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package jalview.ws.dbsources; |
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import jalview.api.FeatureSettingsModelI; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.DBRefSource; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.PDBEntry.Type; |
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import jalview.datamodel.SequenceI; |
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import jalview.io.DataSourceType; |
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import jalview.io.FileFormat; |
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import jalview.io.FileFormatI; |
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import jalview.io.FormatAdapter; |
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import jalview.io.PDBFeatureSettings; |
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import jalview.structure.StructureImportSettings; |
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import jalview.util.MessageManager; |
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import jalview.ws.ebi.EBIFetchClient; |
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import java.io.File; |
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import java.util.ArrayList; |
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import java.util.List; |
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import com.stevesoft.pat.Regex; |
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@author |
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| 6.4% |
Uncovered Elements: 88 (94) |
Complexity: 31 |
Complexity Density: 0.53 |
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public class Pdb extends EbiFileRetrievedProxy |
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{ |
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private static final String SEPARATOR = "|"; |
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private static final String COLON = ":"; |
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private static final int PDB_ID_LENGTH = 4; |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public Pdb()... |
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{ |
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super(); |
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} |
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@see |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public String getAccessionSeparator() |
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{ |
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return null; |
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} |
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@see |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public Regex getAccessionValidator() |
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{ |
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return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)"); |
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} |
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@see |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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2216 |
@Override... |
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public String getDbSource() |
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{ |
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return DBRefSource.PDB; |
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} |
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@see |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public String getDbVersion() |
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{ |
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return "0"; |
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} |
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@see |
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| 0% |
Uncovered Elements: 72 (72) |
Complexity: 21 |
Complexity Density: 0.44 |
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@Override... |
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public AlignmentI getSequenceRecords(String queries) throws Exception |
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{ |
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AlignmentI pdbAlignment = null; |
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String chain = null; |
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String id = null; |
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if (queries.indexOf(COLON) > -1) |
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{ |
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chain = queries.substring(queries.indexOf(COLON) + 1); |
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id = queries.substring(0, queries.indexOf(COLON)); |
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} |
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else |
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{ |
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id = queries; |
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} |
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if (queries.length() > PDB_ID_LENGTH && chain == null) |
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{ |
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chain = queries.substring(PDB_ID_LENGTH, PDB_ID_LENGTH + 1); |
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id = queries.substring(0, PDB_ID_LENGTH); |
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} |
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if (!isValidReference(id)) |
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{ |
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System.err.println("Ignoring invalid pdb query: '" + id + "'"); |
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stopQuery(); |
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return null; |
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} |
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Type pdbFileFormat = StructureImportSettings |
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.getDefaultStructureFileFormat(); |
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String ext = pdbFileFormat.getExtension(); |
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String fetchFormat = pdbFileFormat.getFormat(); |
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EBIFetchClient ebi = new EBIFetchClient(); |
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File tmpFile = ebi.fetchDataAsFile("pdb:" + id, fetchFormat, ext); |
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file = tmpFile.getAbsolutePath(); |
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stopQuery(); |
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if (file == null) |
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{ |
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return null; |
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} |
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try |
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{ |
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FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB |
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: FileFormat.MMCif; |
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pdbAlignment = new FormatAdapter().readFile(tmpFile, DataSourceType.FILE, |
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fileFormat); |
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if (pdbAlignment != null) |
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List<SequenceI> toremove = new ArrayList<SequenceI>(); |
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for (SequenceI pdbcs : pdbAlignment.getSequences()) |
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{ |
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String chid = null; |
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for (PDBEntry pid : pdbcs.getAllPDBEntries()) |
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{ |
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if (pid.getFile() == file) |
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{ |
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chid = pid.getChainCode(); |
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} |
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} |
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if (chain == null || (chid != null && (chid.equals(chain) |
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|| chid.trim().equals(chain.trim()) |
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|| (chain.trim().length() == 0 && chid.equals("_"))))) |
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{ |
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pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR + id |
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+ SEPARATOR + pdbcs.getName()); |
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DBRefEntry dbentry = new DBRefEntry(getDbSource(), |
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getDbVersion(), (chid == null ? id : id + chid)); |
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pdbcs.addDBRef(dbentry); |
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} |
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else |
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{ |
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toremove.add(pdbcs); |
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} |
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} |
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for (SequenceI pdbcs : toremove) |
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{ |
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pdbAlignment.deleteSequence(pdbcs); |
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if (pdbcs.getAnnotation() != null) |
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{ |
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for (AlignmentAnnotation aa : pdbcs.getAnnotation()) |
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{ |
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pdbAlignment.deleteAnnotation(aa); |
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} |
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} |
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} |
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} |
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if (pdbAlignment == null || pdbAlignment.getHeight() < 1) |
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{ |
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throw new Exception(MessageManager.formatMessage( |
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"exception.no_pdb_records_for_chain", new String[] |
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{ id, ((chain == null) ? "' '" : chain) })); |
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} |
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} catch (Exception ex) |
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{ |
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stopQuery(); |
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throw (ex); |
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} |
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return pdbAlignment; |
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} |
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@see |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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0 |
@Override... |
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public boolean isValidReference(String accession) |
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{ |
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Regex r = getAccessionValidator(); |
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return r.search(accession.trim()); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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0 |
@Override... |
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public String getTestQuery() |
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{ |
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return "1QIP"; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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2210 |
@Override... |
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public String getDbName() |
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{ |
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return "PDB"; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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0 |
@Override... |
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public int getTier() |
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{ |
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return 0; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public FeatureSettingsModelI getFeatureColourScheme() |
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{ |
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return new PDBFeatureSettings(); |
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} |
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} |