X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=61c5c0458fe4fa7090d3d2362e8659e3d7187ddf;hb=27c7530b396a5dd1addc4ab346ef2823d34fb335;hp=7586856ab95c47b59c996e6e041b2f72304ed7f9;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 7586856..61c5c04 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,218 +1,283 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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 .
- */
-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, 5);
- id = queries.substring(0, 4);
- }
- if (!isValidReference(id))
- {
- System.err.println("Ignoring invalid pdb query: '" + id + "'");
- stopQuery();
- return null;
- }
- 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";
- }
-
- public String getDbName()
- {
- return "PDB"; // getDbSource();
- }
-
-}
+
+/*
+ * 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 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";
+
+ /*
+ * (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 = 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("_")))))
+ {
+ 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());
+ }
+
+ /**
+ * 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();
+ }
+}