X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=738c4dc831caf71090ddf09bd57ff458f468be44;hb=0ebcd487f08f9873987d9a32edce7df47aa27927;hp=1fd52c36c7a802a487b9862495ca03c548e22ab5;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java index 1fd52c3..738c4dc 100755 --- a/src/jalview/datamodel/DBRefEntry.java +++ b/src/jalview/datamodel/DBRefEntry.java @@ -1,26 +1,32 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * 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. + * 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 . + * 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; -public class DBRefEntry +import jalview.api.DBRefEntryI; + +public class DBRefEntry implements DBRefEntryI { String source = "", version = "", accessionId = ""; + private int startRes, endRes; /** * maps from associated sequence to the database sequence's coordinate system */ @@ -31,6 +37,7 @@ public class DBRefEntry } + public DBRefEntry(String source, String version, String accessionId) { this(source, version, accessionId, null); @@ -57,21 +64,30 @@ public class DBRefEntry this.map = map; } - public DBRefEntry(DBRefEntry entry) + 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) { + // 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 (entry == null) - return false; + } if (equalRef(entry) && ((map == null && entry.map == null) || (map != null && entry.map != null && map.equals(entry.map)))) @@ -82,76 +98,153 @@ public class DBRefEntry } /** + * 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(DBRefEntry 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.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 */ - 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))) + } + 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 - */ + + @Override public void setAccessionId(String accessionId) { this.accessionId = accessionId; } - /** - * @param source - * the source to set - */ + + @Override public void setSource(String source) { this.source = source; } - /** - * @param version - * the version to set - */ + + @Override public void setVersion(String version) { this.version = version; } - /** - * @return the map - */ + + @Override public Mapping getMap() { return map; @@ -180,4 +273,34 @@ public class DBRefEntry return ((source != null) ? source : "") + ":" + ((accessionId != null) ? accessionId : ""); } + + @Override + public String toString() + { + return getSrcAccString(); + } + + @Override + public int getStartRes() + { + return startRes; + } + + @Override + public void setStartRes(int startRes) + { + this.startRes = startRes; + } + + @Override + public int getEndRes() + { + return endRes; + } + + @Override + public void setEndRes(int endRes) + { + this.endRes = endRes; + } }