X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=e4326d1ee4047c706a407a901369fbadb0d61773;hb=dce53361c4b6bb56dc8567ac77e85a2300a5458d;hp=5773171de3746a0a3c7fae129cf2392138d8eb39;hpb=08fbe7c3d40a4077ab519334952a079968c07cd1;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 5773171..e4326d1 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,191 +1,297 @@
-/**
- *
- */
-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 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.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();
+ }
+}