X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=bc8d0cf1d1723e423b1d1d62608ce1a62d2bb6fa;hb=cbeb7ad59d51b468c54ca3db2a2a7693060a2509;hp=c35c8c26d4e8a94c5da9c9be4cc0dab036565d7d;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java index c35c8c2..bc8d0cf 100755 --- a/src/jalview/datamodel/DBRefEntry.java +++ b/src/jalview/datamodel/DBRefEntry.java @@ -1,47 +1,338 @@ -/* - * 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 - * 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. - * - * 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 - */ -package jalview.datamodel; - -public class DBRefEntry -{ - String source, version, accessionId; - - public DBRefEntry(String source, String version, String accessionId) - { - this.source = source; - this.version = version; - this.accessionId = accessionId; - } - - public String getSource() - { - return source; - } - - public String getVersion() - { - return version; - } - - public String getAccessionId() - { - return accessionId; - } - -} +/* + * 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.datamodel; + +import jalview.api.DBRefEntryI; + +import java.util.Arrays; +import java.util.List; + +public class DBRefEntry implements DBRefEntryI +{ + String source = ""; + + String version = ""; + + String accessionId = ""; + + /** + * maps from associated sequence to the database sequence's coordinate system + */ + Mapping map = null; + + public DBRefEntry() + { + + } + + public DBRefEntry(String source, String version, String accessionId) + { + this(source, version, accessionId, null); + } + + /** + * + * @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(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; + } + + @Override + public void setAccessionId(String accessionId) + { + this.accessionId = accessionId; + } + + @Override + public void setSource(String source) + { + this.source = source; + } + + @Override + public void setVersion(String version) + { + this.version = version; + } + + @Override + public Mapping getMap() + { + return map; + } + + /** + * @param map + * the map to set + */ + public void setMap(Mapping map) + { + this.map = map; + } + + 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; + } +}