/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.io.PDBFeatureSettings;
import jalview.structure.StructureImportSettings;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.utils.UrlDownloadClient;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import com.stevesoft.pat.Regex;
/**
* @author JimP
*
*/
public class EBIAlfaFold extends EbiFileRetrievedProxy
{
private static final String SEPARATOR = "|";
private static final String COLON = ":";
private static final int PDB_ID_LENGTH = 4;
public EBIAlfaFold()
{
super();
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
@Override
public String getAccessionSeparator()
{
return null;
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
@Override
public Regex getAccessionValidator()
{
Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
validator.setIgnoreCase(true);
return validator;
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
@Override
public String getDbSource()
{
return "ALPHAFOLD";
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getDbVersion()
*/
@Override
public String getDbVersion()
{
return "1";
}
public static String getAlphaFoldCifDownloadUrl(String id)
{
return "https://alphafold.ebi.ac.uk/files/" + id + "-model_v1.cif";
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
*/
@Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
AlignmentI pdbAlignment = null;
String chain = null;
String id = null;
if (queries.indexOf(COLON) > -1)
{
chain = queries.substring(queries.indexOf(COLON) + 1);
id = queries.substring(0, queries.indexOf(COLON));
}
else
{
id = queries;
}
if (!isValidReference(id))
{
System.err.println(
"(AFClient) Ignoring invalid pdb query: '" + id + "'");
stopQuery();
return null;
}
String alphaFoldCif = getAlphaFoldCifDownloadUrl(id);
try
{
File tmpFile = File.createTempFile(id, ".cif");
UrlDownloadClient.download(alphaFoldCif, tmpFile);
// may not need this check ?
file = tmpFile.getAbsolutePath();
if (file == 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);
}
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 toremove = new ArrayList();
for (SequenceI pdbcs : pdbAlignment.getSequences())
{
String chid = null;
// Mapping map=null;
for (PDBEntry pid : pdbcs.getAllPDBEntries())
{
if (pid.getFile() == file)
{
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
if (dbSource != null)
{
DBRefEntry dbentry = new DBRefEntry(dbSource,
dbVersion, (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)
{
pdbAlignment.deleteSequence(pdbcs);
if (pdbcs.getAnnotation() != null)
{
for (AlignmentAnnotation aa : pdbcs.getAnnotation())
{
pdbAlignment.deleteAnnotation(aa);
}
}
}
}
return pdbAlignment;
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
@Override
public boolean isValidReference(String accession)
{
Regex r = getAccessionValidator();
return r.search(accession.trim());
}
/**
* human glyoxalase
*/
@Override
public String getTestQuery()
{
return "1QIP";
}
@Override
public String getDbName()
{
return "PDB"; // getDbSource();
}
@Override
public int getTier()
{
return 0;
}
/**
* Returns a descriptor for suitable feature display settings with
*
* - ResNums or insertions features visible
* - insertions features coloured red
* - ResNum features coloured by label
* - Insertions displayed above (on top of) ResNums
*
*/
@Override
public FeatureSettingsModelI getFeatureColourScheme()
{
return new PDBFeatureSettings();
}
}