/*
* 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.util;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Hashtable;
import java.util.Map;
import java.util.Vector;
public class DBRefUtils
{
/**
* Utilities for handling DBRef objects and their collections.
*/
/**
*
* @param dbrefs
* Vector of DBRef objects to search
* @param sources
* String[] array of source DBRef IDs to retrieve
* @return Vector
*/
public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs,
String[] sources)
{
if (dbrefs == null)
{
return null;
}
if (sources == null)
{
return dbrefs;
}
Map srcs = new HashMap();
ArrayList res = new ArrayList();
for (int i = 0; i < sources.length; i++)
{
srcs.put(new String(sources[i]), new Integer(i));
}
for (int i = 0, j = dbrefs.length; i < j; i++)
{
if (srcs.containsKey(dbrefs[i].getSource()))
{
res.add(dbrefs[i]);
}
}
if (res.size() > 0)
{
DBRefEntry[] reply = new DBRefEntry[res.size()];
return res.toArray(reply);
}
res = null;
// there are probable memory leaks in the hashtable!
return null;
}
/**
* isDasCoordinateSystem
*
* @param string
* String
* @param dBRefEntry
* DBRefEntry
* @return boolean true if Source DBRefEntry is compatible with DAS
* CoordinateSystem name
*/
public static Hashtable DasCoordinateSystemsLookup = null;
public static boolean isDasCoordinateSystem(String string,
DBRefEntry dBRefEntry)
{
if (DasCoordinateSystemsLookup == null)
{
// TODO: Make a DasCoordinateSystemsLookup properties resource
// Initialise
DasCoordinateSystemsLookup = new Hashtable();
DasCoordinateSystemsLookup.put("pdbresnum",
jalview.datamodel.DBRefSource.PDB);
DasCoordinateSystemsLookup.put("uniprot",
jalview.datamodel.DBRefSource.UNIPROT);
DasCoordinateSystemsLookup.put("EMBL",
jalview.datamodel.DBRefSource.EMBL);
// DasCoordinateSystemsLookup.put("EMBL",
// jalview.datamodel.DBRefSource.EMBLCDS);
}
String coordsys = (String) DasCoordinateSystemsLookup.get(string
.toLowerCase());
if (coordsys != null)
{
return coordsys.equals(dBRefEntry.getSource());
}
return false;
}
public static Hashtable CanonicalSourceNameLookup = null;
/**
* look up source in an internal list of database reference sources and return
* the canonical jalview name for the source, or the original string if it has
* no canonical form.
*
* @param source
* @return canonical jalview source (one of jalview.datamodel.DBRefSource.*)
* or original source
*/
public static String getCanonicalName(String source)
{
if (CanonicalSourceNameLookup == null)
{
CanonicalSourceNameLookup = new Hashtable();
CanonicalSourceNameLookup.put("uniprotkb/swiss-prot",
jalview.datamodel.DBRefSource.UNIPROT);
CanonicalSourceNameLookup.put("uniprotkb/trembl",
jalview.datamodel.DBRefSource.UNIPROT);
CanonicalSourceNameLookup.put("pdb",
jalview.datamodel.DBRefSource.PDB);
}
String canonical = (String) CanonicalSourceNameLookup.get(source
.toLowerCase());
if (canonical == null)
{
return source;
}
return canonical;
}
/**
* find RefEntry corresponding to a particular pattern the equals method of
* each entry is used, from String attributes right down to Mapping
* attributes.
*
* @param ref
* Set of references to search
* @param entry
* pattern to collect - null any entry for wildcard match
* @return
*/
public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry)
{
return searchRefs(ref, entry,
matchDbAndIdAndEitherMapOrEquivalentMapList);
}
public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry,
DbRefComp comparator)
{
if (ref == null || entry == null)
{
return null;
}
Vector rfs = new Vector();
for (int i = 0; i < ref.length; i++)
{
if (comparator.matches(entry, ref[i]))
{
rfs.addElement(ref[i]);
}
}
// TODO Auto-generated method stub
if (rfs.size() > 0)
{
DBRefEntry[] rf = new DBRefEntry[rfs.size()];
rfs.copyInto(rf);
return rf;
}
return null;
}
public interface DbRefComp
{
public boolean matches(DBRefEntry refa, DBRefEntry refb);
}
/**
* match on all non-null fields in refa
*/
public static DbRefComp matchNonNullonA = new DbRefComp()
{
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
if (refa.getSource() == null
|| refb.getSource().equals(refa.getSource()))
{
if (refa.getVersion() == null
|| refb.getVersion().equals(refa.getVersion()))
{
if (refa.getAccessionId() == null
|| refb.getAccessionId().equals(refa.getAccessionId()))
{
if (refa.getMap() == null
|| (refb.getMap() != null && refb.getMap().equals(
refa.getMap())))
{
return true;
}
}
}
}
return false;
}
};
/**
* either field is null or field matches for all of source, version, accession
* id and map.
*/
public static DbRefComp matchEitherNonNull = new DbRefComp()
{
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
if ((refa.getSource() == null || refb.getSource() == null)
|| refb.getSource().equals(refa.getSource()))
{
if ((refa.getVersion() == null || refb.getVersion() == null)
|| refb.getVersion().equals(refa.getVersion()))
{
if ((refa.getAccessionId() == null || refb.getAccessionId() == null)
|| refb.getAccessionId().equals(refa.getAccessionId()))
{
if ((refa.getMap() == null || refb.getMap() == null)
|| (refb.getMap() != null && refb.getMap().equals(
refa.getMap())))
{
return true;
}
}
}
}
return false;
}
};
/**
* accession ID and DB must be identical. Version is ignored. Map is either
* not defined or is a match (or is compatible?)
*/
public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp()
{
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
if (refa.getSource() != null && refb.getSource() != null
&& refb.getSource().equals(refa.getSource()))
{
// We dont care about version
// if ((refa.getVersion()==null || refb.getVersion()==null)
// || refb.getVersion().equals(refa.getVersion()))
// {
if (refa.getAccessionId() != null && refb.getAccessionId() != null
|| refb.getAccessionId().equals(refa.getAccessionId()))
{
if ((refa.getMap() == null || refb.getMap() == null)
|| (refa.getMap() != null && refb.getMap() != null && refb
.getMap().equals(refa.getMap())))
{
return true;
}
}
}
return false;
}
};
/**
* accession ID and DB must be identical. Version is ignored. No map on either
* or map but no maplist on either or maplist of map on a is the complement of
* maplist of map on b.
*/
public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp()
{
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
if (refa.getSource() != null && refb.getSource() != null
&& refb.getSource().equals(refa.getSource()))
{
// We dont care about version
// if ((refa.getVersion()==null || refb.getVersion()==null)
// || refb.getVersion().equals(refa.getVersion()))
// {
if (refa.getAccessionId() != null && refb.getAccessionId() != null
|| refb.getAccessionId().equals(refa.getAccessionId()))
{
if ((refa.getMap() == null && refb.getMap() == null)
|| (refa.getMap() != null && refb.getMap() != null))
{
if ((refb.getMap().getMap() == null && refa.getMap().getMap() == null)
|| (refb.getMap().getMap() != null
&& refa.getMap().getMap() != null && refb
.getMap().getMap().getInverse()
.equals(refa.getMap().getMap())))
{
return true;
}
}
}
}
return false;
}
};
/**
* accession ID and DB must be identical. Version is ignored. No map on both
* or or map but no maplist on either or maplist of map on a is equivalent to
* the maplist of map on b.
*/
public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp()
{
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
if (refa.getSource() != null && refb.getSource() != null
&& refb.getSource().equals(refa.getSource()))
{
// We dont care about version
// if ((refa.getVersion()==null || refb.getVersion()==null)
// || refb.getVersion().equals(refa.getVersion()))
// {
if (refa.getAccessionId() != null && refb.getAccessionId() != null
|| refb.getAccessionId().equals(refa.getAccessionId()))
{
if (refa.getMap() == null && refb.getMap() == null)
{
return true;
}
if (refa.getMap() != null
&& refb.getMap() != null
&& ((refb.getMap().getMap() == null && refa.getMap()
.getMap() == null) || (refb.getMap().getMap() != null
&& refa.getMap().getMap() != null && refb
.getMap().getMap().equals(refa.getMap().getMap()))))
{
return true;
}
}
}
return false;
}
};
/**
* accession ID and DB must be identical. Version is ignored. No map on either
* or map but no maplist on either or maplist of map on a is equivalent to the
* maplist of map on b.
*/
public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp()
{
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
// System.err.println("Comparing A: "+refa.getSrcAccString()+(refa.hasMap()?" has map.":"."));
// System.err.println("Comparing B: "+refb.getSrcAccString()+(refb.hasMap()?" has map.":"."));
if (refa.getSource() != null && refb.getSource() != null
&& refb.getSource().equals(refa.getSource()))
{
// We dont care about version
// if ((refa.getVersion()==null || refb.getVersion()==null)
// || refb.getVersion().equals(refa.getVersion()))
// {
if (refa.getAccessionId() != null && refb.getAccessionId() != null
&& refb.getAccessionId().equals(refa.getAccessionId()))
{
if (refa.getMap() == null || refb.getMap() == null)
{
return true;
}
if ((refa.getMap() != null && refb.getMap() != null)
&& (refb.getMap().getMap() == null && refa.getMap()
.getMap() == null)
|| (refb.getMap().getMap() != null
&& refa.getMap().getMap() != null && (refb
.getMap().getMap().equals(refa.getMap().getMap()))))
{ // getMap().getMap().containsEither(false,refa.getMap().getMap())
return true;
}
}
}
return false;
}
};
/**
* used by file parsers to generate DBRefs from annotation within file (eg
* stockholm)
*
* @param dbname
* @param version
* @param acn
* @param seq
* where to anotate with reference
* @return parsed version of entry that was added to seq (if any)
*/
public static DBRefEntry parseToDbRef(SequenceI seq, String dbname,
String version, String acn)
{
DBRefEntry ref = null;
if (dbname != null)
{
String locsrc = jalview.util.DBRefUtils.getCanonicalName(dbname);
if (locsrc.equals(jalview.datamodel.DBRefSource.PDB))
{
// check for chaincode and mapping
// PFAM style stockhom PDB citation
com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
"([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)");
if (r.search(acn.trim()))
{
String pdbid = r.stringMatched(1);
String chaincode = r.stringMatched(2);
if (chaincode==null)
{
chaincode = " ";
}
String mapstart = r.stringMatched(3);
String mapend = r.stringMatched(4);
if (chaincode.equals(" "))
{
chaincode = "_";
}
// construct pdb ref.
ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
PDBEntry pdbr = new PDBEntry();
pdbr.setId(pdbid);
pdbr.setProperty(new Hashtable());
pdbr.getProperty().put("CHAIN", chaincode);
seq.addPDBId(pdbr);
} else {
System.err.println("Malformed PDB DR line:"+acn);
}
}
else
{
// default:
ref = new DBRefEntry(locsrc, version, acn);
}
}
if (ref != null)
{
seq.addDBRef(ref);
}
return ref;
}
}