X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=aedfd3b793adb47e468834fa9755a5f0bb5127ba;hb=HEAD;hp=8520e5cc2f20abfbb2499e3b1f1472c31caf34ca;hpb=b3a1578f1b29594527e347534f39ffc4e5b37298;p=jalview.git diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java index 8520e5c..aedfd3b 100755 --- a/src/jalview/datamodel/DBRefEntry.java +++ b/src/jalview/datamodel/DBRefEntry.java @@ -20,6 +20,8 @@ */ package jalview.datamodel; +import java.util.Locale; + import jalview.api.DBRefEntryI; import jalview.util.DBRefUtils; import jalview.util.MapList; @@ -28,29 +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"; - String source = ""; - String version = ""; - + private String version = ""; + private String ucversion; - String accessionId = ""; - - String sourceKey; + 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; @@ -60,44 +54,71 @@ public class DBRefEntry implements DBRefEntryI } + /** + * + * @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); } /** * * @param source - * canonical source (uppercase only) + * canonical source (turned to uppercase; cannot be null) * @param version - * (source dependent version string) + * (source dependent version string or null) * @param accessionId - * (source dependent accession number string) + * (source dependent accession number string or null) * @param map * (mapping from local sequence numbering to source accession - * numbering) + * numbering or null) */ public DBRefEntry(String source, String version, String accessionId, - Mapping map) + Mapping map, boolean isCanonical) { - // BH 2019.01.25 made these always non-null. - // Is there a difference between "" and null for version? - // evidence is that source CANNOT be null. - setSource(source); + + this.source = source.toUpperCase(Locale.ROOT); setVersion(version); - setAccessionId(accessionId); + this.accessionId = accessionId; this.map = map; + this.isCanonicalAccession = isCanonical; } + /** + * Clone an entry, this time not allowing any null fields except map. + * + */ public DBRefEntry(DBRefEntryI entry) { - this(entry.getSource(), entry.getVersion(), entry.getAccessionId(), entry.getMap() == null ? null : new Mapping(entry.getMap())); -// 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()))); + 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())), + entry.isCanonical()); } @Override @@ -105,28 +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; } /** @@ -156,6 +175,7 @@ public class DBRefEntry implements DBRefEntryI return true; } + boolean improved = false; /* * source must either match or be both null */ @@ -179,6 +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 @@ -195,12 +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) { @@ -227,21 +263,17 @@ public class DBRefEntry implements DBRefEntryI { return true; } - - // BH 2019.01.25 source, accessionId, and version cannot be null. + + // BH 2019.01.25/2019.02.04 source cannot/should not be null. // for example, StructureChooser has dbRef.getSource().equalsIgnoreCase... - - if (entry != null + + return (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; + && version.equalsIgnoreCase(entry.getVersion()))); } @Override @@ -250,17 +282,26 @@ public class DBRefEntry implements DBRefEntryI return source; } - public String getSourceKey() + public int getSourceKey() { - return sourceKey; + return (sourceKey == Integer.MIN_VALUE + ? (sourceKey = DBRefSource + .getSourceKey(getCanonicalSourceName())) + : sourceKey); } + /** + * can be null + */ @Override public String getVersion() { return version; } + /** + * can be null + */ @Override public String getAccessionId() { @@ -270,22 +311,30 @@ public class DBRefEntry implements DBRefEntryI @Override public void setAccessionId(String accessionId) { - this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase(); + this.accessionId = accessionId; + // this.accessionId = (accessionId == null ? "" : + // accessionId).toUpperCase(Locale.ROOT); } + /** + * CAUTION! allows setting source null or not uppercase! + */ @Override public void setSource(String source) { - this.source = (source == null ? "" : source).toUpperCase(); - this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source); - this.sourceKey = ";" + 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 == null ? "" : version); - this.ucversion = this.version.toUpperCase(); + this.version = version; + this.ucversion = (version == null ? null + : version.toUpperCase(Locale.ROOT)); } @Override @@ -338,14 +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; } @@ -355,36 +404,13 @@ public class DBRefEntry implements DBRefEntryI return false; } } - if (version == null || version == "") + 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[] sources = DBRefSource.allSources(); - for (int i = sources.length; --i >= 0;) - { - if (ucversion.startsWith(sources[i])) // BH 2019.01.25 .toUpperCase() unnecessary here for allSources - { - // 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; - } - /** - * Mappings to chromosome are held with accessionId as "chromosome:id" - * - * @return - */ - public boolean isChromosome() - { - return accessionId != null && accessionId.startsWith(CHROMOSOME + ":"); + return DBRefSource.isPrimaryCandidate(ucversion); } /** @@ -395,9 +421,31 @@ public class DBRefEntry implements DBRefEntryI * * @return */ - public Object getCanonicalSourceName() { - return canonicalSourceName; + public String getCanonicalSourceName() + { + return (canonicalSourceName == null + ? (canonicalSourceName = DBRefUtils + .getCanonicalName(this.source)) + : canonicalSourceName); } + /** + * + * @param canonical + */ + 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; + } }