/*
* 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.bin.Cache;
import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ContactMatrix;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
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;
import jalview.io.FormatAdapter;
import jalview.io.PDBFeatureSettings;
import jalview.javascript.json.JSON;
import jalview.structure.StructureImportSettings;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;
import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.utils.UrlDownloadClient;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.jmol.adapter.readers.simple.JSONReader;
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";
}
public static String getAlphaFoldPaeDownloadUrl(String id)
{
return "https://alphafold.ebi.ac.uk/files/" + id
+ "-predicted_aligned_error_v1.json";
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
*/
@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 (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 alphafold query: '" + id + "'");
stopQuery();
return null;
}
String alphaFoldCif = getAlphaFoldCifDownloadUrl(id);
if (retrievalUrl != null)
{
alphaFoldCif = retrievalUrl;
}
try
{
File tmpFile = File.createTempFile(id, ".cif");
Console.debug("Retrieving structure file for "+id+" from "+alphaFoldCif);
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) }));
}
// import PAE as contact matrix - assume this will work if there was a
// model
File pae = File.createTempFile(id, "pae_json");
String paeURL = getAlphaFoldPaeDownloadUrl(id);
if (retrievalUrl!=null) {
// manufacture the PAE url from a url like ...-model-vN.cif
paeURL = retrievalUrl.replace("model","predicted_aligned_error").replace(".cif",".json");
}
Console.debug("Downloading pae from " + paeURL
+ " to " + pae.toString() + "");
try {
UrlDownloadClient.download(paeURL, pae);
if (!importPaeJSONAsContactMatrix(pdbAlignment, pae))
{
Console.warn("Couln't import contact matrix from " + paeURL
+ " (stored in " + pae.toString() + ")");
}
} catch (Exception pae_ex) {
Console.debug("Couldn't download PAE",pae_ex);
}
} catch (Exception ex) // Problem parsing PDB file
{
stopQuery();
throw (ex);
}
return pdbAlignment;
}
private boolean importPaeJSONAsContactMatrix(AlignmentI pdbAlignment,
File pae) throws Exception
{
FileInputStream pae_input = new FileInputStream(pae);
List