X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=68dda8862ff7240c56d012e4b47ef6f41445e1d1;hb=2b6a2fdd887521f16ec777aab3126d6209f2a0a6;hp=631a79f3854d393ed11d5006269ac1d6abc5f462;hpb=e1d776602ceedd69cae590bcf85836d7b32c5993;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 631a79f..68dda88 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,50 +1,63 @@
+
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.Vector;
-
-import MCview.PDBChain;
-import MCview.PDBfile;
+import java.util.ArrayList;
+import java.util.List;
import com.stevesoft.pat.Regex;
-import jalview.datamodel.AlignmentI;
-import jalview.io.FormatAdapter;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
/**
* @author JimP
*
*/
-public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
+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();
- addDbSourceProperty(DBRefSource.PROTSEQDB);
}
/*
@@ -52,9 +65,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
+ @Override
public String getAccessionSeparator()
{
- // TODO Auto-generated method stub
return null;
}
@@ -63,6 +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]?)");
@@ -73,6 +87,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
+ @Override
public String getDbSource()
{
return DBRefSource.PDB;
@@ -83,6 +98,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getDbVersion()
*/
+ @Override
public String getDbVersion()
{
return "0";
@@ -93,34 +109,44 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
*/
+ @Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
- AlignmentI pdbfile = null;
- Vector result = new Vector();
+ AlignmentI pdbAlignment = null;
String chain = null;
String id = null;
- if (queries.indexOf(":") > -1)
+ if (queries.indexOf(COLON) > -1)
{
- chain = queries.substring(queries.indexOf(":") + 1);
- id = queries.substring(0, queries.indexOf(":"));
+ chain = queries.substring(queries.indexOf(COLON) + 1);
+ id = queries.substring(0, queries.indexOf(COLON));
}
else
{
id = queries;
}
- if (queries.length() > 4 && chain == null)
+
+ /*
+ * 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(4, 5);
- id = queries.substring(0, 4);
+ 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;
}
+ 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)
{
@@ -128,32 +154,36 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
}
try
{
-
- pdbfile = new FormatAdapter().readFile(file,
- jalview.io.AppletFormatAdapter.FILE, "PDB");
- if (pdbfile != null)
+ // todo get rid of Type and use FileFormatI instead?
+ // todo get rid of "ext" and just use "tmp"?
+ FileFormatI fileFormat = pdbFileFormat == Type.PDB ? FileFormat.PDB
+ : FileFormat.MMCif;
+ pdbAlignment = new FormatAdapter().readFile(file,
+ DataSourceType.FILE, fileFormat);
+ if (pdbAlignment != null)
{
- for (SequenceI pdbcs : pdbfile.getSequences())
+ List toremove = new ArrayList();
+ for (SequenceI pdbcs : pdbAlignment.getSequences())
{
String chid = null;
// Mapping map=null;
- for (PDBEntry pid : (Vector) pdbcs.getPDBId())
+ for (PDBEntry pid : pdbcs.getAllPDBEntries())
{
if (pid.getFile() == file)
{
- chid = (String) pid.getProperty().get("CHAIN");
+ 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());
+ // 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
/*
@@ -177,23 +207,38 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
}
else
{
- // remove this sequence from the alignment - since it's not from the
- // right chain
- pdbfile.deleteSequence(pdbcs);
+ // 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 (pdbfile == null || pdbfile.getHeight() < 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);
}
- return pdbfile;
+ return pdbAlignment;
}
/*
@@ -201,6 +246,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
+ @Override
public boolean isValidReference(String accession)
{
Regex r = getAccessionValidator();
@@ -208,13 +254,15 @@ 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();
@@ -225,4 +273,19 @@ 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();
+ }
}