import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeaturesI;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
@Override
public Regex getAccessionValidator()
{
- return new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+ Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+ validator.setIgnoreCase(true);
+ return validator;
}
/*
{
return "1";
}
+
public static String getAlphaFoldCifDownloadUrl(String id)
{
- return "https://alphafold.ebi.ac.uk/files/"+id+"-model_v1.cif";
+ return "https://alphafold.ebi.ac.uk/files/" + id + "-model_v1.cif";
}
+
/*
* (non-Javadoc)
*
@Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
+ return getSequenceRecords(queries, null);
+ }
+ public AlignmentI getSequenceRecords(String queries, String retrievalUrl) throws Exception
+ {
AlignmentI pdbAlignment = null;
String chain = null;
String id = null;
if (!isValidReference(id))
{
- System.err.println("(AFClient) Ignoring invalid pdb query: '" + id + "'");
+ System.err.println(
+ "(AFClient) Ignoring invalid pdb query: '" + id + "'");
stopQuery();
return null;
}
String alphaFoldCif = getAlphaFoldCifDownloadUrl(id);
-
- try {
- File tmpFile = File.createTempFile(id,"cif");
+ if (retrievalUrl != null)
+ {
+ alphaFoldCif = retrievalUrl;
+ }
+
+ try
+ {
+ File tmpFile = File.createTempFile(id, ".cif");
UrlDownloadClient.download(alphaFoldCif, tmpFile);
+
+ // may not need this check ?
file = tmpFile.getAbsolutePath();
if (file == null)
{
- return null;
+ return null;
+ }
+
+ pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile, id, chain, getDbSource(),getDbVersion());
+
+
+ if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
+ {
+ throw new Exception(MessageManager.formatMessage(
+ "exception.no_pdb_records_for_chain", new String[]
+ { id, ((chain == null) ? "' '" : chain) }));
+ }
+
+ } catch (Exception ex) // Problem parsing PDB file
+ {
+ stopQuery();
+ throw (ex);
}
- // todo get rid of Type and use FileFormatI instead?
- FileFormatI fileFormat = FileFormat.MMCif;
- pdbAlignment = new FormatAdapter().readFile(tmpFile, DataSourceType.FILE,
- fileFormat);
- if (pdbAlignment != null)
+ return pdbAlignment;
+ }
+
+ /**
+ * general purpose structure importer - designed to yield alignment useful for transfer of annotation to associated sequences
+ * @param alphaFoldCif
+ * @param tmpFile
+ * @param id
+ * @param chain
+ * @param dbSource
+ * @param dbVersion
+ * @return
+ * @throws Exception
+ */
+ public static AlignmentI importDownloadedStructureFromUrl(String alphaFoldCif,
+ File tmpFile, String id, String chain, String dbSource, String dbVersion) throws Exception
+ {
+ String file = tmpFile.getAbsolutePath();
+ // todo get rid of Type and use FileFormatI instead?
+ FileFormatI fileFormat = FileFormat.MMCif;
+ AlignmentI pdbAlignment = new FormatAdapter().readFile(tmpFile,
+ DataSourceType.FILE, fileFormat);
+ if (pdbAlignment != null)
+ {
+ List<SequenceI> toremove = new ArrayList<SequenceI>();
+ for (SequenceI pdbcs : pdbAlignment.getSequences())
{
- List<SequenceI> toremove = new ArrayList<SequenceI>();
- for (SequenceI pdbcs : pdbAlignment.getSequences())
+ String chid = null;
+ // Mapping map=null;
+ for (PDBEntry pid : pdbcs.getAllPDBEntries())
{
- String chid = null;
- // Mapping map=null;
- for (PDBEntry pid : pdbcs.getAllPDBEntries())
+ if (pid.getFile() == file)
{
- if (pid.getFile() == file)
- {
- chid = pid.getChainCode();
+ chid = pid.getChainCode();
- }
- }
- if (chain == null || (chid != null && (chid.equals(chain)
- || chid.trim().equals(chain.trim())
- || (chain.trim().length() == 0 && chid.equals("_")))))
- {
- // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
- // TODO: suggest simplify naming to 1qip|A as default name defined
- pdbcs.setName(id
- + SEPARATOR + pdbcs.getName());
- // Might need to add more metadata to the PDBEntry object
- // like below
- /*
- * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
- * entry.setId(id); if (entry.getProperty() == null)
- * entry.setProperty(new Hashtable());
- * entry.getProperty().put("chains", pdbchain.id + "=" +
- * sq.getStart() + "-" + sq.getEnd());
- * sq.getDatasetSequence().addPDBId(entry);
- */
- // Add PDB DB Refs
- // We make a DBRefEtntry because we have obtained the PDB file from
- // a
- // verifiable source
- // JBPNote - PDB DBRefEntry should also carry the chain and mapping
- // information
- DBRefEntry dbentry = new DBRefEntry(getDbSource(),
- getDbVersion(), (chid == null ? id : id + chid));
- // dbentry.setMap()
- pdbcs.addDBRef(dbentry);
- }
- else
- {
- // mark this sequence to be removed from the alignment
- // - since it's not from the right chain
- toremove.add(pdbcs);
}
}
- // now remove marked sequences
- for (SequenceI pdbcs : toremove)
+ if (chain == null || (chid != null && (chid.equals(chain)
+ || chid.trim().equals(chain.trim())
+ || (chain.trim().length() == 0 && chid.equals("_")))))
{
- pdbAlignment.deleteSequence(pdbcs);
- if (pdbcs.getAnnotation() != null)
+ // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
+ // TODO: suggest simplify naming to 1qip|A as default name defined
+ pdbcs.setName(id + SEPARATOR + pdbcs.getName());
+ // Might need to add more metadata to the PDBEntry object
+ // like below
+ /*
+ * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
+ * entry.setId(id); if (entry.getProperty() == null)
+ * entry.setProperty(new Hashtable());
+ * entry.getProperty().put("chains", pdbchain.id + "=" +
+ * sq.getStart() + "-" + sq.getEnd());
+ * sq.getDatasetSequence().addPDBId(entry);
+ */
+ // Add PDB DB Refs
+ // We make a DBRefEtntry because we have obtained the PDB file from
+ // a
+ // verifiable source
+ // JBPNote - PDB DBRefEntry should also carry the chain and mapping
+ // information
+ if (dbSource != null)
{
- for (AlignmentAnnotation aa : pdbcs.getAnnotation())
+ DBRefEntry dbentry = new DBRefEntry(dbSource,
+
+ dbVersion, (chid == null ? id : id + chid));
+ // dbentry.setMap()
+ pdbcs.addDBRef(dbentry);
+ // update any feature groups
+ List<SequenceFeature> allsf = pdbcs.getFeatures().getAllFeatures();
+ List<SequenceFeature> newsf = new ArrayList<SequenceFeature>();
+ if (allsf!=null && allsf.size()>0)
{
- pdbAlignment.deleteAnnotation(aa);
+ for (SequenceFeature f:allsf)
+ {
+ if (file.equals(f.getFeatureGroup()))
+ {
+ f = new SequenceFeature(f, f.type, f.begin, f.end, id, f.score);
+ }
+ newsf.add(f);
+ }
+ pdbcs.setSequenceFeatures(newsf);
}
}
}
+ else
+ {
+ // mark this sequence to be removed from the alignment
+ // - since it's not from the right chain
+ toremove.add(pdbcs);
+ }
}
-
- if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
+ // now remove marked sequences
+ for (SequenceI pdbcs : toremove)
{
- throw new Exception(MessageManager.formatMessage(
- "exception.no_pdb_records_for_chain", new String[]
- { id, ((chain == null) ? "' '" : chain) }));
+ pdbAlignment.deleteSequence(pdbcs);
+ if (pdbcs.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation aa : pdbcs.getAnnotation())
+ {
+ pdbAlignment.deleteAnnotation(aa);
+ }
+ }
}
-
- } catch (Exception ex) // Problem parsing PDB file
- {
- stopQuery();
- throw (ex);
}
return pdbAlignment;
}
{
return new PDBFeatureSettings();
}
+
}
git://source.jalview.org / jalview.git / blobdiff