import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
import jalview.util.Format;
import jalview.xml.binding.sifts.Entry;
import jalview.xml.binding.sifts.Entry.Entity;
siftsEntry = parseSIFTs(siftsFile);
}
-
/**
* Parse the given SIFTs File and return a JAXB POJO of parsed data
*
{
siftsDownloadDir.mkdirs();
}
- // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
- 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);
+ // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
+ 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);
return new File(downloadedSiftsFile);
}
public DBRefEntryI getValidSourceDBRef(SequenceI seq)
throws SiftsException
{
- DBRefEntryI sourceDBRef = null;
- sourceDBRef = seq.getSourceDBRef();
- if (sourceDBRef != null && isValidDBRefEntry(sourceDBRef))
+ List<DBRefEntry> dbRefs = seq.getPrimaryDBRefs();
+ if (dbRefs == null || dbRefs.size() < 1)
{
- return sourceDBRef;
+ throw new SiftsException(
+ "Source DBRef could not be determined. DBRefs might not have been retrieved.");
}
- else
+
+ for (DBRefEntry dbRef : dbRefs)
{
- DBRefEntry[] dbRefs = seq.getDBRefs();
- if (dbRefs == null || dbRefs.length < 1)
+ if (dbRef == null || dbRef.getAccessionId() == null
+ || dbRef.getSource() == null)
{
- throw new SiftsException(
- "Source DBRef could not be determined. DBRefs might not have been retrieved.");
+ continue;
}
-
- for (DBRefEntryI dbRef : dbRefs)
+ String canonicalSource = DBRefUtils.getCanonicalName(dbRef
+ .getSource());
+ if (isValidDBRefEntry(dbRef)
+ && (canonicalSource.equalsIgnoreCase(DBRefSource.UNIPROT) || canonicalSource
+ .equalsIgnoreCase(DBRefSource.PDB)))
{
- if (dbRef == null || dbRef.getAccessionId() == null
- || dbRef.getSource() == null)
- {
- continue;
- }
- if (isFoundInSiftsEntry(dbRef.getAccessionId())
- && (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT) || dbRef
- .getSource().equalsIgnoreCase(DBRefSource.PDB)))
- {
- seq.setSourceDBRef(dbRef);
- return dbRef;
- }
+ return dbRef;
}
}
- if (sourceDBRef != null && isValidDBRefEntry(sourceDBRef))
- {
- return sourceDBRef;
- }
throw new SiftsException("Could not get source DB Ref");
}
String pdbFile, String chain) throws SiftsException
{
structId = (chain == null) ? pdbId : pdbId + "|" + chain;
- System.out.println("Getting mapping for: " + pdbId + "|" + chain
- + " : seq- " + seq.getName());
+ System.out.println("Getting SIFTS mapping for " + structId + ": seq "
+ + seq.getName());
final StringBuilder mappingDetails = new StringBuilder(128);
PrintStream ps = new PrintStream(System.out)
String originalSeq = AlignSeq.extractGaps(
jalview.util.Comparison.GapChars, seq.getSequenceAsString());
HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
- DBRefEntryI sourceDBRef = seq.getSourceDBRef();
+ DBRefEntryI sourceDBRef;
sourceDBRef = getValidSourceDBRef(seq);
// TODO ensure sequence start/end is in the same coordinate system and
// consistent with the choosen sourceDBRef
int pdbStart = UNASSIGNED;
int pdbEnd = UNASSIGNED;
- Integer[] keys = mapping.keySet().toArray(new Integer[0]);
- Arrays.sort(keys);
- if (keys.length < 1)
+ if (mapping.isEmpty())
{
- throw new SiftsException(">>> Empty SIFTS mapping generated!!");
+ throw new SiftsException("SIFTS mapping failed");
}
+
+ Integer[] keys = mapping.keySet().toArray(new Integer[0]);
+ Arrays.sort(keys);
seqStart = keys[0];
seqEnd = keys[keys.length - 1];
}
}
}
+
/**
*
* @param chainId
}
}
-
-
@Override
public Entity getEntityById(String id) throws SiftsException
{
if (sPojo[0].entityId != null)
{
+ if (sPojo[0].pid < 1)
+ {
+ return null;
+ }
for (Entity entity : entities)
{
if (!entity.getEntityId().equalsIgnoreCase(sPojo[0].entityId))
{
if ((i + (j * len)) < seqRes.length())
{
- if (seqRes.charAt(i + (j * len)) == strRes
- .charAt(i + (j * len))
+ boolean sameChar = Comparison.compareChars(
+ seqRes.charAt(i + (j * len)),
+ strRes.charAt(i + (j * len)), false);
+ if (sameChar
&& !jalview.util.Comparison.isGap(seqRes.charAt(i
+ (j * len))))
{