-/**\r
- * \r
- */\r
-package jalview.ws.dbsources;\r
-\r
-import jalview.datamodel.Alignment;\r
-import jalview.datamodel.DBRefEntry;\r
-import jalview.datamodel.DBRefSource;\r
-import jalview.datamodel.SequenceI;\r
-\r
-import java.io.BufferedInputStream;\r
-import java.io.InputStream;\r
-import java.io.InputStreamReader;\r
-import java.util.Hashtable;\r
-import java.util.Vector;\r
-\r
-import MCview.PDBChain;\r
-import MCview.PDBfile;\r
-\r
-import com.stevesoft.pat.Regex;\r
-\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.io.FileParse;\r
-import jalview.ws.ebi.EBIFetchClient;\r
-import jalview.ws.seqfetcher.DbSourceProxy;\r
-import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
-\r
-/**\r
- * @author JimP\r
- *\r
- */\r
-public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy\r
-{\r
- public Pdb() {\r
- super();\r
- addDbSourceProperty(DBRefSource.PROTSEQDB);\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getAccessionSeparator()\r
- */\r
- public String getAccessionSeparator()\r
- {\r
- // TODO Auto-generated method stub\r
- return null;\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getAccessionValidator()\r
- */\r
- public Regex getAccessionValidator()\r
- {\r
- return new Regex("[1-9][0-9A-Za-z]{3}[ _A-Za-z0-9]?");\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getDbSource()\r
- */\r
- public String getDbSource()\r
- {\r
- return DBRefSource.PDB;\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getDbVersion()\r
- */\r
- public String getDbVersion()\r
- {\r
- return "0";\r
- }\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])\r
- */\r
- public AlignmentI getSequenceRecords(String queries) throws Exception\r
- {\r
-\r
- Vector result = new Vector();\r
- String chain = null;\r
- String id = null;\r
- if (queries.indexOf(":") > -1)\r
- {\r
- chain = queries.substring(queries.indexOf(":") + 1);\r
- id = queries.substring(0, queries.indexOf(":"));\r
- }\r
- else\r
- {\r
- id = queries;\r
- }\r
- if (queries.length() > 4 && chain == null)\r
- {\r
- chain = queries.substring(4);\r
- id = queries.substring(0, 4);\r
- }\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw")\r
- .getAbsolutePath();\r
- stopQuery();\r
- if (file == null)\r
- {\r
- return null;\r
- }\r
- try\r
- {\r
- \r
- PDBfile pdbfile = new PDBfile(file,\r
- jalview.io.AppletFormatAdapter.FILE);\r
- for (int i = 0; i < pdbfile.chains.size(); i++)\r
- {\r
- if (chain == null\r
- || ((PDBChain) pdbfile.chains.elementAt(i)).id\r
- .toUpperCase().equals(chain))\r
- {\r
- PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);\r
- // Get the Chain's Sequence - who's dataset includes any special features added from the PDB file\r
- SequenceI sq = pdbchain.sequence;\r
- // Specially formatted name for the PDB chain sequences retrieved from the PDB\r
- sq.setName(jalview.datamodel.DBRefSource.PDB+"|" + id + "|" + sq.getName());\r
- // Might need to add more metadata to the PDBEntry object\r
- // like below\r
- /*\r
- * PDBEntry entry = new PDBEntry();\r
- // Construct the PDBEntry\r
- entry.setId(id);\r
- if (entry.getProperty() == null)\r
- entry.setProperty(new Hashtable());\r
- entry.getProperty().put("chains",\r
- pdbchain.id\r
- + "=" + sq.getStart()\r
- + "-" + sq.getEnd());\r
- sq.getDatasetSequence().addPDBId(entry);\r
- */\r
- // Add PDB DB Refs\r
- // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source\r
- // JBPNote - PDB DBRefEntry should also carry the chain and mapping information\r
- DBRefEntry dbentry = new DBRefEntry(getDbSource(),\r
- getDbVersion(), id + pdbchain.id);\r
- sq.addDBRef(dbentry);\r
- // and add seuqence to the retrieved set\r
- result.addElement(sq.deriveSequence());\r
- }\r
- }\r
-\r
- if (result.size() < 1)\r
- {\r
- throw new Exception("No PDB Records for " + id + " chain "\r
- + ((chain == null) ? " " : chain));\r
- }\r
- } catch (Exception ex) // Problem parsing PDB file\r
- {\r
- stopQuery();\r
- throw (ex);\r
- }\r
-\r
- SequenceI[] results = new SequenceI[result.size()];\r
- for (int i = 0, j = result.size(); i < j; i++)\r
- {\r
- results[i] = (SequenceI) result.elementAt(i);\r
- result.setElementAt(null, i);\r
- }\r
- return new Alignment(results);\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)\r
- */\r
- public boolean isValidReference(String accession)\r
- {\r
- Regex r = getAccessionValidator();\r
- return r.search(accession.trim());\r
- }\r
-\r
- /**\r
- * obtain human glyoxalase chain A sequence\r
- */\r
- public String getTestQuery()\r
- {\r
- return "1QIPA";\r
- }\r
-\r
-}\r
+/*
+ * 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.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<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(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
+ * <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