X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=aedfd3b793adb47e468834fa9755a5f0bb5127ba;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=54e8379666c51b3dd6b23ce2fd4b36a127d13287;hpb=beff7ac7ab7be2c24ccb179be16b8816d2c18610;p=jalview.git diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java index 54e8379..aedfd3b 100755 --- a/src/jalview/datamodel/DBRefEntry.java +++ b/src/jalview/datamodel/DBRefEntry.java @@ -20,8 +20,9 @@ */ package jalview.datamodel; +import java.util.Locale; + import jalview.api.DBRefEntryI; -import jalview.io.vamsas.Dbref; import jalview.util.DBRefUtils; import jalview.util.MapList; @@ -29,29 +30,21 @@ import java.util.List; public class DBRefEntry implements DBRefEntryI { - /* - * 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 = ""; + String source = ""; private String version = ""; - + private String ucversion; private String accessionId = ""; - + int sourceKey = Integer.MIN_VALUE; String canonicalSourceName; + boolean isCanonicalAccession = false; - /** + /* * maps from associated sequence to the database sequence's coordinate system */ Mapping map = null; @@ -60,15 +53,34 @@ public class DBRefEntry implements DBRefEntryI { } -/** - * - * @param source may not be null - * @param version may be null - * @param accessionId may be null - */ + + /** + * + * @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); + this(source, version, accessionId, null, false); + } + + /** + * + * @param source + * may not be null + * @param version + * may be null + * @param accessionId + * may be null + */ + public DBRefEntry(String source, String version, String accessionId, + Mapping map) + { + this(source, version, accessionId, map, false); } /** @@ -84,13 +96,14 @@ public class DBRefEntry implements DBRefEntryI * numbering or null) */ public DBRefEntry(String source, String version, String accessionId, - Mapping map) + Mapping map, boolean isCanonical) { - - this.source = source.toUpperCase(); + + this.source = source.toUpperCase(Locale.ROOT); setVersion(version); this.accessionId = accessionId; this.map = map; + this.isCanonicalAccession = isCanonical; } /** @@ -104,7 +117,8 @@ public class DBRefEntry implements DBRefEntryI : new String(entry.getVersion())), (entry.getAccessionId() == null ? "" : new String(entry.getAccessionId())), - (entry.getMap() == null ? null : new Mapping(entry.getMap()))); + (entry.getMap() == null ? null : new Mapping(entry.getMap())), + entry.isCanonical()); } @Override @@ -112,28 +126,26 @@ public class DBRefEntry implements DBRefEntryI { // 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 (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; + 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; } /** @@ -163,6 +175,7 @@ public class DBRefEntry implements DBRefEntryI return true; } + boolean improved = false; /* * source must either match or be both null */ @@ -186,6 +199,19 @@ public class DBRefEntry implements DBRefEntryI return false; } + if (!isCanonicalAccession && other.isCanonical()) + { + isCanonicalAccession = true; + improved = true; + } + else + { + if (isCanonicalAccession && !other.isCanonical()) + { + // other is not an authoritative source of canonical accessions + return false; + } + } /* * if my version is null, "0" or "source:0" then replace with other version, * otherwise the versions have to match @@ -202,12 +228,15 @@ public class DBRefEntry implements DBRefEntryI if (version != null && (otherVersion == null || !version.equalsIgnoreCase(otherVersion))) { - return false; + // FIXME: there may be a problem with old version strings not allowing + // updating of dbrefentries + return improved; } } /* - * if I have no mapping, take that of the other dbref + * if I have no mapping, take that of the other dbref + * - providing it had a version and so do I */ if (map == null) { @@ -234,10 +263,10 @@ public class DBRefEntry implements DBRefEntryI { return true; } - - // BH 2019.01.25/2019.02.04 source cannot/should not be null. + + // 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())) @@ -253,9 +282,12 @@ public class DBRefEntry implements DBRefEntryI return source; } - public int getSourceKey() + public int getSourceKey() { - return (sourceKey == Integer.MIN_VALUE ? (sourceKey = DBRefSource.getSourceKey(getCanonicalSourceName())) : sourceKey); + return (sourceKey == Integer.MIN_VALUE + ? (sourceKey = DBRefSource + .getSourceKey(getCanonicalSourceName())) + : sourceKey); } /** @@ -279,8 +311,9 @@ public class DBRefEntry implements DBRefEntryI @Override public void setAccessionId(String accessionId) { - this.accessionId = accessionId; -// this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase(); + this.accessionId = accessionId; + // this.accessionId = (accessionId == null ? "" : + // accessionId).toUpperCase(Locale.ROOT); } /** @@ -289,18 +322,19 @@ public class DBRefEntry implements DBRefEntryI @Override public void setSource(String source) { - this.source = source; - -// this.source = (source == null ? "" : source).toUpperCase(); -// this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source); -// this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName); + this.source = source; + + // this.source = (source == null ? "" : source).toUpperCase(Locale.ROOT); + // this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source); + // this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName); } @Override public void setVersion(String version) { this.version = version; - this.ucversion = (version == null ? null : version.toUpperCase()); + this.ucversion = (version == null ? null + : version.toUpperCase(Locale.ROOT)); } @Override @@ -353,14 +387,14 @@ public class DBRefEntry implements DBRefEntryI return false; } MapList ml = map.getMap(); - if (ml.getFromRatio() != ml.getToRatio() - || ml.getFromRatio() != 1) + 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) + if ((fromRanges = ml.getFromRanges()).size() != 1 + || (toRanges = ml.getToRanges()).size() != 1) { return false; } @@ -375,31 +409,43 @@ public class DBRefEntry implements DBRefEntryI // 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" + * stores the upper-case canonical name of the source for use in + * Sequence.getPrimaryDBRefs(). + * + * @author Bob Hanson * * @return */ - public boolean isChromosome() + public String getCanonicalSourceName() { - return accessionId != null && accessionId.startsWith(CHROMOSOME + ":"); + return (canonicalSourceName == null + ? (canonicalSourceName = DBRefUtils + .getCanonicalName(this.source)) + : canonicalSourceName); } /** - * stores the upper-case canonical name of the source for use in - * Sequence.getPrimaryDBRefs(). - * - * @author Bob Hanson * - * @return + * @param canonical */ - public String getCanonicalSourceName() { - return (canonicalSourceName == null ? (canonicalSourceName = DBRefUtils.getCanonicalName(this.source)) : canonicalSourceName); + public void setCanonical(boolean canonical) + { + isCanonicalAccession = canonical; } - + /** + * + * @return true if this is the primary canonical accession for the database + * source + */ + public boolean isCanonical() + { + // TODO Auto-generated method stub + return isCanonicalAccession; + } }