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package jalview.ws.sifts; |
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import java.io.File; |
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import java.io.FileInputStream; |
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import java.io.FileOutputStream; |
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import java.io.IOException; |
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import java.io.InputStream; |
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import java.io.PrintStream; |
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import java.net.URL; |
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import java.net.URLConnection; |
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import java.nio.file.Files; |
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import java.nio.file.Path; |
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import java.nio.file.attribute.BasicFileAttributes; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.Collection; |
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import java.util.Collections; |
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import java.util.Date; |
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import java.util.HashMap; |
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import java.util.HashSet; |
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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.Set; |
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import java.util.TreeMap; |
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import java.util.zip.GZIPInputStream; |
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import javax.xml.bind.JAXBContext; |
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import javax.xml.bind.JAXBElement; |
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import javax.xml.bind.Unmarshaller; |
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import javax.xml.stream.XMLInputFactory; |
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import javax.xml.stream.XMLStreamReader; |
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|
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import jalview.analysis.AlignSeq; |
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import jalview.analysis.scoremodels.ScoreMatrix; |
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import jalview.analysis.scoremodels.ScoreModels; |
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import jalview.api.DBRefEntryI; |
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import jalview.api.SiftsClientI; |
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import jalview.bin.Console; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.DBRefSource; |
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import jalview.datamodel.SequenceI; |
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import jalview.io.BackupFiles; |
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import jalview.io.StructureFile; |
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import jalview.schemes.ResidueProperties; |
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import jalview.structure.StructureMapping; |
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import jalview.util.Comparison; |
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import jalview.util.DBRefUtils; |
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import jalview.util.Format; |
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import jalview.util.HttpUtils; |
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import jalview.util.Platform; |
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import jalview.xml.binding.sifts.Entry; |
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import jalview.xml.binding.sifts.Entry.Entity; |
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import jalview.xml.binding.sifts.Entry.Entity.Segment; |
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import jalview.xml.binding.sifts.Entry.Entity.Segment.ListMapRegion.MapRegion; |
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import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue; |
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import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.CrossRefDb; |
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import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.ResidueDetail; |
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import mc_view.Atom; |
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import mc_view.PDBChain; |
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| 6.6% |
Uncovered Elements: 521 (558) |
Complexity: 128 |
Complexity Density: 0.33 |
|
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public class SiftsClient implements SiftsClientI |
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{ |
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private static File mockSiftsFile; |
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private Entry siftsEntry; |
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private StructureFile pdb; |
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private String pdbId; |
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private String structId; |
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private CoordinateSys seqCoordSys = CoordinateSys.UNIPROT; |
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private jalview.datamodel.Mapping seqFromPdbMapping; |
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private static final int BUFFER_SIZE = 4096; |
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public static final int UNASSIGNED = Integer.MIN_VALUE; |
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private static final int PDB_RES_POS = 0; |
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private static final int PDB_ATOM_POS = 1; |
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private static final int PDBE_POS = 2; |
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private static final String NOT_OBSERVED = "Not_Observed"; |
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private static final String SIFTS_SPLIT_FTP_BASE_URL = "https://ftp.ebi.ac.uk/pub/databases/msd/sifts/split_xml/"; |
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private final static String NEWLINE = System.lineSeparator(); |
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private String curSourceDBRef; |
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private HashSet<String> curDBRefAccessionIdsString; |
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| 50% |
Uncovered Elements: 2 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
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private enum CoordinateSys |
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{ |
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UNIPROT("UniProt"), PDB("PDBresnum"), PDBe("PDBe"); |
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private String name; |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
134 |
12 |
private CoordinateSys(String name)... |
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{ |
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this.name = name; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
139 |
0 |
public String getName()... |
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{ |
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return name; |
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} |
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}; |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
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private enum ResidueDetailType |
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{ |
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NAME_SEC_STRUCTURE("nameSecondaryStructure"), |
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CODE_SEC_STRUCTURE("codeSecondaryStructure"), ANNOTATION("Annotation"); |
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private String code; |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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private ResidueDetailType(String code)... |
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{ |
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this.code = code; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
public String getCode()... |
158 |
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{ |
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0 |
return code; |
160 |
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} |
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}; |
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@param |
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@throws |
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| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
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public SiftsClient(StructureFile pdb) throws SiftsException... |
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{ |
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this.pdb = pdb; |
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this.pdbId = pdb.getId(); |
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File siftsFile = getSiftsFile(pdbId); |
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siftsEntry = parseSIFTs(siftsFile); |
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} |
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@param |
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183 |
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@return |
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@throws |
185 |
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186 |
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| 80% |
Uncovered Elements: 2 (10) |
Complexity: 6 |
Complexity Density: 0.6 |
|
187 |
4 |
private Entry parseSIFTs(File siftFile) throws SiftsException... |
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{ |
189 |
4 |
try (InputStream in = new FileInputStream(siftFile); |
190 |
4 |
GZIPInputStream gzis = new GZIPInputStream(in);) |
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{ |
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|
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4 |
JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.sifts"); |
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4 |
XMLStreamReader streamReader = XMLInputFactory.newInstance() |
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.createXMLStreamReader(gzis); |
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Unmarshaller um = jc.createUnmarshaller(); |
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4 |
JAXBElement<Entry> jbe = um.unmarshal(streamReader, Entry.class); |
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4 |
return jbe.getValue(); |
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} catch (Exception e) |
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{ |
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e.printStackTrace(); |
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throw new SiftsException(e.getMessage()); |
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} |
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} |
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@param |
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@return |
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@throws |
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| 37% |
Uncovered Elements: 17 (27) |
Complexity: 6 |
Complexity Density: 0.29 |
|
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4 |
public static File getSiftsFile(String pdbId) throws SiftsException... |
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{ |
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4 |
if (mockSiftsFile != null) |
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{ |
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0 |
return mockSiftsFile; |
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} |
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|
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4 |
String siftsFileName = SiftsSettings.getSiftDownloadDirectory() |
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+ pdbId.toLowerCase(Locale.ROOT) + ".xml.gz"; |
226 |
4 |
File siftsFile = new File(siftsFileName); |
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4 |
if (siftsFile.exists()) |
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{ |
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|
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4 |
jalview.bin.Console |
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.outPrintln(">>> SIFTS File already downloaded for " + pdbId); |
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|
233 |
4 |
if (isFileOlderThanThreshold(siftsFile, |
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SiftsSettings.getCacheThresholdInDays())) |
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{ |
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File oldSiftsFile = new File(siftsFileName + "_old"); |
237 |
0 |
BackupFiles.moveFileToFile(siftsFile, oldSiftsFile); |
238 |
0 |
try |
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{ |
240 |
0 |
siftsFile = downloadSiftsFile(pdbId.toLowerCase(Locale.ROOT)); |
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0 |
oldSiftsFile.delete(); |
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0 |
return siftsFile; |
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} catch (IOException e) |
244 |
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{ |
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0 |
e.printStackTrace(); |
246 |
0 |
BackupFiles.moveFileToFile(oldSiftsFile, siftsFile); |
247 |
0 |
return new File(siftsFileName); |
248 |
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} |
249 |
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} |
250 |
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else |
251 |
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{ |
252 |
4 |
return siftsFile; |
253 |
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} |
254 |
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} |
255 |
0 |
try |
256 |
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{ |
257 |
0 |
siftsFile = downloadSiftsFile(pdbId.toLowerCase(Locale.ROOT)); |
258 |
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} catch (IOException e) |
259 |
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{ |
260 |
0 |
throw new SiftsException(e.getMessage()); |
261 |
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} |
262 |
0 |
return siftsFile; |
263 |
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} |
264 |
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265 |
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266 |
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267 |
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|
268 |
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|
269 |
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@param |
270 |
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|
271 |
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@param |
272 |
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|
273 |
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@return |
274 |
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|
|
|
| 87.5% |
Uncovered Elements: 1 (8) |
Complexity: 2 |
Complexity Density: 0.25 |
|
275 |
4 |
public static boolean isFileOlderThanThreshold(File file, int noOfDays)... |
276 |
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{ |
277 |
4 |
Path filePath = file.toPath(); |
278 |
4 |
BasicFileAttributes attr; |
279 |
4 |
int diffInDays = 0; |
280 |
4 |
try |
281 |
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{ |
282 |
4 |
attr = Files.readAttributes(filePath, BasicFileAttributes.class); |
283 |
4 |
diffInDays = (int) ((new Date().getTime() |
284 |
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- attr.lastModifiedTime().toMillis()) |
285 |
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/ (1000 * 60 * 60 * 24)); |
286 |
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|
287 |
|
} catch (IOException e) |
288 |
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{ |
289 |
0 |
e.printStackTrace(); |
290 |
|
} |
291 |
4 |
return noOfDays <= diffInDays; |
292 |
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} |
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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@param |
298 |
|
@return |
299 |
|
@throws |
300 |
|
@throws |
301 |
|
|
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| 0% |
Uncovered Elements: 30 (30) |
Complexity: 5 |
Complexity Density: 0.23 |
|
302 |
0 |
public static File downloadSiftsFile(String pdbId)... |
303 |
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throws SiftsException, IOException |
304 |
|
{ |
305 |
0 |
if (pdbId.contains(".cif")) |
306 |
|
{ |
307 |
0 |
pdbId = pdbId.replace(".cif", ""); |
308 |
|
} |
309 |
0 |
String siftFile = pdbId + ".xml.gz"; |
310 |
0 |
String siftsFileFTPURL = getDownloadUrlFor(siftFile); |
311 |
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|
312 |
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|
313 |
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|
314 |
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|
315 |
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|
316 |
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|
317 |
0 |
File downloadTo = null; |
318 |
0 |
if (Platform.isJS()) |
319 |
|
{ |
320 |
0 |
downloadTo = File.createTempFile(siftFile, ".xml.gz"); |
321 |
|
} |
322 |
|
else |
323 |
|
{ |
324 |
0 |
downloadTo = new File( |
325 |
|
SiftsSettings.getSiftDownloadDirectory() + siftFile); |
326 |
0 |
File siftsDownloadDir = new File( |
327 |
|
SiftsSettings.getSiftDownloadDirectory()); |
328 |
0 |
if (!siftsDownloadDir.exists()) |
329 |
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{ |
330 |
0 |
siftsDownloadDir.mkdirs(); |
331 |
|
} |
332 |
|
} |
333 |
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|
334 |
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|
335 |
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|
336 |
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|
337 |
0 |
URL url = new URL(siftsFileFTPURL); |
338 |
0 |
URLConnection conn = HttpUtils.openConnection(url); |
339 |
0 |
InputStream inputStream = conn.getInputStream(); |
340 |
0 |
FileOutputStream outputStream = new FileOutputStream(downloadTo); |
341 |
0 |
byte[] buffer = new byte[BUFFER_SIZE]; |
342 |
0 |
int bytesRead = -1; |
343 |
0 |
while ((bytesRead = inputStream.read(buffer)) != -1) |
344 |
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{ |
345 |
0 |
outputStream.write(buffer, 0, bytesRead); |
346 |
|
} |
347 |
0 |
outputStream.close(); |
348 |
0 |
inputStream.close(); |
349 |
|
|
350 |
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|
351 |
|
|
352 |
0 |
return downloadTo; |
353 |
|
} |
354 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
355 |
1 |
public static String getDownloadUrlFor(String siftFile)... |
356 |
|
{ |
357 |
1 |
String durl = SIFTS_SPLIT_FTP_BASE_URL + siftFile.substring(1, 3) + "/" |
358 |
|
+ siftFile; |
359 |
1 |
Console.trace("SIFTS URL for " + siftFile + " is " + durl); |
360 |
1 |
return durl; |
361 |
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|
362 |
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} |
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 |
|
@param |
369 |
|
@return |
370 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
371 |
0 |
public static boolean deleteSiftsFileByPDBId(String pdbId)... |
372 |
|
{ |
373 |
0 |
File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory() |
374 |
|
+ pdbId.toLowerCase(Locale.ROOT) + ".xml.gz"); |
375 |
0 |
if (siftsFile.exists()) |
376 |
|
{ |
377 |
0 |
return siftsFile.delete(); |
378 |
|
} |
379 |
0 |
return true; |
380 |
|
} |
381 |
|
|
382 |
|
|
383 |
|
|
384 |
|
|
385 |
|
@param |
386 |
|
|
387 |
|
@return |
388 |
|
@throws |
389 |
|
|
390 |
|
|
|
|
| 0% |
Uncovered Elements: 16 (16) |
Complexity: 9 |
Complexity Density: 0.9 |
|
391 |
0 |
public DBRefEntryI getValidSourceDBRef(SequenceI seq)... |
392 |
|
throws SiftsException |
393 |
|
{ |
394 |
0 |
List<DBRefEntry> dbRefs = seq.getPrimaryDBRefs(); |
395 |
0 |
if (dbRefs == null || dbRefs.size() < 1) |
396 |
|
{ |
397 |
0 |
throw new SiftsException( |
398 |
|
"Source DBRef could not be determined. DBRefs might not have been retrieved."); |
399 |
|
} |
400 |
|
|
401 |
0 |
for (DBRefEntry dbRef : dbRefs) |
402 |
|
{ |
403 |
0 |
if (dbRef == null || dbRef.getAccessionId() == null |
404 |
|
|| dbRef.getSource() == null) |
405 |
|
{ |
406 |
0 |
continue; |
407 |
|
} |
408 |
0 |
String canonicalSource = DBRefUtils |
409 |
|
.getCanonicalName(dbRef.getSource()); |
410 |
0 |
if (isValidDBRefEntry(dbRef) |
411 |
|
&& (canonicalSource.equalsIgnoreCase(DBRefSource.UNIPROT) |
412 |
|
|| canonicalSource.equalsIgnoreCase(DBRefSource.PDB))) |
413 |
|
{ |
414 |
0 |
return dbRef; |
415 |
|
} |
416 |
|
} |
417 |
0 |
throw new SiftsException("Could not get source DB Ref"); |
418 |
|
} |
419 |
|
|
420 |
|
|
421 |
|
|
422 |
|
|
423 |
|
|
424 |
|
@param |
425 |
|
|
426 |
|
@return |
427 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
428 |
0 |
boolean isValidDBRefEntry(DBRefEntryI entry)... |
429 |
|
{ |
430 |
0 |
return entry != null && entry.getAccessionId() != null |
431 |
|
&& isFoundInSiftsEntry(entry.getAccessionId()); |
432 |
|
} |
433 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
|
434 |
0 |
@Override... |
435 |
|
public HashSet<String> getAllMappingAccession() |
436 |
|
{ |
437 |
0 |
HashSet<String> accessions = new HashSet<String>(); |
438 |
0 |
List<Entity> entities = siftsEntry.getEntity(); |
439 |
0 |
for (Entity entity : entities) |
440 |
|
{ |
441 |
0 |
List<Segment> segments = entity.getSegment(); |
442 |
0 |
for (Segment segment : segments) |
443 |
|
{ |
444 |
0 |
List<MapRegion> mapRegions = segment.getListMapRegion() |
445 |
|
.getMapRegion(); |
446 |
0 |
for (MapRegion mapRegion : mapRegions) |
447 |
|
{ |
448 |
0 |
accessions.add(mapRegion.getDb().getDbAccessionId() |
449 |
|
.toLowerCase(Locale.ROOT)); |
450 |
|
} |
451 |
|
} |
452 |
|
} |
453 |
0 |
return accessions; |
454 |
|
} |
455 |
|
|
|
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 3 |
Complexity Density: 0.27 |
|
456 |
0 |
@Override... |
457 |
|
public StructureMapping getSiftsStructureMapping(SequenceI seq, |
458 |
|
String pdbFile, String chain) throws SiftsException |
459 |
|
{ |
460 |
0 |
SequenceI aseq = seq; |
461 |
0 |
while (seq.getDatasetSequence() != null) |
462 |
|
{ |
463 |
0 |
seq = seq.getDatasetSequence(); |
464 |
|
} |
465 |
0 |
structId = (chain == null) ? pdbId : pdbId + "|" + chain; |
466 |
0 |
jalview.bin.Console.outPrintln("Getting SIFTS mapping for " + structId |
467 |
|
+ ": seq " + seq.getName()); |
468 |
|
|
469 |
0 |
final StringBuilder mappingDetails = new StringBuilder(128); |
470 |
0 |
PrintStream ps = new PrintStream(System.out) |
471 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
472 |
0 |
@Override... |
473 |
|
public void print(String x) |
474 |
|
{ |
475 |
0 |
mappingDetails.append(x); |
476 |
|
} |
477 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
478 |
0 |
@Override... |
479 |
|
public void println() |
480 |
|
{ |
481 |
0 |
mappingDetails.append(NEWLINE); |
482 |
|
} |
483 |
|
}; |
484 |
0 |
HashMap<Integer, int[]> mapping = getGreedyMapping(chain, seq, ps); |
485 |
|
|
486 |
0 |
String mappingOutput = mappingDetails.toString(); |
487 |
0 |
StructureMapping siftsMapping = new StructureMapping(aseq, pdbFile, |
488 |
|
pdbId, chain, mapping, mappingOutput, seqFromPdbMapping); |
489 |
|
|
490 |
0 |
return siftsMapping; |
491 |
|
} |
492 |
|
|
|
|
| 0% |
Uncovered Elements: 113 (113) |
Complexity: 15 |
Complexity Density: 0.16 |
|
493 |
0 |
@Override... |
494 |
|
public HashMap<Integer, int[]> getGreedyMapping(String entityId, |
495 |
|
SequenceI seq, java.io.PrintStream os) throws SiftsException |
496 |
|
{ |
497 |
0 |
List<Integer> omitNonObserved = new ArrayList<>(); |
498 |
0 |
int nonObservedShiftIndex = 0, pdbeNonObserved = 0; |
499 |
|
|
500 |
0 |
Entity entity = null; |
501 |
0 |
entity = getEntityById(entityId); |
502 |
0 |
String originalSeq = AlignSeq.extractGaps( |
503 |
|
jalview.util.Comparison.GapChars, seq.getSequenceAsString()); |
504 |
0 |
HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>(); |
505 |
0 |
DBRefEntryI sourceDBRef; |
506 |
0 |
sourceDBRef = getValidSourceDBRef(seq); |
507 |
|
|
508 |
|
|
509 |
|
|
510 |
|
|
511 |
0 |
if (sourceDBRef.getSource().equalsIgnoreCase(DBRefSource.PDB)) |
512 |
|
{ |
513 |
0 |
seqCoordSys = CoordinateSys.PDB; |
514 |
|
} |
515 |
|
|
516 |
0 |
HashSet<String> dbRefAccessionIdsString = new HashSet<String>(); |
517 |
0 |
for (DBRefEntry dbref : seq.getDBRefs()) |
518 |
|
{ |
519 |
0 |
dbRefAccessionIdsString |
520 |
|
.add(dbref.getAccessionId().toLowerCase(Locale.ROOT)); |
521 |
|
} |
522 |
0 |
dbRefAccessionIdsString |
523 |
|
.add(sourceDBRef.getAccessionId().toLowerCase(Locale.ROOT)); |
524 |
|
|
525 |
0 |
curDBRefAccessionIdsString = dbRefAccessionIdsString; |
526 |
0 |
curSourceDBRef = sourceDBRef.getAccessionId(); |
527 |
|
|
528 |
0 |
TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>(); |
529 |
0 |
List<Segment> segments = entity.getSegment(); |
530 |
0 |
SegmentHelperPojo shp = new SegmentHelperPojo(seq, mapping, resNumMap, |
531 |
|
omitNonObserved, nonObservedShiftIndex, pdbeNonObserved); |
532 |
0 |
processSegments(segments, shp); |
533 |
0 |
try |
534 |
|
{ |
535 |
0 |
populateAtomPositions(entityId, mapping); |
536 |
|
} catch (Exception e) |
537 |
|
{ |
538 |
0 |
e.printStackTrace(); |
539 |
|
} |
540 |
0 |
if (seqCoordSys == CoordinateSys.UNIPROT) |
541 |
|
{ |
542 |
0 |
padWithGaps(resNumMap, omitNonObserved); |
543 |
|
} |
544 |
0 |
int seqStart = UNASSIGNED; |
545 |
0 |
int seqEnd = UNASSIGNED; |
546 |
0 |
int pdbStart = UNASSIGNED; |
547 |
0 |
int pdbEnd = UNASSIGNED; |
548 |
|
|
549 |
0 |
if (mapping.isEmpty()) |
550 |
|
{ |
551 |
0 |
throw new SiftsException("SIFTS mapping failed for " + entityId |
552 |
|
+ " and " + seq.getName()); |
553 |
|
} |
554 |
|
|
555 |
|
|
556 |
|
|
557 |
0 |
Integer[] keys = mapping.keySet().toArray(new Integer[0]); |
558 |
0 |
Arrays.sort(keys); |
559 |
0 |
seqStart = keys[0]; |
560 |
0 |
seqEnd = keys[keys.length - 1]; |
561 |
0 |
List<int[]> from = new ArrayList<>(), to = new ArrayList<>(); |
562 |
0 |
int[] _cfrom = null, _cto = null; |
563 |
0 |
String matchedSeq = originalSeq; |
564 |
0 |
if (seqStart != UNASSIGNED) |
565 |
|
|
566 |
|
{ |
567 |
0 |
for (int seqps : keys) |
568 |
|
{ |
569 |
0 |
int pdbpos = mapping.get(seqps)[PDBE_POS]; |
570 |
0 |
if (pdbpos == UNASSIGNED) |
571 |
|
{ |
572 |
|
|
573 |
0 |
continue; |
574 |
|
} |
575 |
0 |
if (_cfrom == null || seqps != _cfrom[1] + 1) |
576 |
|
{ |
577 |
0 |
_cfrom = new int[] { seqps, seqps }; |
578 |
0 |
from.add(_cfrom); |
579 |
0 |
_cto = null; |
580 |
|
} |
581 |
|
else |
582 |
|
{ |
583 |
0 |
_cfrom[1] = seqps; |
584 |
|
} |
585 |
0 |
if (_cto == null || pdbpos != 1 + _cto[1]) |
586 |
|
{ |
587 |
0 |
_cto = new int[] { pdbpos, pdbpos }; |
588 |
0 |
to.add(_cto); |
589 |
|
} |
590 |
|
else |
591 |
|
{ |
592 |
0 |
_cto[1] = pdbpos; |
593 |
|
} |
594 |
|
} |
595 |
0 |
_cfrom = new int[from.size() * 2]; |
596 |
0 |
_cto = new int[to.size() * 2]; |
597 |
0 |
int p = 0; |
598 |
0 |
for (int[] range : from) |
599 |
|
{ |
600 |
0 |
_cfrom[p++] = range[0]; |
601 |
0 |
_cfrom[p++] = range[1]; |
602 |
|
} |
603 |
0 |
; |
604 |
0 |
p = 0; |
605 |
0 |
for (int[] range : to) |
606 |
|
{ |
607 |
0 |
_cto[p++] = range[0]; |
608 |
0 |
_cto[p++] = range[1]; |
609 |
|
} |
610 |
0 |
; |
611 |
|
|
612 |
0 |
seqFromPdbMapping = new jalview.datamodel.Mapping(null, _cto, _cfrom, |
613 |
|
1, 1); |
614 |
0 |
pdbStart = mapping.get(seqStart)[PDB_RES_POS]; |
615 |
0 |
pdbEnd = mapping.get(seqEnd)[PDB_RES_POS]; |
616 |
0 |
int orignalSeqStart = seq.getStart(); |
617 |
0 |
if (orignalSeqStart >= 1) |
618 |
|
{ |
619 |
0 |
int subSeqStart = (seqStart >= orignalSeqStart) |
620 |
|
? seqStart - orignalSeqStart |
621 |
|
: 0; |
622 |
0 |
int subSeqEnd = seqEnd - (orignalSeqStart - 1); |
623 |
0 |
subSeqEnd = originalSeq.length() < subSeqEnd ? originalSeq.length() |
624 |
|
: subSeqEnd; |
625 |
0 |
matchedSeq = originalSeq.substring(subSeqStart, subSeqEnd); |
626 |
|
} |
627 |
|
else |
628 |
|
{ |
629 |
0 |
matchedSeq = originalSeq.substring(1, originalSeq.length()); |
630 |
|
} |
631 |
|
} |
632 |
|
|
633 |
0 |
StringBuilder targetStrucSeqs = new StringBuilder(); |
634 |
0 |
for (String res : resNumMap.values()) |
635 |
|
{ |
636 |
0 |
targetStrucSeqs.append(res); |
637 |
|
} |
638 |
|
|
639 |
0 |
if (os != null) |
640 |
|
{ |
641 |
0 |
MappingOutputPojo mop = new MappingOutputPojo(); |
642 |
0 |
mop.setSeqStart(seqStart); |
643 |
0 |
mop.setSeqEnd(seqEnd); |
644 |
0 |
mop.setSeqName(seq.getName()); |
645 |
0 |
mop.setSeqResidue(matchedSeq); |
646 |
|
|
647 |
0 |
mop.setStrStart(pdbStart); |
648 |
0 |
mop.setStrEnd(pdbEnd); |
649 |
0 |
mop.setStrName(structId); |
650 |
0 |
mop.setStrResidue(targetStrucSeqs.toString()); |
651 |
|
|
652 |
0 |
mop.setType("pep"); |
653 |
0 |
os.print(getMappingOutput(mop).toString()); |
654 |
0 |
os.println(); |
655 |
|
} |
656 |
0 |
return mapping; |
657 |
|
} |
658 |
|
|
|
|
| 0% |
Uncovered Elements: 68 (68) |
Complexity: 15 |
Complexity Density: 0.36 |
|
659 |
0 |
void processSegments(List<Segment> segments, SegmentHelperPojo shp)... |
660 |
|
{ |
661 |
0 |
SequenceI seq = shp.getSeq(); |
662 |
0 |
HashMap<Integer, int[]> mapping = shp.getMapping(); |
663 |
0 |
TreeMap<Integer, String> resNumMap = shp.getResNumMap(); |
664 |
0 |
List<Integer> omitNonObserved = shp.getOmitNonObserved(); |
665 |
0 |
int nonObservedShiftIndex = shp.getNonObservedShiftIndex(); |
666 |
0 |
int pdbeNonObservedCount = shp.getPdbeNonObserved(); |
667 |
0 |
int firstPDBResNum = UNASSIGNED; |
668 |
0 |
for (Segment segment : segments) |
669 |
|
{ |
670 |
|
|
671 |
|
|
672 |
|
|
673 |
0 |
List<Residue> residues = segment.getListResidue().getResidue(); |
674 |
0 |
for (Residue residue : residues) |
675 |
|
{ |
676 |
0 |
boolean isObserved = isResidueObserved(residue); |
677 |
0 |
int pdbeIndex = getLeadingIntegerValue(residue.getDbResNum(), |
678 |
|
UNASSIGNED); |
679 |
0 |
int currSeqIndex = UNASSIGNED; |
680 |
0 |
List<CrossRefDb> cRefDbs = residue.getCrossRefDb(); |
681 |
0 |
CrossRefDb pdbRefDb = null; |
682 |
0 |
for (CrossRefDb cRefDb : cRefDbs) |
683 |
|
{ |
684 |
0 |
if (cRefDb.getDbSource().equalsIgnoreCase(DBRefSource.PDB)) |
685 |
|
{ |
686 |
0 |
pdbRefDb = cRefDb; |
687 |
0 |
if (firstPDBResNum == UNASSIGNED) |
688 |
|
{ |
689 |
0 |
firstPDBResNum = getLeadingIntegerValue(cRefDb.getDbResNum(), |
690 |
|
UNASSIGNED); |
691 |
|
} |
692 |
|
else |
693 |
|
{ |
694 |
0 |
if (isObserved) |
695 |
|
{ |
696 |
|
|
697 |
0 |
firstPDBResNum++; |
698 |
|
} |
699 |
|
} |
700 |
|
} |
701 |
0 |
if (cRefDb.getDbCoordSys().equalsIgnoreCase(seqCoordSys.getName()) |
702 |
|
&& isAccessionMatched(cRefDb.getDbAccessionId())) |
703 |
|
{ |
704 |
0 |
currSeqIndex = getLeadingIntegerValue(cRefDb.getDbResNum(), |
705 |
|
UNASSIGNED); |
706 |
0 |
if (pdbRefDb != null) |
707 |
|
{ |
708 |
0 |
break; |
709 |
|
} |
710 |
|
} |
711 |
|
} |
712 |
0 |
if (!isObserved) |
713 |
|
{ |
714 |
0 |
++pdbeNonObservedCount; |
715 |
|
} |
716 |
0 |
if (seqCoordSys == seqCoordSys.PDB) |
717 |
|
|
718 |
|
{ |
719 |
|
|
720 |
|
|
721 |
|
|
722 |
0 |
currSeqIndex = seq.getStart() - 1 + pdbeIndex; |
723 |
|
} |
724 |
0 |
if (!isObserved) |
725 |
|
{ |
726 |
0 |
if (seqCoordSys != CoordinateSys.UNIPROT) |
727 |
|
|
728 |
|
{ |
729 |
|
|
730 |
|
|
731 |
|
|
732 |
0 |
omitNonObserved.add(currSeqIndex); |
733 |
0 |
++nonObservedShiftIndex; |
734 |
|
} |
735 |
|
} |
736 |
0 |
if (currSeqIndex == UNASSIGNED) |
737 |
|
{ |
738 |
|
|
739 |
|
|
740 |
|
|
741 |
0 |
continue; |
742 |
|
} |
743 |
|
|
744 |
|
|
745 |
|
|
746 |
|
|
747 |
|
|
748 |
|
|
749 |
|
|
750 |
|
|
751 |
|
{ |
752 |
|
|
753 |
0 |
int resNum = (pdbRefDb == null) |
754 |
|
? getLeadingIntegerValue(residue.getDbResNum(), |
755 |
|
UNASSIGNED) |
756 |
|
: getLeadingIntegerValue(pdbRefDb.getDbResNum(), |
757 |
|
UNASSIGNED); |
758 |
|
|
759 |
0 |
if (isObserved) |
760 |
|
{ |
761 |
0 |
char resCharCode = ResidueProperties |
762 |
|
.getSingleCharacterCode(ResidueProperties |
763 |
|
.getCanonicalAminoAcid(residue.getDbResName())); |
764 |
0 |
resNumMap.put(currSeqIndex, String.valueOf(resCharCode)); |
765 |
|
|
766 |
0 |
int[] mappingcols = new int[] { Integer.valueOf(resNum), |
767 |
0 |
UNASSIGNED, isObserved ? firstPDBResNum : UNASSIGNED }; |
768 |
|
|
769 |
0 |
mapping.put(currSeqIndex - nonObservedShiftIndex, mappingcols); |
770 |
|
} |
771 |
|
} |
772 |
|
} |
773 |
|
} |
774 |
|
} |
775 |
|
|
776 |
|
|
777 |
|
|
778 |
|
|
779 |
|
@param |
780 |
|
|
781 |
|
@param |
782 |
|
|
783 |
|
@return |
784 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 5 |
Complexity Density: 0.83 |
|
785 |
0 |
static int getLeadingIntegerValue(String input, int failValue)... |
786 |
|
{ |
787 |
0 |
if (input == null) |
788 |
|
{ |
789 |
0 |
return failValue; |
790 |
|
} |
791 |
0 |
String[] parts = input.split("(?=\\D)(?<=\\d)"); |
792 |
0 |
if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+")) |
793 |
|
{ |
794 |
0 |
return Integer.valueOf(parts[0]); |
795 |
|
} |
796 |
0 |
return failValue; |
797 |
|
} |
798 |
|
|
799 |
|
|
800 |
|
|
801 |
|
@param |
802 |
|
|
803 |
|
@param |
804 |
|
|
805 |
|
@throws |
806 |
|
|
807 |
|
@throws |
808 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 6 |
Complexity Density: 0.67 |
|
809 |
0 |
void populateAtomPositions(String chainId, Map<Integer, int[]> mapping)... |
810 |
|
throws IllegalArgumentException, SiftsException |
811 |
|
{ |
812 |
0 |
try |
813 |
|
{ |
814 |
0 |
PDBChain chain = pdb.findChain(chainId); |
815 |
|
|
816 |
0 |
if (chain == null || mapping == null) |
817 |
|
{ |
818 |
0 |
throw new IllegalArgumentException( |
819 |
|
"Chain id or mapping must not be null."); |
820 |
|
} |
821 |
0 |
for (int[] map : mapping.values()) |
822 |
|
{ |
823 |
0 |
if (map[PDB_RES_POS] != UNASSIGNED) |
824 |
|
{ |
825 |
0 |
map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms); |
826 |
|
} |
827 |
|
} |
828 |
|
} catch (NullPointerException e) |
829 |
|
{ |
830 |
0 |
throw new SiftsException(e.getMessage()); |
831 |
|
} catch (Exception e) |
832 |
|
{ |
833 |
0 |
throw new SiftsException(e.getMessage()); |
834 |
|
} |
835 |
|
} |
836 |
|
|
837 |
|
|
838 |
|
|
839 |
|
@param |
840 |
|
|
841 |
|
@param |
842 |
|
|
843 |
|
@return |
844 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
845 |
0 |
int getAtomIndex(int residueIndex, Collection<Atom> atoms)... |
846 |
|
{ |
847 |
0 |
if (atoms == null) |
848 |
|
{ |
849 |
0 |
throw new IllegalArgumentException( |
850 |
|
"atoms collection must not be null!"); |
851 |
|
} |
852 |
0 |
for (Atom atom : atoms) |
853 |
|
{ |
854 |
0 |
if (atom.resNumber == residueIndex) |
855 |
|
{ |
856 |
0 |
return atom.atomIndex; |
857 |
|
} |
858 |
|
} |
859 |
0 |
return UNASSIGNED; |
860 |
|
} |
861 |
|
|
862 |
|
|
863 |
|
|
864 |
|
|
865 |
|
@param |
866 |
|
@return |
867 |
|
|
|
|
| 0% |
Uncovered Elements: 11 (11) |
Complexity: 4 |
Complexity Density: 0.57 |
|
868 |
0 |
private boolean isResidueObserved(Residue residue)... |
869 |
|
{ |
870 |
0 |
Set<String> annotations = getResidueAnnotaitons(residue, |
871 |
|
ResidueDetailType.ANNOTATION); |
872 |
0 |
if (annotations == null || annotations.isEmpty()) |
873 |
|
{ |
874 |
0 |
return true; |
875 |
|
} |
876 |
0 |
for (String annotation : annotations) |
877 |
|
{ |
878 |
0 |
if (annotation.equalsIgnoreCase(NOT_OBSERVED)) |
879 |
|
{ |
880 |
0 |
return false; |
881 |
|
} |
882 |
|
} |
883 |
0 |
return true; |
884 |
|
} |
885 |
|
|
886 |
|
|
887 |
|
|
888 |
|
|
889 |
|
@param |
890 |
|
@param |
891 |
|
@return |
892 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
893 |
0 |
private Set<String> getResidueAnnotaitons(Residue residue,... |
894 |
|
ResidueDetailType type) |
895 |
|
{ |
896 |
0 |
HashSet<String> foundAnnotations = new HashSet<String>(); |
897 |
0 |
List<ResidueDetail> resDetails = residue.getResidueDetail(); |
898 |
0 |
for (ResidueDetail resDetail : resDetails) |
899 |
|
{ |
900 |
0 |
if (resDetail.getProperty().equalsIgnoreCase(type.getCode())) |
901 |
|
{ |
902 |
0 |
foundAnnotations.add(resDetail.getContent()); |
903 |
|
} |
904 |
|
} |
905 |
0 |
return foundAnnotations; |
906 |
|
} |
907 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
908 |
0 |
@Override... |
909 |
|
public boolean isAccessionMatched(String accession) |
910 |
|
{ |
911 |
0 |
boolean isStrictMatch = true; |
912 |
0 |
return isStrictMatch ? curSourceDBRef.equalsIgnoreCase(accession) |
913 |
|
: curDBRefAccessionIdsString |
914 |
|
.contains(accession.toLowerCase(Locale.ROOT)); |
915 |
|
} |
916 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
917 |
0 |
private boolean isFoundInSiftsEntry(String accessionId)... |
918 |
|
{ |
919 |
0 |
Set<String> siftsDBRefs = getAllMappingAccession(); |
920 |
0 |
return accessionId != null |
921 |
|
&& siftsDBRefs.contains(accessionId.toLowerCase(Locale.ROOT)); |
922 |
|
} |
923 |
|
|
924 |
|
|
925 |
|
|
926 |
|
|
927 |
|
@param |
928 |
|
|
|
|
| 0% |
Uncovered Elements: 14 (14) |
Complexity: 6 |
Complexity Density: 0.75 |
|
929 |
0 |
void padWithGaps(Map<Integer, String> resNumMap,... |
930 |
|
List<Integer> omitNonObserved) |
931 |
|
{ |
932 |
0 |
if (resNumMap == null || resNumMap.isEmpty()) |
933 |
|
{ |
934 |
0 |
return; |
935 |
|
} |
936 |
0 |
Integer[] keys = resNumMap.keySet().toArray(new Integer[0]); |
937 |
|
|
938 |
0 |
int firstIndex = keys[0]; |
939 |
0 |
int lastIndex = keys[keys.length - 1]; |
940 |
|
|
941 |
|
|
942 |
0 |
for (int x = firstIndex; x <= lastIndex; x++) |
943 |
|
{ |
944 |
0 |
if (!resNumMap.containsKey(x) && !omitNonObserved.contains(x)) |
945 |
|
{ |
946 |
0 |
resNumMap.put(x, "-"); |
947 |
|
} |
948 |
|
} |
949 |
|
} |
950 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
951 |
0 |
@Override... |
952 |
|
public Entity getEntityById(String id) throws SiftsException |
953 |
|
{ |
954 |
|
|
955 |
|
|
956 |
0 |
Entity entity = getEntityByMostOptimalMatchedId(id); |
957 |
0 |
if (entity != null) |
958 |
|
{ |
959 |
0 |
return entity; |
960 |
|
} |
961 |
0 |
throw new SiftsException("Entity " + id + " not found"); |
962 |
|
} |
963 |
|
|
964 |
|
|
965 |
|
|
966 |
|
|
967 |
|
|
968 |
|
|
969 |
|
@param |
970 |
|
@return |
971 |
|
|
|
|
| 0% |
Uncovered Elements: 38 (38) |
Complexity: 6 |
Complexity Density: 0.21 |
|
972 |
0 |
public Entity getEntityByMostOptimalMatchedId(String chainId)... |
973 |
|
{ |
974 |
|
|
975 |
|
|
976 |
|
|
977 |
0 |
List<Entity> entities = siftsEntry.getEntity(); |
978 |
0 |
SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()]; |
979 |
0 |
int count = 0; |
980 |
0 |
for (Entity entity : entities) |
981 |
|
{ |
982 |
0 |
sPojo[count] = new SiftsEntitySortPojo(); |
983 |
0 |
sPojo[count].entityId = entity.getEntityId(); |
984 |
|
|
985 |
0 |
List<Segment> segments = entity.getSegment(); |
986 |
0 |
for (Segment segment : segments) |
987 |
|
{ |
988 |
0 |
List<Residue> residues = segment.getListResidue().getResidue(); |
989 |
0 |
for (Residue residue : residues) |
990 |
|
{ |
991 |
0 |
List<CrossRefDb> cRefDbs = residue.getCrossRefDb(); |
992 |
0 |
for (CrossRefDb cRefDb : cRefDbs) |
993 |
|
{ |
994 |
0 |
if (!cRefDb.getDbSource().equalsIgnoreCase("PDB")) |
995 |
|
{ |
996 |
0 |
continue; |
997 |
|
} |
998 |
0 |
++sPojo[count].resCount; |
999 |
0 |
if (cRefDb.getDbChainId().equalsIgnoreCase(chainId)) |
1000 |
|
{ |
1001 |
0 |
++sPojo[count].chainIdFreq; |
1002 |
|
} |
1003 |
|
} |
1004 |
|
} |
1005 |
|
} |
1006 |
0 |
sPojo[count].pid = (100 * sPojo[count].chainIdFreq) |
1007 |
|
/ sPojo[count].resCount; |
1008 |
0 |
++count; |
1009 |
|
} |
1010 |
0 |
Arrays.sort(sPojo, Collections.reverseOrder()); |
1011 |
|
|
1012 |
|
|
1013 |
|
|
1014 |
|
|
1015 |
0 |
if (sPojo[0].entityId != null) |
1016 |
|
{ |
1017 |
0 |
if (sPojo[0].pid < 1) |
1018 |
|
{ |
1019 |
0 |
return null; |
1020 |
|
} |
1021 |
0 |
for (Entity entity : entities) |
1022 |
|
{ |
1023 |
0 |
if (!entity.getEntityId().equalsIgnoreCase(sPojo[0].entityId)) |
1024 |
|
{ |
1025 |
0 |
continue; |
1026 |
|
} |
1027 |
0 |
return entity; |
1028 |
|
} |
1029 |
|
} |
1030 |
0 |
return null; |
1031 |
|
} |
1032 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 1 |
|
1033 |
|
private class SiftsEntitySortPojo |
1034 |
|
implements Comparable<SiftsEntitySortPojo> |
1035 |
|
{ |
1036 |
|
public String entityId; |
1037 |
|
|
1038 |
|
public int chainIdFreq; |
1039 |
|
|
1040 |
|
public int pid; |
1041 |
|
|
1042 |
|
public int resCount; |
1043 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1044 |
0 |
@Override... |
1045 |
|
public int compareTo(SiftsEntitySortPojo o) |
1046 |
|
{ |
1047 |
0 |
return this.pid - o.pid; |
1048 |
|
} |
1049 |
|
} |
1050 |
|
|
|
|
| 0% |
Uncovered Elements: 31 (31) |
Complexity: 13 |
Complexity Density: 0.72 |
|
1051 |
|
private class SegmentHelperPojo |
1052 |
|
{ |
1053 |
|
private SequenceI seq; |
1054 |
|
|
1055 |
|
private HashMap<Integer, int[]> mapping; |
1056 |
|
|
1057 |
|
private TreeMap<Integer, String> resNumMap; |
1058 |
|
|
1059 |
|
private List<Integer> omitNonObserved; |
1060 |
|
|
1061 |
|
private int nonObservedShiftIndex; |
1062 |
|
|
1063 |
|
|
1064 |
|
|
1065 |
|
|
1066 |
|
|
1067 |
|
|
1068 |
|
private int pdbeNonObserved; |
1069 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
1070 |
0 |
public SegmentHelperPojo(SequenceI seq, HashMap<Integer, int[]> mapping,... |
1071 |
|
TreeMap<Integer, String> resNumMap, |
1072 |
|
List<Integer> omitNonObserved, int nonObservedShiftIndex, |
1073 |
|
int pdbeNonObserved) |
1074 |
|
{ |
1075 |
0 |
setSeq(seq); |
1076 |
0 |
setMapping(mapping); |
1077 |
0 |
setResNumMap(resNumMap); |
1078 |
0 |
setOmitNonObserved(omitNonObserved); |
1079 |
0 |
setNonObservedShiftIndex(nonObservedShiftIndex); |
1080 |
0 |
setPdbeNonObserved(pdbeNonObserved); |
1081 |
|
|
1082 |
|
} |
1083 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1084 |
0 |
public void setPdbeNonObserved(int pdbeNonObserved2)... |
1085 |
|
{ |
1086 |
0 |
this.pdbeNonObserved = pdbeNonObserved2; |
1087 |
|
} |
1088 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1089 |
0 |
public int getPdbeNonObserved()... |
1090 |
|
{ |
1091 |
0 |
return pdbeNonObserved; |
1092 |
|
} |
1093 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1094 |
0 |
public SequenceI getSeq()... |
1095 |
|
{ |
1096 |
0 |
return seq; |
1097 |
|
} |
1098 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1099 |
0 |
public void setSeq(SequenceI seq)... |
1100 |
|
{ |
1101 |
0 |
this.seq = seq; |
1102 |
|
} |
1103 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1104 |
0 |
public HashMap<Integer, int[]> getMapping()... |
1105 |
|
{ |
1106 |
0 |
return mapping; |
1107 |
|
} |
1108 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1109 |
0 |
public void setMapping(HashMap<Integer, int[]> mapping)... |
1110 |
|
{ |
1111 |
0 |
this.mapping = mapping; |
1112 |
|
} |
1113 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1114 |
0 |
public TreeMap<Integer, String> getResNumMap()... |
1115 |
|
{ |
1116 |
0 |
return resNumMap; |
1117 |
|
} |
1118 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1119 |
0 |
public void setResNumMap(TreeMap<Integer, String> resNumMap)... |
1120 |
|
{ |
1121 |
0 |
this.resNumMap = resNumMap; |
1122 |
|
} |
1123 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1124 |
0 |
public List<Integer> getOmitNonObserved()... |
1125 |
|
{ |
1126 |
0 |
return omitNonObserved; |
1127 |
|
} |
1128 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1129 |
0 |
public void setOmitNonObserved(List<Integer> omitNonObserved)... |
1130 |
|
{ |
1131 |
0 |
this.omitNonObserved = omitNonObserved; |
1132 |
|
} |
1133 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1134 |
0 |
public int getNonObservedShiftIndex()... |
1135 |
|
{ |
1136 |
0 |
return nonObservedShiftIndex; |
1137 |
|
} |
1138 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1139 |
0 |
public void setNonObservedShiftIndex(int nonObservedShiftIndex)... |
1140 |
|
{ |
1141 |
0 |
this.nonObservedShiftIndex = nonObservedShiftIndex; |
1142 |
|
} |
1143 |
|
|
1144 |
|
} |
1145 |
|
|
|
|
| 0% |
Uncovered Elements: 92 (92) |
Complexity: 16 |
Complexity Density: 0.24 |
|
1146 |
0 |
@Override... |
1147 |
|
public StringBuilder getMappingOutput(MappingOutputPojo mp) |
1148 |
|
throws SiftsException |
1149 |
|
{ |
1150 |
0 |
String seqRes = mp.getSeqResidue(); |
1151 |
0 |
String seqName = mp.getSeqName(); |
1152 |
0 |
int sStart = mp.getSeqStart(); |
1153 |
0 |
int sEnd = mp.getSeqEnd(); |
1154 |
|
|
1155 |
0 |
String strRes = mp.getStrResidue(); |
1156 |
0 |
String strName = mp.getStrName(); |
1157 |
0 |
int pdbStart = mp.getStrStart(); |
1158 |
0 |
int pdbEnd = mp.getStrEnd(); |
1159 |
|
|
1160 |
0 |
String type = mp.getType(); |
1161 |
|
|
1162 |
0 |
int maxid = (seqName.length() >= strName.length()) ? seqName.length() |
1163 |
|
: strName.length(); |
1164 |
0 |
int len = 72 - maxid - 1; |
1165 |
|
|
1166 |
0 |
int nochunks = ((seqRes.length()) / len) |
1167 |
0 |
+ ((seqRes.length()) % len > 0 ? 1 : 0); |
1168 |
|
|
1169 |
0 |
StringBuilder output = new StringBuilder(512); |
1170 |
0 |
output.append(NEWLINE); |
1171 |
0 |
output.append("Sequence \u27f7 Structure mapping details") |
1172 |
|
.append(NEWLINE); |
1173 |
0 |
output.append("Method: SIFTS"); |
1174 |
0 |
output.append(NEWLINE).append(NEWLINE); |
1175 |
|
|
1176 |
0 |
output.append(new Format("%" + maxid + "s").form(seqName)); |
1177 |
0 |
output.append(" : "); |
1178 |
0 |
output.append(String.valueOf(sStart)); |
1179 |
0 |
output.append(" - "); |
1180 |
0 |
output.append(String.valueOf(sEnd)); |
1181 |
0 |
output.append(" Maps to "); |
1182 |
0 |
output.append(NEWLINE); |
1183 |
0 |
output.append(new Format("%" + maxid + "s").form(structId)); |
1184 |
0 |
output.append(" : "); |
1185 |
0 |
output.append(String.valueOf(pdbStart)); |
1186 |
0 |
output.append(" - "); |
1187 |
0 |
output.append(String.valueOf(pdbEnd)); |
1188 |
0 |
output.append(NEWLINE).append(NEWLINE); |
1189 |
|
|
1190 |
0 |
ScoreMatrix pam250 = ScoreModels.getInstance().getPam250(); |
1191 |
0 |
int matchedSeqCount = 0; |
1192 |
0 |
for (int j = 0; j < nochunks; j++) |
1193 |
|
{ |
1194 |
|
|
1195 |
0 |
output.append(new Format("%" + (maxid) + "s").form(seqName)) |
1196 |
|
.append(" "); |
1197 |
|
|
1198 |
0 |
for (int i = 0; i < len; i++) |
1199 |
|
{ |
1200 |
0 |
if ((i + (j * len)) < seqRes.length()) |
1201 |
|
{ |
1202 |
0 |
output.append(seqRes.charAt(i + (j * len))); |
1203 |
|
} |
1204 |
|
} |
1205 |
|
|
1206 |
0 |
output.append(NEWLINE); |
1207 |
0 |
output.append(new Format("%" + (maxid) + "s").form(" ")).append(" "); |
1208 |
|
|
1209 |
|
|
1210 |
|
|
1211 |
|
|
1212 |
|
|
1213 |
|
|
1214 |
|
|
1215 |
0 |
for (int i = 0; i < len; i++) |
1216 |
|
{ |
1217 |
0 |
try |
1218 |
|
{ |
1219 |
0 |
if ((i + (j * len)) < seqRes.length()) |
1220 |
|
{ |
1221 |
0 |
char c1 = seqRes.charAt(i + (j * len)); |
1222 |
0 |
char c2 = strRes.charAt(i + (j * len)); |
1223 |
0 |
boolean sameChar = Comparison.isSameResidue(c1, c2, false); |
1224 |
0 |
if (sameChar && !Comparison.isGap(c1)) |
1225 |
|
{ |
1226 |
0 |
matchedSeqCount++; |
1227 |
0 |
output.append("|"); |
1228 |
|
} |
1229 |
0 |
else if (type.equals("pep")) |
1230 |
|
{ |
1231 |
0 |
if (pam250.getPairwiseScore(c1, c2) > 0) |
1232 |
|
{ |
1233 |
0 |
output.append("."); |
1234 |
|
} |
1235 |
|
else |
1236 |
|
{ |
1237 |
0 |
output.append(" "); |
1238 |
|
} |
1239 |
|
} |
1240 |
|
else |
1241 |
|
{ |
1242 |
0 |
output.append(" "); |
1243 |
|
} |
1244 |
|
} |
1245 |
|
} catch (IndexOutOfBoundsException e) |
1246 |
|
{ |
1247 |
0 |
continue; |
1248 |
|
} |
1249 |
|
} |
1250 |
|
|
1251 |
0 |
output = output.append(NEWLINE); |
1252 |
0 |
output = output.append(new Format("%" + (maxid) + "s").form(strName)) |
1253 |
|
.append(" "); |
1254 |
0 |
for (int i = 0; i < len; i++) |
1255 |
|
{ |
1256 |
0 |
if ((i + (j * len)) < strRes.length()) |
1257 |
|
{ |
1258 |
0 |
output.append(strRes.charAt(i + (j * len))); |
1259 |
|
} |
1260 |
|
} |
1261 |
0 |
output.append(NEWLINE).append(NEWLINE); |
1262 |
|
} |
1263 |
0 |
float pid = (float) matchedSeqCount / seqRes.length() * 100; |
1264 |
0 |
if (pid < SiftsSettings.getFailSafePIDThreshold()) |
1265 |
|
{ |
1266 |
0 |
throw new SiftsException(">>> Low PID detected for SIFTs mapping..."); |
1267 |
|
} |
1268 |
0 |
output.append("Length of alignment = " + seqRes.length()) |
1269 |
|
.append(NEWLINE); |
1270 |
0 |
output.append(new Format("Percentage ID = %2.2f").form(pid)); |
1271 |
0 |
return output; |
1272 |
|
} |
1273 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1274 |
0 |
@Override... |
1275 |
|
public int getEntityCount() |
1276 |
|
{ |
1277 |
0 |
return siftsEntry.getEntity().size(); |
1278 |
|
} |
1279 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1280 |
0 |
@Override... |
1281 |
|
public String getDbAccessionId() |
1282 |
|
{ |
1283 |
0 |
return siftsEntry.getDbAccessionId(); |
1284 |
|
} |
1285 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1286 |
0 |
@Override... |
1287 |
|
public String getDbCoordSys() |
1288 |
|
{ |
1289 |
0 |
return siftsEntry.getDbCoordSys(); |
1290 |
|
} |
1291 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1292 |
0 |
@Override... |
1293 |
|
public String getDbSource() |
1294 |
|
{ |
1295 |
0 |
return siftsEntry.getDbSource(); |
1296 |
|
} |
1297 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1298 |
0 |
@Override... |
1299 |
|
public String getDbVersion() |
1300 |
|
{ |
1301 |
0 |
return siftsEntry.getDbVersion(); |
1302 |
|
} |
1303 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1304 |
0 |
public static void setMockSiftsFile(File file)... |
1305 |
|
{ |
1306 |
0 |
mockSiftsFile = file; |
1307 |
|
} |
1308 |
|
|
1309 |
|
} |