/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * 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 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 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
-import java.util.*;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
-import jalview.datamodel.*;
+import com.stevesoft.pat.Regex;
+/**
+ * Utilities for handling DBRef objects and their collections.
+ */
public class DBRefUtils
{
- /**
- * Utilities for handling DBRef objects and their collections.
+ /*
+ * lookup from lower-case form of a name to its canonical (standardised) form
*/
- /**
- *
- * @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;
- }
- Hashtable srcs = new Hashtable();
- Vector res = new Vector();
+ private static Map<String, String> canonicalSourceNameLookup = new HashMap<>();
- 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.addElement(dbrefs[i]);
- }
- }
+ public final static int DB_SOURCE = 1;
+ public final static int DB_VERSION = 2;
+ public final static int DB_ID = 4;
+ public final static int DB_MAP = 8;
- if (res.size() > 0)
- {
- DBRefEntry[] reply = new DBRefEntry[res.size()];
- for (int i = 0; i < res.size(); i++)
- {
- reply[i] = (DBRefEntry) res.elementAt(i);
- }
- return reply;
- }
- res = null;
- // there are probable memory leaks in the hashtable!
- return null;
- }
+ public final static int SEARCH_MODE_NO_MAP_NO_VERSION = DB_SOURCE | DB_ID;
+ public final static int SEARCH_MODE_FULL = DB_SOURCE | DB_VERSION | DB_ID | DB_MAP;
- /**
- * isDasCoordinateSystem
- *
- * @param string
- * String
- * @param dBRefEntry
- * DBRefEntry
- * @return boolean true if Source DBRefEntry is compatible with DAS
- * CoordinateSystem name
- */
- public static Hashtable DasCoordinateSystemsLookup = null;
+ static
+ {
+ // TODO load these from a resource file?
+ canonicalSourceNameLookup.put("uniprotkb/swiss-prot", DBRefSource.UNIPROT);
+ canonicalSourceNameLookup.put("uniprotkb/trembl", DBRefSource.UNIPROT);
- 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);
- }
+ // Ensembl values for dbname in xref REST service:
+ canonicalSourceNameLookup.put("uniprot/sptrembl", DBRefSource.UNIPROT);
+ canonicalSourceNameLookup.put("uniprot/swissprot", DBRefSource.UNIPROT);
- String coordsys = (String) DasCoordinateSystemsLookup.get(string
- .toLowerCase());
- if (coordsys != null)
- {
- return coordsys.equals(dBRefEntry.getSource());
- }
- return false;
- }
+ canonicalSourceNameLookup.put("pdb", DBRefSource.PDB);
+ canonicalSourceNameLookup.put("ensembl", DBRefSource.ENSEMBL);
+ // Ensembl Gn and Tr are for Ensembl genomic and transcript IDs as served
+ // from ENA.
+ canonicalSourceNameLookup.put("ensembl-tr", DBRefSource.ENSEMBL);
+ canonicalSourceNameLookup.put("ensembl-gn", DBRefSource.ENSEMBL);
- public static Hashtable CanonicalSourceNameLookup = null;
+ // guarantee we always have lowercase entries for canonical string lookups
+ for (String k : canonicalSourceNameLookup.keySet())
+ {
+ canonicalSourceNameLookup.put(k.toLowerCase(),
+ canonicalSourceNameLookup.get(k));
+ }
+ }
/**
- * 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.
+ * Returns those DBRefEntry objects whose source identifier (once converted to
+ * Jalview's canonical form) is in the list of sources to search for. Returns
+ * null if no matches found.
*
- * @param source
- * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*)
- * or original source
+ * @param dbrefs DBRefEntry objects to search
+ * @param sources array of sources to select
+ * @return
*/
- public static String getCanonicalName(String source)
+ public static List<DBRefEntry> selectRefs(List<DBRefEntry> dbrefs, String[] sources)
{
- 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;
+ if (dbrefs == null || sources == null)
+ {
+ return dbrefs;
+ }
+
+ // BH TODO (what?)
+ HashSet<String> srcs = new HashSet<>();
+ for (String src : sources)
+ {
+ srcs.add(src.toUpperCase());
+ }
+
+ int nrefs = dbrefs.size();
+ List<DBRefEntry> res = new ArrayList<>();
+ for (int ib = 0; ib < nrefs; ib++)
+ {
+ DBRefEntry dbr = dbrefs.get(ib);
+ String source = getCanonicalName(dbr.getSource());
+ if (srcs.contains(source.toUpperCase()))
+ {
+ res.add(dbr);
+ }
+ }
+ if (res.size() > 0)
+ {
+ // List<DBRefEntry> reply = new DBRefEntry[res.size()];
+ return res;// .toArray(reply);
+ }
+ return null;
+ }
+
+ private static boolean selectRefsBS(List<DBRefEntry> dbrefs, int sourceKeys, BitSet bsSelect)
+ {
+ if (dbrefs == null || sourceKeys == 0)
+ {
+ return false;
+ }
+ for (int i = 0, n = dbrefs.size(); i < n; i++)
+ {
+ DBRefEntry dbr = dbrefs.get(i);
+ if ((dbr.getSourceKey() & sourceKeys) != 0)
+ {
+ bsSelect.clear(i);
+ }
+ }
+ return !bsSelect.isEmpty();
}
/**
- * find RefEntry corresponding to a particular pattern the equals method of
- * each entry is used, from String attributes right down to Mapping
- * attributes.
+ * Returns a (possibly empty) list of those references that match the given
+ * entry, according to the given comparator.
*
- * @param ref
- * Set of references to search
+ * @param refs
+ * an array of database references to search
* @param entry
- * pattern to collect - null any entry for wildcard match
+ * an entry to compare against
+ * @param comparator
* @return
*/
- public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry)
- {
- return searchRefs(ref, entry,
- matchDbAndIdAndEitherMapOrEquivalentMapList);
- }
-
- public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry,
+ static List<DBRefEntry> searchRefs(DBRefEntry[] refs, DBRefEntry entry,
DbRefComp comparator)
{
- if (ref == null || entry == null)
- return null;
- Vector rfs = new Vector();
- for (int i = 0; i < ref.length; i++)
+ List<DBRefEntry> rfs = new ArrayList<>();
+ if (refs == null || entry == null)
{
- if (comparator.matches(entry, ref[i]))
- {
- rfs.addElement(ref[i]);
- }
+ return rfs;
}
- // TODO Auto-generated method stub
- if (rfs.size() > 0)
+ for (int i = 0; i < refs.length; i++)
{
- DBRefEntry[] rf = new DBRefEntry[rfs.size()];
- rfs.copyInto(rf);
- return rf;
+ if (comparator.matches(entry, refs[i]))
+ {
+ rfs.add(refs[i]);
+ }
}
- return null;
+ return rfs;
}
- public interface DbRefComp
- {
- public boolean matches(DBRefEntry refa, DBRefEntry refb);
- }
+ /**
+ * 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 (source == null)
+ {
+ return null;
+ }
+ String canonical = canonicalSourceNameLookup.get(source.toLowerCase());
+ return canonical == null ? source : canonical;
+ }
- /**
- * 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;
- }
- };
+ /**
+ * Returns a (possibly empty) list of those references that match the given
+ * entry. Currently uses a comparator which matches if
+ * <ul>
+ * <li>database sources are the same</li>
+ * <li>accession ids are the same</li>
+ * <li>both have no mapping, or the mappings are the same</li>
+ * </ul>
+ *
+ * @param ref Set of references to search
+ * @param entry pattern to match
+ * @param mode SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION optional
+ * @return
+ */
+ public static List<DBRefEntry> searchRefs(List<DBRefEntry> ref, DBRefEntry entry, int mode) {
+ return searchRefs(ref, entry, matchDbAndIdAndEitherMapOrEquivalentMapList, mode);
+ }
- /**
- * 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;
- }
- };
+ /**
+ * Returns a list of those references that match the given accession id
+ * <ul>
+ * <li>database sources are the same</li>
+ * <li>accession ids are the same</li>
+ * <li>both have no mapping, or the mappings are the same</li>
+ * </ul>
+ *
+ * @param refs Set of references to search
+ * @param accId accession id to match
+ * @return
+ */
+ public static List<DBRefEntry> searchRefs(List<DBRefEntry> refs, String accId) {
+ List<DBRefEntry> rfs = new ArrayList<>();
+ if (refs == null || accId == null) {
+ return rfs;
+ }
+ for (int i = 0, n = refs.size(); i < n; i++) {
+ DBRefEntry e = refs.get(i);
+ if (accId.equals(e.getAccessionId())) {
+ rfs.add(e);
+ }
+ }
+ return rfs;
+// return searchRefs(refs, new DBRefEntry("", "", accId), matchId, SEARCH_MODE_FULL);
+ }
- /**
- * 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;
- }
- };
+ /**
+ * Returns a (possibly empty) list of those references that match the given
+ * entry, according to the given comparator.
+ *
+ * @param refs an array of database references to search
+ * @param entry an entry to compare against
+ * @param comparator
+ * @param mode SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION
+ * optional
+ * @return
+ */
+ static List<DBRefEntry> searchRefs(List<DBRefEntry> refs, DBRefEntry entry, DbRefComp comparator, int mode) {
+ List<DBRefEntry> rfs = new ArrayList<>();
+ if (refs == null || entry == null) {
+ return rfs;
+ }
+ for (int i = 0, n = refs.size(); i < n; i++) {
+ DBRefEntry e = refs.get(i);
+ if (comparator.matches(entry, e, SEARCH_MODE_FULL)) {
+ rfs.add(e);
+ }
+ }
+ return rfs;
+ }
- /**
- * 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;
- }
- };
+ interface DbRefComp {
+ default public boolean matches(DBRefEntry refa, DBRefEntry refb) {
+ return matches(refa, refb, SEARCH_MODE_FULL);
+ };
- /**
- * 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 boolean matches(DBRefEntry refa, DBRefEntry refb, int mode);
+ }
+
+ /**
+ * match on all non-null fields in refa
+ */
+ // TODO unused - remove? would be broken by equating "" with null
+ public static DbRefComp matchNonNullonA = new DbRefComp() {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
+ if ((mode & DB_SOURCE) != 0 &&
+ (refa.getSource() == null || DBRefUtils.getCanonicalName(refb.getSource())
+ .equals(DBRefUtils.getCanonicalName(refa.getSource())))) {
+ if ((mode & DB_VERSION) != 0 &&
+ (refa.getVersion() == null || refb.getVersion().equals(refa.getVersion()))) {
+ if ((mode & DB_ID) != 0 &&
+ (refa.getAccessionId() == null || refb.getAccessionId().equals(refa.getAccessionId()))) {
+ if ((mode & DB_MAP) != 0 &&
+ (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.
+ */
+ // TODO unused - remove?
+ public static DbRefComp matchEitherNonNull = new DbRefComp() {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
+ if (nullOrEqualSource(refa.getSource(), refb.getSource())
+ && nullOrEqual(refa.getVersion(), refb.getVersion())
+ && nullOrEqual(refa.getAccessionId(), refb.getAccessionId())
+ && nullOrEqual(refa.getMap(), refb.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?)
+ */
+ // TODO unused - remove?
+ public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp() {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
+ if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource())
+ .equals(DBRefUtils.getCanonicalName(refa.getSource()))) {
+ // We dont care about version
+ if (refa.getAccessionId() != null && refb.getAccessionId() != null
+ // FIXME should be && not || here?
+ || 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.
+ */
+ // TODO unused - remove?
+ public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp() {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
+ if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource())
+ .equals(DBRefUtils.getCanonicalName(refa.getSource()))) {
+ // We dont care about version
+ 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.
+ */
+ // TODO unused - remove?
+ public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp() {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
+ if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource())
+ .equals(DBRefUtils.getCanonicalName(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, or null on a. 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()
+ {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
+ {
+ if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource())
+ .equals(DBRefUtils.getCanonicalName(refa.getSource())))
+ {
+ // We dont care about version
+ if (refa.getAccessionId() == null || refa.getAccessionId().equals(refb.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;
+ }
+ };
+
+ /**
+ * Returns the (possibly empty) list of those supplied dbrefs which have the
+ * specified source database, with a case-insensitive match of source name
+ *
+ * @param dbRefs
+ * @param source
+ * @return
*/
- public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp()
+ public static List<DBRefEntry> searchRefsForSource(DBRefEntry[] dbRefs,
+ String source)
{
- public boolean matches(DBRefEntry refa, DBRefEntry refb)
+ List<DBRefEntry> matches = new ArrayList<>();
+ if (dbRefs != null && source != null)
{
- if (refa.getSource() != null && refb.getSource() != null
- && refb.getSource().equals(refa.getSource()))
+ for (DBRefEntry dbref : dbRefs)
{
- // 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 (source.equalsIgnoreCase(dbref.getSource()))
{
- 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;
- }
+ matches.add(dbref);
}
}
- return false;
}
- };
+ return matches;
+ }
- /**
- * 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()
+ private static Regex PARSE_REGEX;
+
+ private static Regex getParseRegex()
{
- public boolean matches(DBRefEntry refa, DBRefEntry refb)
+ return (PARSE_REGEX == null ? PARSE_REGEX = Platform.newRegex(
+ "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)", null)
+ : PARSE_REGEX);
+ }
+ /**
+ * Parses a DBRefEntry and adds it to the sequence, also a PDBEntry if the
+ * database is PDB.
+ * <p>
+ * Used by file parsers to generate DBRefs from annotation within file (eg
+ * Stockholm)
+ *
+ * @param dbname
+ * @param version
+ * @param acn
+ * @param seq where to annotate 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 = DBRefUtils.getCanonicalName(dbname);
+ if (locsrc.equals(DBRefSource.PDB)) {
+ /*
+ * Check for PFAM style stockhom PDB accession id citation e.g. "1WRI A; 7-80;"
+ */
+ Regex r = getParseRegex();
+ 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.setType(PDBEntry.Type.PDB);
+ pdbr.setChainCode(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;
+ }
+
+ /**
+ * Returns true if either object is null, or they are equal
+ *
+ * @param o1
+ * @param o2
+ * @return
+ */
+ public static boolean nullOrEqual(Object o1, Object o2) {
+ if (o1 == null || o2 == null) {
+ return true;
+ }
+ return o1.equals(o2);
+ }
+
+ /**
+ * canonicalise source string before comparing. null is always wildcard
+ *
+ * @param o1 - null or source string to compare
+ * @param o2 - null or source string to compare
+ * @return true if either o1 or o2 are null, or o1 equals o2 under
+ * DBRefUtils.getCanonicalName
+ * (o1).equals(DBRefUtils.getCanonicalName(o2))
+ */
+ public static boolean nullOrEqualSource(String o1, String o2) {
+ if (o1 == null || o2 == null) {
+ return true;
+ }
+ return DBRefUtils.getCanonicalName(o1).equals(DBRefUtils.getCanonicalName(o2));
+ }
+
+ /**
+ * Selects just the DNA or protein references from a set of references
+ *
+ * @param selectDna if true, select references to 'standard' DNA databases, else
+ * to 'standard' peptide databases
+ * @param refs a set of references to select from
+ * @return
+ */
+ public static List<DBRefEntry> selectDbRefs(boolean selectDna, List<DBRefEntry> refs) {
+ return selectRefs(refs, selectDna ? DBRefSource.DNACODINGDBS : DBRefSource.PROTEINDBS);
+ // could attempt to find other cross
+ // refs here - ie PDB xrefs
+ // (not dna, not protein seq)
+ }
+
+ /**
+ * Returns the (possibly empty) list of those supplied dbrefs which have the
+ * specified source database, with a case-insensitive match of source name
+ *
+ * @param dbRefs
+ * @param source
+ * @return
+ */
+ public static List<DBRefEntry> searchRefsForSource(List<DBRefEntry> dbRefs, String source) {
+ List<DBRefEntry> matches = new ArrayList<>();
+ if (dbRefs != null && source != null) {
+ for (DBRefEntry dbref : dbRefs) {
+ if (source.equalsIgnoreCase(dbref.getSource())) {
+ matches.add(dbref);
+ }
+ }
+ }
+ return matches;
+ }
+
+ /**
+ * promote direct database references to primary for nucleotide or protein
+ * sequences if they have an appropriate primary ref
+ * <table>
+ * <tr>
+ * <th>Seq Type</th>
+ * <th>Primary DB</th>
+ * <th>Direct which will be promoted</th>
+ * </tr>
+ * <tr align=center>
+ * <td>peptides</td>
+ * <td>Ensembl</td>
+ * <td>Uniprot</td>
+ * </tr>
+ * <tr align=center>
+ * <td>peptides</td>
+ * <td>Ensembl</td>
+ * <td>Uniprot</td>
+ * </tr>
+ * <tr align=center>
+ * <td>dna</td>
+ * <td>Ensembl</td>
+ * <td>ENA</td>
+ * </tr>
+ * </table>
+ *
+ * @param sequence
+ */
+ public static void ensurePrimaries(SequenceI sequence, List<DBRefEntry> pr) {
+ if (pr.size() == 0) {
+ // nothing to do
+ return;
+ }
+ int sstart = sequence.getStart();
+ int send = sequence.getEnd();
+ boolean isProtein = sequence.isProtein();
+ BitSet bsSelect = new BitSet();
+
+// List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
+// {
+
+// List<DBRefEntry> selddfs = selectDbRefs(!isprot, sequence.getDBRefs());
+// if (selfs == null || selfs.size() == 0)
+// {
+// // nothing to do
+// return;
+// }
+
+ List<DBRefEntry> dbrefs = sequence.getDBRefs();
+ bsSelect.set(0, dbrefs.size());
+
+ if (!selectRefsBS(dbrefs, isProtein ? DBRefSource.PROTEIN_MASK : DBRefSource.DNA_CODING_MASK, bsSelect))
{
- 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;
}
- };
- /**
- * 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*;([0-9]+)-([0-9]+)");
- if (r.search(acn.trim()))
+// selfs.addAll(selfArray);
+// }
+
+ // filter non-primary refs
+ for (int ip = pr.size(); --ip >= 0;) {
+ DBRefEntry p = pr.get(ip);
+ for (int i = bsSelect.nextSetBit(0); i >= 0; i = bsSelect.nextSetBit(i + 1)) {
+ if (dbrefs.get(i) == p)
{
- String pdbid = r.stringMatched(1);
- String chaincode = r.stringMatched(2);
- 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);
- seq.addPDBId(pdbr);
+ bsSelect.clear(i);
}
- }
- else
+ }
+// while (selfs.contains(p))
+// {
+// selfs.remove(p);
+// }
+ }
+// List<DBRefEntry> toPromote = new ArrayList<DBRefEntry>();
+
+ for (int ip = pr.size(), keys = 0; --ip >= 0 && keys != DBRefSource.PRIMARY_MASK;) {
+ DBRefEntry p = pr.get(ip);
+ if (isProtein) {
+ switch (getCanonicalName(p.getSource())) {
+ case DBRefSource.UNIPROT:
+ keys |= DBRefSource.UNIPROT_MASK;
+ break;
+ case DBRefSource.ENSEMBL:
+ keys |= DBRefSource.ENSEMBL_MASK;
+ break;
+ }
+ } else {
+ // TODO: promote transcript refs ??
+ }
+ if (keys == 0 || !selectRefsBS(dbrefs, keys, bsSelect))
{
- // default:
- ref = new DBRefEntry(locsrc, version, acn);
+ return;
}
- }
- if (ref != null)
- {
- seq.addDBRef(ref);
- }
- return ref;
- }
+// if (candidates != null)
+ {
+ for (int ic = bsSelect.nextSetBit(0); ic >= 0; ic = bsSelect.nextSetBit(ic + 1))
+// for (int ic = 0, n = candidates.size(); ic < n; ic++)
+ {
+ DBRefEntry cand = dbrefs.get(ic);// candidates.get(ic);
+ if (cand.hasMap()) {
+ Mapping map = cand.getMap();
+ SequenceI cto = map.getTo();
+ if (cto != null && cto != sequence) {
+ // can't promote refs with mappings to other sequences
+ continue;
+ }
+ MapList mlist = map.getMap();
+ if (mlist.getFromLowest() != sstart && mlist.getFromHighest() != send) {
+ // can't promote refs with mappings from a region of this sequence
+ // - eg CDS
+ continue;
+ }
+ }
+ // and promote - not that version must be non-null here,
+ // as p must have passed isPrimaryCandidate()
+ cand.setVersion(p.getVersion() + " (promoted)");
+ bsSelect.clear(ic);
+ // selfs.remove(cand);
+// toPromote.add(cand);
+ if (!cand.isPrimaryCandidate()) {
+ System.out.println("Warning: Couldn't promote dbref " + cand.toString() + " for sequence "
+ + sequence.toString());
+ }
+ }
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff