X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=0004abe7068b971dece2c1e8b87224627fc909f8;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=887a7511068b36d9ccc6f96d7eef95b9ec19963a;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java index 887a751..0004abe 100755 --- a/src/jalview/datamodel/DBRefEntry.java +++ b/src/jalview/datamodel/DBRefEntry.java @@ -1,26 +1,54 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.datamodel; -public class DBRefEntry +import jalview.api.DBRefEntryI; +import jalview.util.DBRefUtils; +import jalview.util.MapList; + +import java.util.List; + +public class DBRefEntry implements DBRefEntryI { - String source = "", version = "", accessionId = ""; + /* + * the mapping to chromosome (genome) is held as an instance with + * source = speciesId + * version = assemblyId + * accessionId = "chromosome:" + chromosomeId + * map = mapping from sequence to reference assembly + */ + public static final String CHROMOSOME = "chromosome"; + + private String source = ""; + + private String version = ""; + + private String ucversion = ""; + + private String accessionId = ""; + + int sourceKey = Integer.MIN_VALUE; + + String canonicalSourceName; + /** * maps from associated sequence to the database sequence's coordinate system @@ -31,7 +59,12 @@ public class DBRefEntry { } - +/** + * + * @param source may not be null + * @param version may be null + * @param accessionId may be null + */ public DBRefEntry(String source, String version, String accessionId) { this(source, version, accessionId, null); @@ -40,46 +73,146 @@ public class DBRefEntry /** * * @param source - * canonical source (uppercase only) + * canonical source (turned to uppercase; cannot be null) * @param version - * (source dependent version string) + * (source dependent version string or null) * @param accessionId - * (source dependent accession number string) + * (source dependent accession number string or null) * @param map - * (mapping from local sequence numbering to source accession - * numbering) + * (mapping from local sequence numbering to source accession + * numbering or null) */ public DBRefEntry(String source, String version, String accessionId, Mapping map) { + this.source = source.toUpperCase(); - this.version = version; + setVersion(version); this.accessionId = accessionId; this.map = map; } - public DBRefEntry(DBRefEntry entry) + /** + * Clone an entry, this time not allowing any null fields except map. + * + */ + public DBRefEntry(DBRefEntryI entry) { - this( - (entry.source == null ? "" : new String(entry.source)), - (entry.version == null ? "" : new String(entry.version)), - (entry.accessionId == null ? "" : new String(entry.accessionId)), - (entry.map == null ? null : new Mapping(entry.map))); + this((entry.getSource() == null ? "" : new String(entry.getSource())), + (entry.getVersion() == null ? "" + : new String(entry.getVersion())), + (entry.getAccessionId() == null ? "" + : new String(entry.getAccessionId())), + (entry.getMap() == null ? null : new Mapping(entry.getMap()))); } - public boolean equals(DBRefEntry entry) + @Override + public boolean equals(Object o) { - if (entry == this) - return true; - if (entry == null) + // TODO should also override hashCode to ensure equal objects have equal + // hashcodes + + +// if (o == null || !(o instanceof DBRefEntry)) +// { +// return false; +// } +// DBRefEntry entry = (DBRefEntry) o; +// if (entry == this) +// { +// return true; +// } + Mapping em; + return (o != null && o instanceof DBRefEntry + && (o == this + || equalRef((DBRefEntry) o) + && (map == null) == ((em = ((DBRefEntry) o).map) == null) + && (map == null || map.equals(em)))); +// +// { +// return true; +// } +// return false; + } + + /** + * Answers true if this object is either equivalent to, or can be 'improved' + * by, the given entry. Specifically, answers true if + * + * + * @param other + * @return + */ + @Override + public boolean updateFrom(DBRefEntryI other) + { + if (other == null) + { return false; - if (equalRef(entry) - && ((map == null && entry.map == null) || (map != null - && entry.map != null && map.equals(entry.map)))) + } + if (other == this) { return true; } - return false; + + /* + * source must either match or be both null + */ + String otherSource = other.getSource(); + if ((source == null && otherSource != null) + || (source != null && otherSource == null) + || (source != null && !source.equalsIgnoreCase(otherSource))) + { + return false; + } + + /* + * accession id must either match or be both null + */ + String otherAccession = other.getAccessionId(); + if ((accessionId == null && otherAccession != null) + || (accessionId != null && otherAccession == null) + || (accessionId != null + && !accessionId.equalsIgnoreCase(otherAccession))) + { + return false; + } + + /* + * if my version is null, "0" or "source:0" then replace with other version, + * otherwise the versions have to match + */ + String otherVersion = other.getVersion(); + + if ((version == null || version.equals("0") || version.endsWith(":0")) + && otherVersion != null) + { + setVersion(otherVersion); + } + else + { + if (version != null && (otherVersion == null + || !version.equalsIgnoreCase(otherVersion))) + { + return false; + } + } + + /* + * if I have no mapping, take that of the other dbref + */ + if (map == null) + { + setMap(other.getMap()); + } + return true; } /** @@ -88,71 +221,88 @@ public class DBRefEntry * @param entry * @return true if source, accession and version are equal with those of entry */ - public boolean equalRef(DBRefEntry entry) + @Override + public boolean equalRef(DBRefEntryI entry) { + // TODO is this method and equals() not needed? if (entry == null) { return false; } if (entry == this) - return true; - if ((source != null && entry.source != null && source - .equalsIgnoreCase(entry.source)) - && (accessionId != null && entry.accessionId != null && accessionId - .equalsIgnoreCase(entry.accessionId)) - && (version != null && entry.version != null && version - .equalsIgnoreCase(entry.version))) { return true; } - return false; + + // BH 2019.01.25/2019.02.04 source cannot/should not be null. + // for example, StructureChooser has dbRef.getSource().equalsIgnoreCase... + + return (entry != null + && (source != null && entry.getSource() != null + && source.equalsIgnoreCase(entry.getSource())) + && (accessionId != null && entry.getAccessionId() != null + && accessionId.equalsIgnoreCase(entry.getAccessionId())) + && (version != null && entry.getVersion() != null + && version.equalsIgnoreCase(entry.getVersion()))); } + @Override public String getSource() { return source; } + public int getSourceKey() + { + return (sourceKey == Integer.MIN_VALUE ? (sourceKey = DBRefSource.getSourceKey(getCanonicalSourceName())) : sourceKey); + } + + /** + * can be null + */ + @Override public String getVersion() { return version; } + /** + * can be null + */ + @Override public String getAccessionId() { return accessionId; } - /** - * @param accessionId - * the accessionId to set - */ + @Override public void setAccessionId(String accessionId) { - this.accessionId = accessionId; + this.accessionId = accessionId; +// this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase(); } /** - * @param source - * the source to set + * CAUTION! allows setting source null or not uppercase! */ + @Override public void setSource(String source) { - this.source = source; + this.source = source; + +// this.source = (source == null ? "" : source).toUpperCase(); +// this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source); +// this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName); } - /** - * @param version - * the version to set - */ + @Override public void setVersion(String version) { this.version = version; + this.ucversion = (version == null ? null : version.toUpperCase()); } - /** - * @return the map - */ + @Override public Mapping getMap() { return map; @@ -160,7 +310,7 @@ public class DBRefEntry /** * @param map - * the map to set + * the map to set */ public void setMap(Mapping map) { @@ -181,4 +331,74 @@ public class DBRefEntry return ((source != null) ? source : "") + ":" + ((accessionId != null) ? accessionId : ""); } + + @Override + public String toString() + { + return getSrcAccString(); + } + + @Override + public boolean isPrimaryCandidate() + { + /* + * if a map is present, unless it is 1:1 and has no SequenceI mate, it cannot be a primary reference. + */ + if (map != null) + { + SequenceI mto = map.getTo(); + if (mto != null) + { + return false; + } + MapList ml = map.getMap(); + if (ml.getFromRatio() != ml.getToRatio() + || ml.getFromRatio() != 1) + { + return false; + } + // check map is between identical single contiguous ranges + List fromRanges, toRanges; + if ((fromRanges = ml.getFromRanges()).size() != 1 || (toRanges = ml.getToRanges()).size() != 1) + { + return false; + } + if (fromRanges.get(0)[0] != toRanges.get(0)[0] + || fromRanges.get(0)[1] != toRanges.get(0)[1]) + { + return false; + } + } + if (version == null) + { + // no version string implies the reference has not been verified at all. + return false; + } + + return DBRefSource.isPrimaryCandidate(ucversion); + } + + /** + * Mappings to chromosome are held with accessionId as "chromosome:id" + * + * @return + */ + public boolean isChromosome() + { + return accessionId != null && accessionId.startsWith(CHROMOSOME + ":"); + } + + /** + * stores the upper-case canonical name of the source for use in + * Sequence.getPrimaryDBRefs(). + * + * @author Bob Hanson + * + * @return + */ + public String getCanonicalSourceName() { + return (canonicalSourceName == null ? (canonicalSourceName = DBRefUtils.getCanonicalName(this.source)) : canonicalSourceName); + } + + }