X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=757ab834292d4346c5e09c24a8da26df93c38e6a;hb=8b27085fa7fc5f2877e078421284c2636b85b8c6;hp=af8676f57ec7631e2447ac5d435e8653dee8f0f5;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index af8676f..757ab83 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,56 +1,70 @@
+
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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 .
+ * 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.datamodel.Alignment;
+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.util.ArrayList;
+import java.util.List;
import java.util.Vector;
-import MCview.PDBChain;
-import MCview.PDBfile;
-
import com.stevesoft.pat.Regex;
-import jalview.datamodel.AlignmentI;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
/**
* @author JimP
*
*/
-public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
+public class Pdb extends EbiFileRetrievedProxy
{
public Pdb()
{
super();
- addDbSourceProperty(DBRefSource.PROTSEQDB);
}
+ 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
@@ -62,6 +76,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
+ @Override
public Regex getAccessionValidator()
{
return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
@@ -72,6 +87,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
+ @Override
public String getDbSource()
{
return DBRefSource.PDB;
@@ -82,6 +98,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getDbVersion()
*/
+ @Override
public String getDbVersion()
{
return "0";
@@ -92,9 +109,10 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
*
* @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;
@@ -118,8 +136,12 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
stopQuery();
return null;
}
+ Type pdbFileFormat = StructureImportSettings
+ .getDefaultStructureFileFormat();
+ String ext = "." + pdbFileFormat.getExtension();
EBIFetchClient ebi = new EBIFetchClient();
- file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
+ file = ebi.fetchDataAsFile("pdb:" + id, pdbFileFormat.getFormat(), ext)
+ .getAbsolutePath();
stopQuery();
if (file == null)
{
@@ -127,63 +149,90 @@ 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++)
+ // convert Type.PDB/MMCIF to FileFormat.PDB/MMCIF
+ // todo get rid of Type?
+ FileFormatI fileFormat = FileFormat.valueOf(pdbFileFormat.toString());
+ pdbAlignment = new FormatAdapter().readFile(file,
+ DataSourceType.FILE, fileFormat);
+ if (pdbAlignment != null)
{
- if (chain == null
- || ((PDBChain) pdbfile.chains.elementAt(i)).id
- .toUpperCase().equals(chain))
+ 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)
{
- 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());
+ pdbAlignment.deleteSequence(pdbcs);
+ if (pdbcs.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation aa : pdbcs.getAnnotation())
+ {
+ pdbAlignment.deleteAnnotation(aa);
+ }
+ }
}
}
- if (result.size() < 1)
+ if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
{
- throw new Exception("No PDB Records for " + id + " chain "
- + ((chain == null) ? "' '" : chain));
+ 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);
}
-
- 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 pdbAlignment;
}
/*
@@ -191,6 +240,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
+ @Override
public boolean isValidReference(String accession)
{
Regex r = getAccessionValidator();
@@ -198,13 +248,15 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
}
/**
- * obtain human glyoxalase chain A sequence
+ * human glyoxalase
*/
+ @Override
public String getTestQuery()
{
- return "1QIPA";
+ return "1QIP";
}
+ @Override
public String getDbName()
{
return "PDB"; // getDbSource();
@@ -215,4 +267,20 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
{
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();
+ }
}