X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=511287bc2da6a2b8649d1cb7bd01b5edc5ccadc6;hb=d867cf856b9c0cdcb3d9732691f2c3afe861697c;hp=bc8d0cf1d1723e423b1d1d62608ce1a62d2bb6fa;hpb=cbeb7ad59d51b468c54ca3db2a2a7693060a2509;p=jalview.git diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java index bc8d0cf..511287b 100755 --- a/src/jalview/datamodel/DBRefEntry.java +++ b/src/jalview/datamodel/DBRefEntry.java @@ -21,19 +21,28 @@ package jalview.datamodel; import jalview.api.DBRefEntryI; +import jalview.util.DBRefUtils; +import jalview.util.MapList; -import java.util.Arrays; import java.util.List; public class DBRefEntry implements DBRefEntryI { String source = ""; - String version = ""; + private String version = ""; + + private String ucversion; - String accessionId = ""; + private String accessionId = ""; + + int sourceKey = Integer.MIN_VALUE; - /** + String canonicalSourceName; + + boolean isCanonicalAccession; + + /* * maps from associated sequence to the database sequence's coordinate system */ Mapping map = null; @@ -43,32 +52,60 @@ 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 - * canonical source (uppercase only) + * may not be null * @param version - * (source dependent version string) + * may be null * @param accessionId - * (source dependent accession number string) + * may be null + */ + public DBRefEntry(String source, String version, String accessionId, Mapping map) + { + this(source, version, accessionId, map,false); + } + /** + * + * @param source + * canonical source (turned to uppercase; cannot be null) + * @param version + * (source dependent version string or null) + * @param accessionId + * (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) { + this.source = source.toUpperCase(); - this.version = version; + setVersion(version); 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() == null ? "" : new String(entry.getSource())), @@ -76,7 +113,7 @@ 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 @@ -84,21 +121,28 @@ 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 (equalRef(entry) && ((map == null && entry.map == null) - || (map != null && entry.map != null && map.equals(entry.map)))) - { - return true; - } - return false; + + +// 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; } /** @@ -128,6 +172,7 @@ public class DBRefEntry implements DBRefEntryI return true; } + boolean improved=false; /* * source must either match or be both null */ @@ -151,6 +196,19 @@ 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 @@ -167,12 +225,15 @@ 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) { @@ -199,17 +260,17 @@ public class DBRefEntry implements DBRefEntryI { return true; } - if (entry != 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())) && (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 @@ -218,12 +279,23 @@ public class DBRefEntry implements DBRefEntryI return source; } + public int getSourceKey() + { + 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() { @@ -233,19 +305,28 @@ public class DBRefEntry implements DBRefEntryI @Override public void setAccessionId(String accessionId) { - this.accessionId = accessionId; + this.accessionId = accessionId; +// this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase(); } + /** + * CAUTION! allows setting source null or not uppercase! + */ @Override public void setSource(String source) { - this.source = source; + this.source = source; + +// this.source = (source == null ? "" : source).toUpperCase(); +// 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()); } @Override @@ -292,19 +373,20 @@ public class DBRefEntry implements DBRefEntryI */ if (map != null) { - if (map.getTo() != null) + SequenceI mto = map.getTo(); + if (mto != null) { return false; } - if (map.getMap().getFromRatio() != map.getMap().getToRatio() - || map.getMap().getFromRatio() != 1) + MapList ml = map.getMap(); + if (ml.getFromRatio() != ml.getToRatio() + || ml.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) + List fromRanges, toRanges; + if ((fromRanges = ml.getFromRanges()).size() != 1 || (toRanges = ml.getToRanges()).size() != 1) { return false; } @@ -319,20 +401,37 @@ public class DBRefEntry implements DBRefEntryI // 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; + + return DBRefSource.isPrimaryCandidate(ucversion); + } + + /** + * stores the upper-case canonical name of the source for use in + * Sequence.getPrimaryDBRefs(). + * + * @author Bob Hanson + * + * @return + */ + 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; } }