X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=f7837f75c0b8fd7a563b8b6f9bef3755ab18bd82;hb=2b3ff3507854925d5bbaf4ad031bf020af176d47;hp=8bbb5f7b58a100f0fbe5ba31b317d351a36c8a8c;hpb=385e63c78d289d4beae9c1ad2b187c0ea311ffbc;p=jalview.git diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java index 8bbb5f7..f7837f7 100755 --- a/src/jalview/datamodel/DBRefEntry.java +++ b/src/jalview/datamodel/DBRefEntry.java @@ -1,119 +1,334 @@ /* - * 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 ($$Version-Rel$$) + * 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. - * - * 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.datamodel; -public class DBRefEntry +import jalview.api.DBRefEntryI; + +import java.util.Arrays; +import java.util.List; + +public class DBRefEntry implements DBRefEntryI { - String source="", version="", accessionId=""; + String source = "", version = "", accessionId = ""; + /** * maps from associated sequence to the database sequence's coordinate system */ - Mapping map=null; - public DBRefEntry() { - + Mapping map = null; + + public DBRefEntry() + { + } + public DBRefEntry(String source, String version, String accessionId) { this(source, version, accessionId, null); } - public DBRefEntry(String source, String version, String accessionId, Mapping map) { - this.source = source; + + /** + * + * @param source + * canonical source (uppercase only) + * @param version + * (source dependent version string) + * @param accessionId + * (source dependent accession number string) + * @param map + * (mapping from local sequence numbering to source accession + * numbering) + */ + public DBRefEntry(String source, String version, String accessionId, + Mapping map) + { + this.source = source.toUpperCase(); this.version = version; this.accessionId = accessionId; this.map = map; } - public DBRefEntry(DBRefEntry entry) - { - this(new String(entry.source), new String(entry.version), new String(entry.accessionId), new Mapping(entry.map)); - } - public boolean equals(DBRefEntry entry) { - if (entry==this) - return true; - if (entry==null) - return false; - if ((source!=null && entry.source!=null && source.equals(entry.source)) - && - (accessionId!=null && entry.accessionId!=null && accessionId.equals(entry.accessionId)) - && - (version!=null && entry.version!=null && version.equals(entry.version)) - && - ((map==null && entry.map==null) || (map!=null && entry.map!=null && map.equals(entry.map)))) { - return true; - } + + public DBRefEntry(DBRefEntryI entry) + { + 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()))); + } + + @Override + public boolean equals(Object o) + { + // 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; + } + if (equalRef(entry) && ((map == null && entry.map == null) + || (map != null && entry.map != null && map.equals(entry.map)))) + { + 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 (other == this) + { + return true; + } + + /* + * 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; + } + + /** + * test for similar DBRef attributes, except for the map object. + * + * @param entry + * @return true if source, accession and version are equal with those of 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 (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()))) + { + return true; + } + return false; } + + @Override public String getSource() { return source; } + @Override public String getVersion() { return version; } + @Override public String getAccessionId() { return accessionId; } -/** - * @param accessionId the accessionId to set - */ -public void setAccessionId(String accessionId) { + + @Override + public void setAccessionId(String accessionId) + { this.accessionId = accessionId; -} -/** - * @param source the source to set - */ -public void setSource(String source) { + } + + @Override + public void setSource(String source) + { this.source = source; -} -/** - * @param version the version to set - */ -public void setVersion(String version) { + } + + @Override + public void setVersion(String version) + { this.version = version; -} -/** - * @return the map - */ -public Mapping getMap() { + } + + @Override + public Mapping getMap() + { return map; -} -/** - * @param map the map to set - */ -public void setMap(Mapping map) { + } + + /** + * @param map + * the map to set + */ + public void setMap(Mapping map) + { this.map = map; -} -public boolean hasMap() -{ - // TODO Auto-generated method stub - return map!=null; -} -/** - * - * @return source+":"+accessionId - */ -public String getSrcAccString() -{ - return ((source!=null) ? source : "") - + ":" + ((accessionId!=null) ? accessionId : ""); -} + } + + public boolean hasMap() + { + return map != null; + } + + /** + * + * @return source+":"+accessionId + */ + public String getSrcAccString() + { + 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) + { + if (map.getTo() != null) + { + return false; + } + if (map.getMap().getFromRatio() != map.getMap().getToRatio() + || map.getMap().getFromRatio() != 1) + { + return false; + } + // check map is between identical single contiguous ranges + List fromRanges = map.getMap().getFromRanges(); + List toRanges = map.getMap().getToRanges(); + if (fromRanges.size() != 1 || toRanges.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; + } + // tricky - this test really needs to search the sequence's set of dbrefs to + // see if there is a primary reference that derived this reference. + String ucv = version.toUpperCase(); + for (String primsrc : Arrays.asList(DBRefSource.allSources())) + { + if (ucv.startsWith(primsrc.toUpperCase())) + { + // by convention, many secondary references inherit the primary + // reference's + // source string as a prefix for any version information from the + // secondary reference. + return false; + } + } + return true; + } }