+++ /dev/null
-/*
- * 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 <http://www.gnu.org/licenses/>.
- * 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.SequenceI;
-import jalview.io.FormatAdapter;
-import jalview.io.PDBFeatureSettings;
-import jalview.util.MessageManager;
-import jalview.ws.ebi.EBIFetchClient;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Vector;
-
-import com.stevesoft.pat.Regex;
-
-/**
- * @author JimP
- *
- */
-public class Pdb extends EbiFileRetrievedProxy
-{
- public Pdb()
- {
- super();
- }
-
- public static final String FEATURE_INSERTION = "INSERTION";
-
- public static final String FEATURE_RES_NUM = "RESNUM";
-
- private static String currentDefaultFormat = DBRefSource.PDB;
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
- */
- @Override
- public String getAccessionSeparator()
- {
- // TODO Auto-generated method stub
- 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;
- 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, 5);
- id = queries.substring(0, 4);
- }
- if (!isValidReference(id))
- {
- System.err.println("Ignoring invalid pdb query: '" + id + "'");
- stopQuery();
- return null;
- }
- String ext = getCurrentDefaultFormat().equalsIgnoreCase("mmcif") ? ".cif"
- : ".xml";
- EBIFetchClient ebi = new EBIFetchClient();
- file = ebi.fetchDataAsFile("pdb:" + id,
-<<<<<<< HEAD
- getCurrentDefaultFomart().toLowerCase(), ext)
-=======
- getCurrentDefaultFormat().toLowerCase(), "raw", ext)
->>>>>>> develop
- .getAbsolutePath();
- stopQuery();
- if (file == null)
- {
- return null;
- }
- try
- {
-
- pdbAlignment = new FormatAdapter().readFile(file,
- jalview.io.AppletFormatAdapter.FILE,
- getCurrentDefaultFormat());
- 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("_")))))
- {
- pdbcs.setName(jalview.datamodel.DBRefSource.PDB + "|" + id
- + "|" + 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());
- }
-
- /**
- * obtain human glyoxalase chain A sequence
- */
- @Override
- public String getTestQuery()
- {
- return "1QIPA";
- }
-
- @Override
- public String getDbName()
- {
- return "PDB"; // getDbSource();
- }
-
- @Override
- public int getTier()
- {
- return 0;
- }
-
- public static String getCurrentDefaultFormat()
- {
- return currentDefaultFormat;
- }
-
- public static void setCurrentDefaultFormat(String currentDefaultFomart)
- {
- Pdb.currentDefaultFormat = currentDefaultFomart;
- }
-
- /**
- * Returns a descriptor for suitable feature display settings with
- * <ul>
- * <li>ResNums or insertions features visible</li>
- * <li>insertions features coloured red</li>
- * <li>ResNum features coloured by label</li>
- * <li>Insertions displayed above (on top of) ResNums</li>
- * </ul>
- */
- @Override
- public FeatureSettingsModelI getFeatureColourScheme()
- {
- return new PDBFeatureSettings();
- }
-}
git://source.jalview.org / jalview.git / blobdiff