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;
@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 "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)
*
@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 + "'");
+ "(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");
+ 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;
}
- // todo get rid of Type and use FileFormatI instead?
- FileFormatI fileFormat = FileFormat.MMCif;
- pdbAlignment = new FormatAdapter().readFile(tmpFile,
- DataSourceType.FILE, fileFormat);
- if (pdbAlignment != null)
- {
- List<SequenceI> toremove = new ArrayList<SequenceI>();
- 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
- 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)
- {
- pdbAlignment.deleteSequence(pdbcs);
- if (pdbcs.getAnnotation() != null)
- {
- for (AlignmentAnnotation aa : pdbcs.getAnnotation())
- {
- pdbAlignment.deleteAnnotation(aa);
- }
- }
- }
- }
+ pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile, id, chain, getDbSource(),getDbVersion());
+
if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
{
{ 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);
- UrlDownloadClient.download(paeURL, pae);
++
++ 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))
+ {
- Cache.log.debug("Couln't import contact matrix from " + paeURL
++ 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();
return pdbAlignment;
}
+ private boolean importPaeJSONAsContactMatrix(AlignmentI pdbAlignment,
+ File pae) throws Exception
+ {
+ FileInputStream pae_input = new FileInputStream(pae);
+
+ List<Object> pae_obj = (List<Object>) Platform
+ .parseJSON(pae_input);
+ if (pae_obj == null)
+ {
+ return false;
+ }
+ ContactMatrixI matrix = new PAEContactMatrix(
+ pdbAlignment.getSequenceAt(0), (Map<String, Object>)pae_obj.get(0));
+
+ pdbAlignment.getSequenceAt(0).addAlignmentAnnotation(pdbAlignment.addContactList(matrix));
+ return true;
+ }
+
+ /**
+ * 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())
+ {
+ 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);
+ // update any feature groups
+ List<SequenceFeature> allsf = pdbcs.getFeatures().getAllFeatures();
+ List<SequenceFeature> newsf = new ArrayList<SequenceFeature>();
+ if (allsf!=null && allsf.size()>0)
+ {
+ 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);
+ }
+ }
+ // 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)
*
@Override
public String getTestQuery()
{
- return "1QIP";
+ return "AF-O15552-F1";
}
@Override
public String getDbName()
{
- return "PDB"; // getDbSource();
+ return "ALPHAFOLD"; // getDbSource();
}
@Override
{
return new PDBFeatureSettings();
}
+
}
*/
package jalview.ws.seqfetcher;
+import static org.testng.Assert.assertNotEquals;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import jalview.analysis.CrossRef;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.FeatureProperties;
+ import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
import jalview.util.DBRefUtils;
+ import jalview.ws.DBRefFetcher;
import jalview.ws.SequenceFetcher;
+import jalview.ws.dbsources.EBIAlfaFold;
import jalview.ws.dbsources.Pdb;
import jalview.ws.dbsources.Uniprot;
import java.util.Arrays;
import java.util.List;
+import org.junit.Assert;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- jalview.bin.Cache.initLogger();
+ jalview.bin.Console.initLogger();
}
/**
{
}
+ @Test(groups= {"Network"})
+ public void checkUniprotCanonicalFlagSet()
+ {
+ // TODO - mock this - for moment it is a live request.
+ SequenceI uniprotSeq = new Sequence("FER1_SPIOL",
+ "MAATTTTMMGMATTFVPKPQAPPMMAALPSNTGRSLFGLKTGSRGGRMTMAAYKVTLVTPTGNVEFQCPDDV"
+ + "YILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEE"
+ + "LTA");
+ DBRefFetcher dbr = new DBRefFetcher(new SequenceI[] { uniprotSeq });
+ dbr.fetchDBRefs(true);
+ List<DBRefEntry> primRefs = uniprotSeq.getPrimaryDBRefs();
+ assertNotNull(primRefs);
+ assertTrue(primRefs.size()>0);
+ boolean canonicalUp=false;
+ for (DBRefEntry ref:primRefs) {
+ assertEquals(DBRefSource.UNIPROT, ref.getCanonicalSourceName());
+ canonicalUp |= ref.isCanonical();
+ }
+ assertTrue("No Canonical Uniprot reference detected", canonicalUp);
+ }
/**
* Tests that standard protein database sources include Uniprot (as the first)
* and also PDB. (Additional sources are dependent on availability of DAS
assertEquals(dr.get(0).getSource() + "|" + dr.get(0).getAccessionId(),
proteinSeq.getName());
}
+
+ /**
+ * Tests retrieval of one entry from EMBLCDS. Test is dependent on
+ * availability of network and the EMBLCDS service.
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "External" })
+ public void testAlphaFoldClien() throws Exception
+ {
+ DbSourceProxy alphafold = new EBIAlfaFold();
+ AlignmentI resp = alphafold.getSequenceRecords(alphafold.getTestQuery());
+ assertNotNull(resp);
+ assertEquals("One sequence only",resp.getHeight(), 1);
+ for (AlignmentAnnotation aa:resp.getAlignmentAnnotation()) {
+ if (aa.graph == AlignmentAnnotation.CUSTOMRENDERER)
+ {
+ assertTrue("Contact map didn't provide valid contact",resp.getContactListFor(aa, 1).getContactAt(1)!=-1d);
+ // test passes
+ return;
+ }
+ }
+ Assert.fail();
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff