/* * 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.MessageManager; import jalview.ws.ebi.EBIFetchClient; import java.io.File; import java.util.ArrayList; import java.util.List; import com.stevesoft.pat.Regex; /** * @author JimP * */ public class Pdb extends EbiFileRetrievedProxy { private static final String SEPARATOR = "|"; private static final String COLON = ":"; private static final int PDB_ID_LENGTH = 4; public Pdb() { 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() { return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)"); } /* * (non-Javadoc) * * @see jalview.ws.DbSourceProxy#getDbSource() */ @Override public String getDbSource() { return DBRefSource.PDB; } /* * (non-Javadoc) * * @see jalview.ws.DbSourceProxy#getDbVersion() */ @Override public String getDbVersion() { return "0"; } /* * (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; } /* * extract chain code if it is appended to the id and we * don't already have one */ if (queries.length() > PDB_ID_LENGTH && chain == null) { chain = queries.substring(PDB_ID_LENGTH, PDB_ID_LENGTH + 1); id = queries.substring(0, PDB_ID_LENGTH); } if (!isValidReference(id)) { System.err.println("Ignoring invalid pdb query: '" + id + "'"); stopQuery(); return null; } /* * ensure that an mmCIF format structure file is saved with extension.cif, * because the Chimera "open" command recognises this extension */ Type pdbFileFormat = StructureImportSettings .getDefaultStructureFileFormat(); String ext = pdbFileFormat.getExtension(); String fetchFormat = pdbFileFormat.getFormat(); EBIFetchClient ebi = new EBIFetchClient(); File tmpFile = ebi.fetchDataAsFile("pdb:" + id, fetchFormat, ext); file = tmpFile.getAbsolutePath(); stopQuery(); if (file == null) { return null; } try { // todo get rid of Type and use FileFormatI instead? FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB : FileFormat.MMCif; pdbAlignment = new FormatAdapter().readFile(file, 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(jalview.datamodel.DBRefSource.PDB + SEPARATOR + 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); } } } } 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; } /* * (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(); } }