import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Set;
import java.util.TreeMap;
import java.util.zip.GZIPInputStream;
import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
import javax.xml.bind.Unmarshaller;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamReader;
-import MCview.Atom;
-import MCview.PDBChain;
import jalview.analysis.AlignSeq;
import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.util.Comparison;
import jalview.util.DBRefUtils;
import jalview.util.Format;
+import jalview.util.Platform;
import jalview.xml.binding.sifts.Entry;
import jalview.xml.binding.sifts.Entry.Entity;
import jalview.xml.binding.sifts.Entry.Entity.Segment;
import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue;
import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.CrossRefDb;
import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.ResidueDetail;
+import mc_view.Atom;
+import mc_view.PDBChain;
public class SiftsClient implements SiftsClientI
{
private final static String NEWLINE = System.lineSeparator();
+ private static final boolean GET_STREAM = false;
+ private static final boolean CACHE_FILE = true;
private String curSourceDBRef;
private HashSet<String> curDBRefAccessionIdsString;
+ private boolean doCache = false;
private enum CoordinateSys
{
UNIPROT("UniProt"), PDB("PDBresnum"), PDBe("PDBe");
-
private String name;
private CoordinateSys(String name)
{
NAME_SEC_STRUCTURE("nameSecondaryStructure"),
CODE_SEC_STRUCTURE("codeSecondaryStructure"), ANNOTATION("Annotation");
-
private String code;
private ResidueDetailType(String code)
{
this.pdb = pdb;
this.pdbId = pdb.getId();
- File siftsFile = getSiftsFile(pdbId);
- siftsEntry = parseSIFTs(siftsFile);
+ if (doCache) {
+ File siftsFile = getSiftsFile(pdbId);
+ siftsEntry = parseSIFTs(siftsFile);
+ } else {
+ siftsEntry = parseSIFTSStreamFor(pdbId);
+ }
+ }
+
+ /**
+ * A more streamlined version of SIFT reading that allows for streaming of the data.
+ *
+ * @param pdbId
+ * @return
+ * @throws SiftsException
+ */
+ private static Entry parseSIFTSStreamFor(String pdbId) throws SiftsException
+ {
+ try
+ {
+ InputStream is = (InputStream) downloadSifts(pdbId, GET_STREAM);
+ return parseSIFTs(is);
+ } catch (Exception e)
+ {
+ throw new SiftsException(e.getMessage());
+ }
}
/**
*/
private Entry parseSIFTs(File siftFile) throws SiftsException
{
- try (InputStream in = new FileInputStream(siftFile);
- GZIPInputStream gzis = new GZIPInputStream(in);)
+ try (InputStream in = new FileInputStream(siftFile)) {
+ return parseSIFTs(in);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ throw new SiftsException(e.getMessage());
+ }
+ }
+
+ private static Entry parseSIFTs(InputStream in) throws Exception {
+ try (GZIPInputStream gzis = new GZIPInputStream(in);)
{
// System.out.println("File : " + siftFile.getAbsolutePath());
JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.sifts");
XMLStreamReader streamReader = XMLInputFactory.newInstance()
.createXMLStreamReader(gzis);
Unmarshaller um = jc.createUnmarshaller();
- return (Entry) um.unmarshal(streamReader);
- } catch (Exception e)
- {
- e.printStackTrace();
- throw new SiftsException(e.getMessage());
+ JAXBElement<Entry> jbe = um.unmarshal(streamReader, Entry.class);
+ return jbe.getValue();
}
}
}
String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
- + pdbId.toLowerCase() + ".xml.gz";
+ + pdbId.toLowerCase(Locale.ROOT) + ".xml.gz";
File siftsFile = new File(siftsFileName);
if (siftsFile.exists())
{
// The line below is required for unit testing... don't comment it out!!!
System.out.println(">>> SIFTS File already downloaded for " + pdbId);
- if (isFileOlderThanThreshold(siftsFile,
+ if (Platform.isFileOlderThanThreshold(siftsFile,
SiftsSettings.getCacheThresholdInDays()))
{
File oldSiftsFile = new File(siftsFileName + "_old");
BackupFiles.moveFileToFile(siftsFile, oldSiftsFile);
try
{
- siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ siftsFile = downloadSiftsFile(pdbId.toLowerCase(Locale.ROOT));
oldSiftsFile.delete();
return siftsFile;
} catch (IOException e)
}
try
{
- siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ siftsFile = downloadSiftsFile(pdbId.toLowerCase(Locale.ROOT));
} catch (IOException e)
{
throw new SiftsException(e.getMessage());
}
/**
- * This method enables checking if a cached file has exceeded a certain
- * threshold(in days)
- *
- * @param file
- * the cached file
- * @param noOfDays
- * the threshold in days
- * @return
- */
- public static boolean isFileOlderThanThreshold(File file, int noOfDays)
- {
- Path filePath = file.toPath();
- BasicFileAttributes attr;
- int diffInDays = 0;
- try
- {
- attr = Files.readAttributes(filePath, BasicFileAttributes.class);
- diffInDays = (int) ((new Date().getTime()
- - attr.lastModifiedTime().toMillis())
- / (1000 * 60 * 60 * 24));
- // System.out.println("Diff in days : " + diffInDays);
- } catch (IOException e)
- {
- e.printStackTrace();
- }
- return noOfDays <= diffInDays;
- }
-
- /**
* Download a SIFTs XML file for a given PDB Id from an FTP repository
*
* @param pdbId
*/
public static File downloadSiftsFile(String pdbId)
throws SiftsException, IOException
+ {
+ return (File) downloadSifts(pdbId, CACHE_FILE);
+ }
+
+ /**
+ * Download SIFTs XML with the option to cache a file or to get a stream.
+ *
+ * @param pdbId
+ * @param asFile
+ * @return
+ * @throws IOException
+ */
+ private static Object downloadSifts(String pdbId, boolean asFile) throws IOException
{
+ pdbId = pdbId.toLowerCase(Locale.ROOT);
if (pdbId.contains(".cif"))
{
pdbId = pdbId.replace(".cif", "");
}
String siftFile = pdbId + ".xml.gz";
- String siftsFileFTPURL = SIFTS_FTP_BASE_URL + siftFile;
- String downloadedSiftsFile = SiftsSettings.getSiftDownloadDirectory()
- + siftFile;
- File siftsDownloadDir = new File(
- SiftsSettings.getSiftDownloadDirectory());
- if (!siftsDownloadDir.exists())
+ File downloadTo = null;
+ if (asFile)
{
- siftsDownloadDir.mkdirs();
+ downloadTo = new File(
+ SiftsSettings.getSiftDownloadDirectory() + siftFile);
+ File siftsDownloadDir = new File(SiftsSettings.getSiftDownloadDirectory());
+ if (!siftsDownloadDir.exists())
+ {
+ siftsDownloadDir.mkdirs();
+ }
}
- // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
- // long now = System.currentTimeMillis();
+
+ String siftsFileFTPURL = SIFTS_FTP_BASE_URL + siftFile;
URL url = new URL(siftsFileFTPURL);
URLConnection conn = url.openConnection();
- InputStream inputStream = conn.getInputStream();
- FileOutputStream outputStream = new FileOutputStream(
- downloadedSiftsFile);
- byte[] buffer = new byte[BUFFER_SIZE];
- int bytesRead = -1;
- while ((bytesRead = inputStream.read(buffer)) != -1)
- {
- outputStream.write(buffer, 0, bytesRead);
- }
- outputStream.close();
- inputStream.close();
- // System.out.println(">>> File downloaded : " + downloadedSiftsFile
- // + " took " + (System.currentTimeMillis() - now) + "ms");
- return new File(downloadedSiftsFile);
+ InputStream is = conn.getInputStream();
+ if (!asFile)
+ return is;
+ // This is MUCH more efficent in JavaScript, as we already have the bytes
+ Platform.streamToFile(is, downloadTo);
+ is.close();
+ return downloadTo;
}
/**
public static boolean deleteSiftsFileByPDBId(String pdbId)
{
File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
- + pdbId.toLowerCase() + ".xml.gz");
+ + pdbId.toLowerCase(Locale.ROOT) + ".xml.gz");
if (siftsFile.exists())
{
return siftsFile.delete();
.getMapRegion();
for (MapRegion mapRegion : mapRegions)
{
- accessions
- .add(mapRegion.getDb().getDbAccessionId().toLowerCase());
+ accessions.add(mapRegion.getDb().getDbAccessionId()
+ .toLowerCase(Locale.ROOT));
}
}
}
SequenceI seq, java.io.PrintStream os) throws SiftsException
{
List<Integer> omitNonObserved = new ArrayList<>();
- int nonObservedShiftIndex = 0, pdbeNonObserved = 0;
+ int nonObservedShiftIndex = 0,pdbeNonObserved=0;
// System.out.println("Generating mappings for : " + entityId);
Entity entity = null;
entity = getEntityById(entityId);
HashSet<String> dbRefAccessionIdsString = new HashSet<String>();
for (DBRefEntry dbref : seq.getDBRefs())
{
- dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase());
+ dbRefAccessionIdsString
+ .add(dbref.getAccessionId().toLowerCase(Locale.ROOT));
}
- dbRefAccessionIdsString.add(sourceDBRef.getAccessionId().toLowerCase());
+ dbRefAccessionIdsString
+ .add(sourceDBRef.getAccessionId().toLowerCase(Locale.ROOT));
curDBRefAccessionIdsString = dbRefAccessionIdsString;
curSourceDBRef = sourceDBRef.getAccessionId();
TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>();
List<Segment> segments = entity.getSegment();
SegmentHelperPojo shp = new SegmentHelperPojo(seq, mapping, resNumMap,
- omitNonObserved, nonObservedShiftIndex, pdbeNonObserved);
+ omitNonObserved, nonObservedShiftIndex,pdbeNonObserved);
processSegments(segments, shp);
try
{
{
throw new SiftsException("SIFTS mapping failed");
}
- // also construct a mapping object between the seq-coord sys and the PDB
- // seq's coord sys
+ // also construct a mapping object between the seq-coord sys and the PDB seq's coord sys
Integer[] keys = mapping.keySet().toArray(new Integer[0]);
Arrays.sort(keys);
seqStart = keys[0];
seqEnd = keys[keys.length - 1];
- List<int[]> from = new ArrayList<>(), to = new ArrayList<>();
- int[] _cfrom = null, _cto = null;
+ List<int[]> from=new ArrayList<>(),to=new ArrayList<>();
+ int[]_cfrom=null,_cto=null;
String matchedSeq = originalSeq;
- if (seqStart != UNASSIGNED) // fixme! seqStart can map to -1 for a pdb
- // sequence that starts <-1
+ if (seqStart != UNASSIGNED) // fixme! seqStart can map to -1 for a pdb sequence that starts <-1
{
- for (int seqps : keys)
+ for (int seqps:keys)
{
int pdbpos = mapping.get(seqps)[PDBE_POS];
if (pdbpos == UNASSIGNED)
// not correct - pdbpos might be -1, but leave it for now
continue;
}
- if (_cfrom == null || seqps != _cfrom[1] + 1)
+ if (_cfrom==null || seqps!=_cfrom[1]+1)
{
- _cfrom = new int[] { seqps, seqps };
+ _cfrom = new int[] { seqps,seqps};
from.add(_cfrom);
_cto = null; // discontinuity
+ } else {
+ _cfrom[1]= seqps;
}
- else
+ if (_cto==null || pdbpos!=1+_cto[1])
{
- _cfrom[1] = seqps;
- }
- if (_cto == null || pdbpos != 1 + _cto[1])
- {
- _cto = new int[] { pdbpos, pdbpos };
+ _cto = new int[] { pdbpos,pdbpos};
to.add(_cto);
- }
- else
- {
+ } else {
_cto[1] = pdbpos;
}
}
;
seqFromPdbMapping = new jalview.datamodel.Mapping(null, _cto, _cfrom,
- 1, 1);
+ 1,
+ 1);
pdbStart = mapping.get(seqStart)[PDB_RES_POS];
pdbEnd = mapping.get(seqEnd)[PDB_RES_POS];
int orignalSeqStart = seq.getStart();
for (Residue residue : residues)
{
boolean isObserved = isResidueObserved(residue);
- int pdbeIndex = getLeadingIntegerValue(residue.getDbResNum(),
+ int pdbeIndex = Platform.getLeadingIntegerValue(residue.getDbResNum(),
UNASSIGNED);
int currSeqIndex = UNASSIGNED;
List<CrossRefDb> cRefDbs = residue.getCrossRefDb();
pdbRefDb = cRefDb;
if (firstPDBResNum == UNASSIGNED)
{
- firstPDBResNum = getLeadingIntegerValue(cRefDb.getDbResNum(),
+ firstPDBResNum = Platform.getLeadingIntegerValue(cRefDb.getDbResNum(),
UNASSIGNED);
}
else
if (cRefDb.getDbCoordSys().equalsIgnoreCase(seqCoordSys.getName())
&& isAccessionMatched(cRefDb.getDbAccessionId()))
{
- currSeqIndex = getLeadingIntegerValue(cRefDb.getDbResNum(),
+ currSeqIndex = Platform.getLeadingIntegerValue(cRefDb.getDbResNum(),
UNASSIGNED);
if (pdbRefDb != null)
{
}
// if (currSeqIndex >= seq.getStart() && currSeqIndex <= seqlength) //
// true
- // numbering
- // is
- // not
- // up
- // to
- // seq.getEnd()
+ // numbering
+ // is
+ // not
+ // up
+ // to
+ // seq.getEnd()
{
int resNum = (pdbRefDb == null)
- ? getLeadingIntegerValue(residue.getDbResNum(),
+ ? Platform.getLeadingIntegerValue(residue.getDbResNum(),
UNASSIGNED)
- : getLeadingIntegerValue(pdbRefDb.getDbResNum(),
+ : Platform.getLeadingIntegerValue(pdbRefDb.getDbResNum(),
UNASSIGNED);
if (isObserved)
}
/**
- * Get the leading integer part of a string that begins with an integer.
- *
- * @param input
- * - the string input to process
- * @param failValue
- * - value returned if unsuccessful
- * @return
- */
- static int getLeadingIntegerValue(String input, int failValue)
- {
- if (input == null)
- {
- return failValue;
- }
- String[] parts = input.split("(?=\\D)(?<=\\d)");
- if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
- {
- return Integer.valueOf(parts[0]);
- }
- return failValue;
- }
-
- /**
*
* @param chainId
* Target chain to populate mapping of its atom positions.
{
boolean isStrictMatch = true;
return isStrictMatch ? curSourceDBRef.equalsIgnoreCase(accession)
- : curDBRefAccessionIdsString.contains(accession.toLowerCase());
+ : curDBRefAccessionIdsString
+ .contains(accession.toLowerCase(Locale.ROOT));
}
private boolean isFoundInSiftsEntry(String accessionId)
{
Set<String> siftsDBRefs = getAllMappingAccession();
return accessionId != null
- && siftsDBRefs.contains(accessionId.toLowerCase());
+ && siftsDBRefs.contains(accessionId.toLowerCase(Locale.ROOT));
}
/**
{
return pdbeNonObserved;
}
-
public SequenceI getSeq()
{
return seq;
git://source.jalview.org / jalview.git / blobdiff