos, seqPos); |
1797 |
|
|
1798 |
0 |
if (!mappedRanges.isEmpty()) |
1799 |
|
{ |
1800 |
0 |
String value = sf.getDescription(); |
1801 |
0 |
if (value == null || value.length() == 0) |
1802 |
|
{ |
1803 |
0 |
value = type; |
1804 |
|
} |
1805 |
0 |
float score = sf.getScore(); |
1806 |
0 |
if (score != 0f && !Float.isNaN(score)) |
1807 |
|
{ |
1808 |
0 |
value = Float.toString(score); |
1809 |
|
} |
1810 |
0 |
Map<Object, AtomSpecModel> featureValues = theMap.get(type); |
1811 |
0 |
if (featureValues == null) |
1812 |
|
{ |
1813 |
0 |
featureValues = new HashMap<>(); |
1814 |
0 |
theMap.put(type, featureValues); |
1815 |
|
} |
1816 |
0 |
for (int[] range : mappedRanges) |
1817 |
|
{ |
1818 |
0 |
addAtomSpecRange(featureValues, value, modelNumber, range[0], |
1819 |
|
range[1], structureMapping.getChain()); |
1820 |
|
} |
1821 |
|
} |
1822 |
|
} |
1823 |
|
} |
1824 |
|
} |
1825 |
|
} |
1826 |
|
|
1827 |
|
|
1828 |
|
|
1829 |
|
|
1830 |
|
|
1831 |
|
|
1832 |
|
@param |
1833 |
|
@param |
1834 |
|
@param |
1835 |
|
@param |
1836 |
|
@param |
1837 |
|
|
|
|
| 0% |
Uncovered Elements: 29 (29) |
Complexity: 8 |
Complexity Density: 0.42 |
|
1838 |
0 |
protected static void scanSequenceFeatures(List<String> visibleFeatures,... |
1839 |
|
StructureMapping mapping, SequenceI seq, |
1840 |
|
Map<String, Map<Object, AtomSpecModel>> theMap, String modelId) |
1841 |
|
{ |
1842 |
0 |
List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures( |
1843 |
|
visibleFeatures.toArray(new String[visibleFeatures.size()])); |
1844 |
0 |
for (SequenceFeature sf : sfs) |
1845 |
|
{ |
1846 |
0 |
String type = sf.getType(); |
1847 |
|
|
1848 |
|
|
1849 |
|
|
1850 |
|
|
1851 |
0 |
if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP |
1852 |
|
.equals(sf.getFeatureGroup())) |
1853 |
|
{ |
1854 |
0 |
continue; |
1855 |
|
} |
1856 |
|
|
1857 |
0 |
List<int[]> mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(), |
1858 |
|
sf.getEnd()); |
1859 |
|
|
1860 |
0 |
if (!mappedRanges.isEmpty()) |
1861 |
|
{ |
1862 |
0 |
String value = sf.getDescription(); |
1863 |
0 |
if (value == null || value.length() == 0) |
1864 |
|
{ |
1865 |
0 |
value = type; |
1866 |
|
} |
1867 |
0 |
float score = sf.getScore(); |
1868 |
0 |
if (score != 0f && !Float.isNaN(score)) |
1869 |
|
{ |
1870 |
0 |
value = Float.toString(score); |
1871 |
|
} |
1872 |
0 |
Map<Object, AtomSpecModel> featureValues = theMap.get(type); |
1873 |
0 |
if (featureValues == null) |
1874 |
|
{ |
1875 |
0 |
featureValues = new HashMap<>(); |
1876 |
0 |
theMap.put(type, featureValues); |
1877 |
|
} |
1878 |
0 |
for (int[] range : mappedRanges) |
1879 |
|
{ |
1880 |
0 |
addAtomSpecRange(featureValues, value, modelId, range[0], |
1881 |
|
range[1], mapping.getChain()); |
1882 |
|
} |
1883 |
|
} |
1884 |
|
} |
1885 |
|
} |
1886 |
|
|
1887 |
|
|
1888 |
|
|
1889 |
|
|
1890 |
|
|
1891 |
|
|
1892 |
|
@return |
1893 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
1894 |
150 |
public int getMappedStructureCount()... |
1895 |
|
{ |
1896 |
150 |
String[] files = getStructureFiles(); |
1897 |
150 |
return files == null ? 0 : files.length; |
1898 |
|
} |
1899 |
|
|
1900 |
|
|
1901 |
|
|
1902 |
|
|
1903 |
|
|
1904 |
|
|
1905 |
|
|
1906 |
|
@param |
1907 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1908 |
0 |
protected void startExternalViewerMonitor(Process p)... |
1909 |
|
{ |
1910 |
0 |
externalViewerMonitor = new Thread(new Runnable() |
1911 |
|
{ |
1912 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 3 |
Complexity Density: 0.6 |
|
1913 |
0 |
@Override... |
1914 |
|
public void run() |
1915 |
|
{ |
1916 |
0 |
try |
1917 |
|
{ |
1918 |
0 |
p.waitFor(); |
1919 |
0 |
JalviewStructureDisplayI display = getViewer(); |
1920 |
0 |
if (display != null) |
1921 |
|
{ |
1922 |
0 |
display.closeViewer(false); |
1923 |
|
} |
1924 |
|
} catch (InterruptedException e) |
1925 |
|
{ |
1926 |
|
|
1927 |
|
} |
1928 |
|
} |
1929 |
|
}); |
1930 |
0 |
externalViewerMonitor.start(); |
1931 |
|
} |
1932 |
|
|
1933 |
|
|
1934 |
|
|
1935 |
|
|
1936 |
|
|
1937 |
|
|
1938 |
|
@param |
1939 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1940 |
0 |
protected void startListening(String uri)... |
1941 |
|
{ |
1942 |
0 |
List<StructureCommandI> commands = getCommandGenerator() |
1943 |
|
.startNotifications(uri); |
1944 |
0 |
if (commands != null) |
1945 |
|
{ |
1946 |
0 |
executeCommands(commands, false, null); |
1947 |
|
} |
1948 |
|
} |
1949 |
|
|
1950 |
|
|
1951 |
|
|
1952 |
|
|
1953 |
|
|
|
|
| 60% |
Uncovered Elements: 2 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1954 |
22 |
protected void stopListening()... |
1955 |
|
{ |
1956 |
22 |
List<StructureCommandI> commands = getCommandGenerator() |
1957 |
|
.stopNotifications(); |
1958 |
22 |
if (commands != null) |
1959 |
|
{ |
1960 |
0 |
executeCommands(commands, false, null); |
1961 |
|
} |
1962 |
|
} |
1963 |
|
|
1964 |
|
|
1965 |
|
|
1966 |
|
|
1967 |
|
|
1968 |
|
|
1969 |
|
@param |
1970 |
|
@param |
1971 |
|
@return |
1972 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
|
1973 |
0 |
public int copyStructureAttributesToFeatures(String attName,... |
1974 |
|
AlignmentPanel alignmentPanel) |
1975 |
|
{ |
1976 |
0 |
StructureCommandI cmd = getCommandGenerator() |
1977 |
|
.getResidueAttributes(attName); |
1978 |
0 |
if (cmd == null) |
1979 |
|
{ |
1980 |
0 |
return 0; |
1981 |
|
} |
1982 |
0 |
List<String> residueAttributes = executeCommand(cmd, true); |
1983 |
|
|
1984 |
0 |
int featuresAdded = createFeaturesForAttributes(attName, |
1985 |
|
residueAttributes); |
1986 |
0 |
if (featuresAdded > 0) |
1987 |
|
{ |
1988 |
0 |
alignmentPanel.getFeatureRenderer().featuresAdded(); |
1989 |
|
} |
1990 |
0 |
return featuresAdded; |
1991 |
|
} |
1992 |
|
|
1993 |
|
|
1994 |
|
|
1995 |
|
|
1996 |
|
|
1997 |
|
|
1998 |
|
|
1999 |
|
|
2000 |
|
|
2001 |
|
@param |
2002 |
|
@param |
2003 |
|
@return |
2004 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2005 |
0 |
protected int createFeaturesForAttributes(String attName,... |
2006 |
|
List<String> residueAttributes) |
2007 |
|
{ |
2008 |
0 |
return 0; |
2009 |
|
} |
2010 |
|
|
2011 |
|
|
2012 |
|
|
2013 |
|
|
2014 |
|
@return |
2015 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2016 |
0 |
public Map<String, String> getHetatmNames()... |
2017 |
|
{ |
2018 |
0 |
return Collections.EMPTY_MAP; |
2019 |
|
} |
2020 |
|
|
2021 |
|
|
2022 |
|
|
2023 |
|
|
2024 |
|
@param |
2025 |
|
|
2026 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2027 |
0 |
public void showHetatms(List<String> toShow)... |
2028 |
|
{ |
2029 |
0 |
executeCommands(commandGenerator.showHetatms(toShow), false, |
2030 |
|
"Adjusting hetatm visibility"); |
2031 |
|
} |
2032 |
|
|
2033 |
|
} |