import java.io.PrintStream;
import java.net.URL;
import java.net.URLConnection;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.attribute.BasicFileAttributes;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
+import java.util.Collections;
+import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
private final static String NEWLINE = System.lineSeparator();
+ private final static int THRESHOLD_IN_DAYS = 2;
+
private String curSourceDBRef;
private HashSet<String> curDBRefAccessionIdsString;
try (InputStream in = new FileInputStream(siftFile);
GZIPInputStream gzis = new GZIPInputStream(in);)
{
- System.out.println("File : " + siftFile.getAbsolutePath());
+ // System.out.println("File : " + siftFile.getAbsolutePath());
JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.sifts");
XMLStreamReader streamReader = XMLInputFactory.newInstance()
.createXMLStreamReader(gzis);
public static File getSiftsFile(String pdbId) throws SiftsException
{
File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
- + pdbId.toLowerCase()
- + ".xml.gz");
+ + pdbId.toLowerCase() + ".xml.gz");
if (siftsFile.exists())
{
- // TODO it may be worth performing an age check to determine if a
- // new SIFTs file should be re-downloaded as SIFTs entries are usually
- // updated weekly
+ // 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, THRESHOLD_IN_DAYS))
+ {
+ // System.out.println("Downloaded file is out of date, hence re-downloading...");
+ siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ }
return siftsFile;
}
siftsFile = downloadSiftsFile(pdbId.toLowerCase());
}
/**
+ * 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
}
try
{
- System.out.println(">> Download ftp url : " + siftsFileFTPURL);
+ // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
URL url = new URL(siftsFileFTPURL);
URLConnection conn = url.openConnection();
InputStream inputStream = conn.getInputStream();
}
outputStream.close();
inputStream.close();
- System.out.println(">>> File downloaded : " + downloadedSiftsFile);
+ // System.out.println(">>> File downloaded : " + downloadedSiftsFile);
} catch (IOException ex)
{
throw new SiftsException(ex.getMessage());
public static boolean deleteSiftsFileByPDBId(String pdbId)
{
File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
- + pdbId.toLowerCase()
- + ".xml.gz");
+ + pdbId.toLowerCase() + ".xml.gz");
if (siftsFile.exists())
{
return siftsFile.delete();
return true;
}
-
/**
* Get a valid SIFTs DBRef for the given sequence current SIFTs entry
*
throw new SiftsException("Could not get source DB Ref");
}
-
/**
* Check that the DBRef Entry is properly populated and is available in this
* SiftClient instance
String mappingOutput = mappingDetails.toString();
StructureMapping siftsMapping = new StructureMapping(seq, pdbFile,
- pdbId, chain, mapping,
- mappingOutput);
+ pdbId, chain, mapping, mappingOutput);
return siftsMapping;
}
@Override
- public HashMap<Integer, int[]> getGreedyMapping(String entityId, SequenceI seq,
- java.io.PrintStream os)
- throws SiftsException
+ public HashMap<Integer, int[]> getGreedyMapping(String entityId,
+ SequenceI seq, java.io.PrintStream os) throws SiftsException
{
ArrayList<Integer> omitNonObserved = new ArrayList<Integer>();
int nonObservedShiftIndex = 0;
Entity entity = null;
entity = getEntityById(entityId);
String originalSeq = AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- seq.getSequenceAsString());
+ jalview.util.Comparison.GapChars, seq.getSequenceAsString());
HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
DBRefEntryI sourceDBRef = seq.getSourceDBRef();
if (sourceDBRef == null)
String resNumIndexString = cRefDb.getDbResNum()
.equalsIgnoreCase("None") ? String.valueOf(UNASSIGNED)
: cRefDb.getDbResNum();
- currSeqIndex = Integer.valueOf(resNumIndexString);
+ try
+ {
+ currSeqIndex = Integer.valueOf(resNumIndexString);
+ } catch (NumberFormatException nfe)
+ {
+ currSeqIndex = Integer.valueOf(resNumIndexString
+ .split("[a-zA-Z]")[0]);
+ }
if (pdbRefDb != null)
{
break;// exit loop if pdb and uniprot are already found
try
{
resNum = (pdbRefDb == null) ? Integer.valueOf(residue
- .getDbResNum()) : Integer.valueOf(pdbRefDb.getDbResNum());
+ .getDbResNum()) : Integer.valueOf(pdbRefDb
+ .getDbResNum());
} catch (NumberFormatException nfe)
{
resNum = (pdbRefDb == null) ? Integer.valueOf(residue
{
e.printStackTrace();
}
- padWithGaps(resNumMap, omitNonObserved);
+ if (seqCoordSys == CoordinateSys.UNIPROT)
+ {
+ padWithGaps(resNumMap, omitNonObserved);
+ }
int seqStart = UNASSIGNED;
int seqEnd = UNASSIGNED;
int pdbStart = UNASSIGNED;
}
}
-
/**
*
* @param chainId
}
return entity;
}
+ Entity entity = getEntityByMostOptimalMatchedId(id);
+ if (entity != null)
+ {
+ return entity;
+ }
throw new SiftsException("Entity " + id + " not found");
}
+ /**
+ * This method was added because EntityId is NOT always equal to ChainId.
+ * Hence, it provides the logic to greedily detect the "true" Entity for a
+ * given chainId where discrepancies exist.
+ *
+ * @param chainId
+ * @return
+ */
+ public Entity getEntityByMostOptimalMatchedId(String chainId)
+ {
+ System.out
+ .println("--------------> advanced greedy entityId matching block entered..");
+ List<Entity> entities = siftsEntry.getEntity();
+ SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()];
+ int count = 0;
+ for (Entity entity : entities)
+ {
+ sPojo[count] = new SiftsEntitySortPojo();
+ sPojo[count].entityId = entity.getEntityId();
+
+ List<Segment> segments = entity.getSegment();
+ for (Segment segment : segments)
+ {
+ List<Residue> residues = segment.getListResidue().getResidue();
+ for (Residue residue : residues)
+ {
+ List<CrossRefDb> cRefDbs = residue.getCrossRefDb();
+ for (CrossRefDb cRefDb : cRefDbs)
+ {
+ if (!cRefDb.getDbSource().equalsIgnoreCase("PDB"))
+ {
+ continue;
+ }
+ ++sPojo[count].resCount;
+ if (cRefDb.getDbChainId().equalsIgnoreCase(chainId))
+ {
+ ++sPojo[count].chainIdFreq;
+ }
+ }
+ }
+ }
+ sPojo[count].pid = 100 * (sPojo[count].chainIdFreq / sPojo[count].resCount);
+ ++count;
+ }
+ Arrays.sort(sPojo, Collections.reverseOrder());
+ System.out.println("highest matched entity : " + sPojo[0].entityId);
+ System.out.println("highest matched pid : " + sPojo[0].pid);
+
+ if (sPojo[0].entityId != null)
+ {
+ for (Entity entity : entities)
+ {
+ if (!entity.getEntityId().equalsIgnoreCase(sPojo[0].entityId))
+ {
+ continue;
+ }
+ return entity;
+ }
+ }
+ return null;
+ }
+
+ public class SiftsEntitySortPojo implements
+ Comparable<SiftsEntitySortPojo>
+ {
+ public String entityId;
+
+ public int chainIdFreq;
+
+ public int pid;
+
+ public int resCount;
+
+ @Override
+ public int compareTo(SiftsEntitySortPojo o)
+ {
+ return this.pid - o.pid;
+ }
+ }
+
@Override
public String[] getEntryDBs()
{
String strName = mp.getStrName();
int pdbStart = mp.getStrStart();
int pdbEnd = mp.getStrEnd();
-
+
String type = mp.getType();
-
+
int maxid = (seqName.length() >= strName.length()) ? seqName.length()
: strName.length();
int len = 72 - maxid - 1;
output.append(" - ");
output.append(String.valueOf(pdbEnd));
output.append(NEWLINE).append(NEWLINE);
-
+
int matchedSeqCount = 0;
for (int j = 0; j < nochunks; j++)
{
{
try
{
- if ((i + (j * len)) < seqRes.length())
- {
- if (seqRes.charAt(i + (j * len)) == strRes.charAt(i + (j * len))
- && !jalview.util.Comparison.isGap(seqRes.charAt(i
- + (j * len))))
+ if ((i + (j * len)) < seqRes.length())
{
+ if (seqRes.charAt(i + (j * len)) == strRes
+ .charAt(i + (j * len))
+ && !jalview.util.Comparison.isGap(seqRes.charAt(i
+ + (j * len))))
+ {
matchedSeqCount++;
- output.append("|");
- }
- else if (type.equals("pep"))
- {
- if (ResidueProperties.getPAM250(seqRes.charAt(i + (j * len)),
- strRes.charAt(i + (j * len))) > 0)
+ output.append("|");
+ }
+ else if (type.equals("pep"))
{
- output.append(".");
+ if (ResidueProperties.getPAM250(seqRes.charAt(i + (j * len)),
+ strRes.charAt(i + (j * len))) > 0)
+ {
+ output.append(".");
+ }
+ else
+ {
+ output.append(" ");
+ }
}
else
{
output.append(" ");
}
}
- else
- {
- output.append(" ");
- }
- }
} catch (IndexOutOfBoundsException e)
{
continue;
{
throw new SiftsException("Low PID detected for SIFTs mapping...");
}
- output.append("Length of alignment = " + seqRes.length())
- .append(NEWLINE);
+ output.append("Length of alignment = " + seqRes.length()).append(
+ NEWLINE);
output.append(new Format("Percentage ID = %2.2f").form(pid));
output.append(NEWLINE);
return output;
}
-
+
@Override
public int getEntityCount()
{
{
return siftsEntry.getDbVersion();
}
+
}
git://source.jalview.org / jalview.git / commitdiff