X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=11fe95e36330a721254024d17bde26b939ecdb4d;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=054858319930513ba036719d99185186abc4125e;hpb=0eda2ac2f334f55f6e5f137789453a9f4dfe4d73;p=jalview.git diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java index 0548583..11fe95e 100644 --- a/src/jalview/ws/dbsources/Pdb.java +++ b/src/jalview/ws/dbsources/Pdb.java @@ -1,180 +1,286 @@ -/** - * - */ -package jalview.ws.dbsources; - -import jalview.datamodel.Alignment; -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.DBRefSource; -import jalview.datamodel.SequenceI; - -import java.io.BufferedInputStream; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.util.Hashtable; -import java.util.Vector; - -import MCview.PDBChain; -import MCview.PDBfile; - -import com.stevesoft.pat.Regex; - -import jalview.datamodel.AlignmentI; -import jalview.io.FileParse; -import jalview.ws.ebi.EBIFetchClient; -import jalview.ws.seqfetcher.DbSourceProxy; -import jalview.ws.seqfetcher.DbSourceProxyImpl; - -/** - * @author JimP - * - */ -public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy -{ - public Pdb() { - super(); - addDbSourceProperty(DBRefSource.PROTSEQDB); - } - - /* (non-Javadoc) - * @see jalview.ws.DbSourceProxy#getAccessionSeparator() - */ - public String getAccessionSeparator() - { - // TODO Auto-generated method stub - return null; - } - - /* (non-Javadoc) - * @see jalview.ws.DbSourceProxy#getAccessionValidator() - */ - public Regex getAccessionValidator() - { - return new Regex("[1-9][0-9A-Za-z]{3}[ _A-Za-z0-9]?"); - } - - /* (non-Javadoc) - * @see jalview.ws.DbSourceProxy#getDbSource() - */ - public String getDbSource() - { - return DBRefSource.PDB; - } - - /* (non-Javadoc) - * @see jalview.ws.DbSourceProxy#getDbVersion() - */ - public String getDbVersion() - { - return "0"; - } - /* (non-Javadoc) - * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[]) - */ - public AlignmentI getSequenceRecords(String queries) throws Exception - { - - Vector result = new Vector(); - String chain = null; - String id = null; - if (queries.indexOf(":") > -1) - { - chain = queries.substring(queries.indexOf(":") + 1); - id = queries.substring(0, queries.indexOf(":")); - } - else - { - id = queries; - } - if (queries.length() > 4 && chain == null) - { - chain = queries.substring(4); - id = queries.substring(0, 4); - } - EBIFetchClient ebi = new EBIFetchClient(); - file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw") - .getAbsolutePath(); - stopQuery(); - if (file == null) - { - return null; - } - try - { - - PDBfile pdbfile = new PDBfile(file, - jalview.io.AppletFormatAdapter.FILE); - for (int i = 0; i < pdbfile.chains.size(); i++) - { - if (chain == null - || ((PDBChain) pdbfile.chains.elementAt(i)).id - .toUpperCase().equals(chain)) - { - PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i); - // Get the Chain's Sequence - who's dataset includes any special features added from the PDB file - SequenceI sq = pdbchain.sequence; - // Specially formatted name for the PDB chain sequences retrieved from the PDB - sq.setName(jalview.datamodel.DBRefSource.PDB+"|" + id + "|" + sq.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(), id + pdbchain.id); - sq.addDBRef(dbentry); - // and add seuqence to the retrieved set - result.addElement(sq.deriveSequence()); - } - } - - if (result.size() < 1) - { - throw new Exception("No PDB Records for " + id + " chain " - + ((chain == null) ? " " : chain)); - } - } catch (Exception ex) // Problem parsing PDB file - { - stopQuery(); - throw (ex); - } - - SequenceI[] results = new SequenceI[result.size()]; - for (int i = 0, j = result.size(); i < j; i++) - { - results[i] = (SequenceI) result.elementAt(i); - result.setElementAt(null, i); - } - return new Alignment(results); - } - - /* (non-Javadoc) - * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String) - */ - public boolean isValidReference(String accession) - { - Regex r = getAccessionValidator(); - return r.search(accession.trim()); - } - - /** - * obtain human glyoxalase chain A sequence - */ - public String getTestQuery() - { - return "1QIPA"; - } - -} +/* + * 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.FormatAdapter; +import jalview.io.PDBFeatureSettings; +import jalview.structure.StructureImportSettings; +import jalview.util.MessageManager; +import jalview.ws.ebi.EBIFetchClient; + +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; + } + String ext = StructureImportSettings.getDefaultStructureFileFormat() + .equalsIgnoreCase(Type.MMCIF.toString()) ? ".cif" : ".xml"; + EBIFetchClient ebi = new EBIFetchClient(); + file = ebi.fetchDataAsFile( + "pdb:" + id, + StructureImportSettings.getDefaultStructureFileFormat() + .toLowerCase(), ext).getAbsolutePath(); + stopQuery(); + if (file == null) + { + return null; + } + try + { + + pdbAlignment = new FormatAdapter().readFile(file, + jalview.io.AppletFormatAdapter.FILE, + StructureImportSettings.getDefaultStructureFileFormat()); + 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(); + } +}