X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=bc8d0cf1d1723e423b1d1d62608ce1a62d2bb6fa;hb=cbeb7ad59d51b468c54ca3db2a2a7693060a2509;hp=6dc6641a9043fc9dfc0a22f6bcd29cec0eeb56f9;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java index 6dc6641..bc8d0cf 100755 --- a/src/jalview/datamodel/DBRefEntry.java +++ b/src/jalview/datamodel/DBRefEntry.java @@ -1,26 +1,37 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) - * Copyright (C) 2014 The Jalview Authors + * 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; + +import java.util.Arrays; +import java.util.List; + +public class DBRefEntry implements DBRefEntryI { - String source = "", version = "", accessionId = ""; + String source = ""; + + String version = ""; + + String accessionId = ""; /** * maps from associated sequence to the database sequence's coordinate system @@ -58,24 +69,32 @@ 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)))) + } + if (equalRef(entry) && ((map == null && entry.map == null) + || (map != null && entry.map != null && map.equals(entry.map)))) { return true; } @@ -83,76 +102,153 @@ 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(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 */ - 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; @@ -181,4 +277,62 @@ 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) + { + 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; + } }