From: jprocter Date: Sat, 17 Nov 2012 21:24:42 +0000 (+0000) Subject: return alignmentI created from pdbfile class directly to preserve all annotation X-Git-Tag: Jalview_2_9~265^2~5 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5730402f9459bf91e9eab40755433bc7c85a326d;p=jalview.git return alignmentI created from pdbfile class directly to preserve all annotation --- diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java index b432dff..219008d 100644 --- a/src/jalview/ws/dbsources/Pdb.java +++ b/src/jalview/ws/dbsources/Pdb.java @@ -20,6 +20,7 @@ package jalview.ws.dbsources; import jalview.datamodel.Alignment; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; +import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import java.util.Vector; @@ -30,6 +31,7 @@ import MCview.PDBfile; import com.stevesoft.pat.Regex; import jalview.datamodel.AlignmentI; +import jalview.io.FormatAdapter; import jalview.ws.ebi.EBIFetchClient; import jalview.ws.seqfetcher.DbSourceProxy; @@ -93,7 +95,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy */ public AlignmentI getSequenceRecords(String queries) throws Exception { - + AlignmentI pdbfile = null; Vector result = new Vector(); String chain = null; String id = null; @@ -127,45 +129,61 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy try { - PDBfile pdbfile = new PDBfile(file, - jalview.io.AppletFormatAdapter.FILE); - for (int i = 0; i < pdbfile.chains.size(); i++) + pdbfile = new FormatAdapter().readFile(file, + jalview.io.AppletFormatAdapter.FILE, "PDB"); + if (pdbfile != null) { - if (chain == null - || ((PDBChain) pdbfile.chains.elementAt(i)).id - .toUpperCase().equals(chain)) + for (SequenceI pdbcs : pdbfile.getSequences()) { - 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()); + String chid = null; + // Mapping map=null; + for (PDBEntry pid : (Vector) pdbcs.getPDBId()) + { + if (pid.getFile() == file) + { + chid = (String) pid.getProperty().get("CHAIN"); + + } + ; + + } + 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 + { + // remove this sequence from the alignment - since it's not from the + // right chain + pdbfile.deleteSequence(pdbcs); + } } } - - if (result.size() < 1) + if (pdbfile == null || pdbfile.getHeight() < 1) { throw new Exception("No PDB Records for " + id + " chain " + ((chain == null) ? "' '" : chain)); @@ -175,14 +193,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy 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); + return pdbfile; } /*