X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=b7d55592f0cbc19059a570144ae8f7cd9fe68972;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=d94e234f7833d7dcf5358b9707738bb58f892ba4;hpb=c4ac57368086aeed8330c598ed6d0f6f83a6f625;p=jalview.git
diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index d94e234..b7d5559 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -1,20 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
@@ -28,12 +30,15 @@ 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
+ *
+ * @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)
+ public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs,
+ String[] sources)
{
if (dbrefs == null)
{
@@ -68,91 +73,113 @@ public class DBRefUtils
return reply;
}
res = null;
- // there are probable memory leaks in the hashtable!
+ // 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
+ *
+ * @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)
+ DBRefEntry dBRefEntry)
{
if (DasCoordinateSystemsLookup == null)
- { // Initialise
+ {
+ // TODO: Make a DasCoordinateSystemsLookup properties resource
+ // Initialise
DasCoordinateSystemsLookup = new Hashtable();
DasCoordinateSystemsLookup.put("pdbresnum",
- jalview.datamodel.DBRefSource.PDB);
+ jalview.datamodel.DBRefSource.PDB);
DasCoordinateSystemsLookup.put("uniprot",
- jalview.datamodel.DBRefSource.UNIPROT);
+ jalview.datamodel.DBRefSource.UNIPROT);
DasCoordinateSystemsLookup.put("EMBL",
jalview.datamodel.DBRefSource.EMBL);
- //DasCoordinateSystemsLookup.put("EMBL",
- // jalview.datamodel.DBRefSource.EMBLCDS);
+ // DasCoordinateSystemsLookup.put("EMBL",
+ // jalview.datamodel.DBRefSource.EMBLCDS);
}
- String coordsys = (String) DasCoordinateSystemsLookup.get(string.
- toLowerCase());
+ String coordsys = (String) DasCoordinateSystemsLookup.get(string
+ .toLowerCase());
if (coordsys != null)
{
return coordsys.equals(dBRefEntry.getSource());
}
return false;
}
- public static Hashtable CanonicalSourceNameLookup=null;
+
+ 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.
+ * 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
+ * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*)
+ * or original source
*/
public static String getCanonicalName(String source)
{
- if (CanonicalSourceNameLookup==null) {
+ 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);
+ 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)
+ 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
+ * 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);
+ return searchRefs(ref, entry,
+ matchDbAndIdAndEitherMapOrEquivalentMapList);
}
- public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry, DbRefComp comparator)
+
+ public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry,
+ DbRefComp comparator)
{
- if (ref==null || entry==null)
+ if (ref == null || entry == null)
return null;
Vector rfs = new Vector();
- for (int i=0; i0)
+ if (rfs.size() > 0)
{
DBRefEntry[] rf = new DBRefEntry[rfs.size()];
rfs.copyInto(rf);
@@ -160,185 +187,274 @@ public class DBRefUtils
}
return null;
}
- public interface DbRefComp {
+
+ 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)
{
- 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.getSource()==null || refb.getSource().equals(refa.getSource()))
+ if (refa.getMap() == null
+ || (refb.getMap() != null && refb.getMap().equals(
+ refa.getMap())))
{
- 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 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()
+ }
+ }
+ 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)
{
- 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.getSource()==null || refb.getSource()==null)
- || refb.getSource().equals(refa.getSource()))
+ if ((refa.getMap() == null || refb.getMap() == null)
+ || (refb.getMap() != null && refb.getMap().equals(
+ refa.getMap())))
{
- 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 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()
+ }
+ }
+ 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)
{
- 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())))
{
- 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;
+ return true;
}
- };
- /**
- * 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()
+ }
+ }
+ 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)
{
- public boolean matches(DBRefEntry refa, DBRefEntry refb)
- {
- if (refa.getSource()!=null && refb.getSource()!=null
- && refb.getSource().equals(refa.getSource()))
+ 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())))
{
- // 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;
+ 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;
}
- };
- /**
- * 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()
+ }
+ }
+ 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)
{
- 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)
{
- 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;
+ 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;
}
- };
- /**
- * 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()
+ }
+ }
+ 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)
{
- public boolean matches(DBRefEntry refa, DBRefEntry refb)
+ 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)
{
- 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;
+ 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;
+ }
+
}