X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=ae06650f2ce9914fdf49fa1b9355b38d0489c3a4;hb=d0d660cab06c31659e7bb0a1780317b3d2231eb6;hp=8520e5cc2f20abfbb2499e3b1f1472c31caf34ca;hpb=b3a1578f1b29594527e347534f39ffc4e5b37298;p=jalview.git diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java index 8520e5c..ae06650 100755 --- a/src/jalview/datamodel/DBRefEntry.java +++ b/src/jalview/datamodel/DBRefEntry.java @@ -28,29 +28,21 @@ 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 = ""; + private String accessionId = ""; - String sourceKey; + int sourceKey = Integer.MIN_VALUE; String canonicalSourceName; + + boolean isCanonicalAccession; - - /** + /* * maps from associated sequence to the database sequence's coordinate system */ Mapping map = null; @@ -60,44 +52,68 @@ 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) { - // 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(); 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()))); } @Override @@ -228,20 +244,16 @@ 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 +262,23 @@ 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 +288,28 @@ 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(); } + /** + * 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(); +// 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()); } @Override @@ -355,49 +379,42 @@ 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; + + 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() - { - return accessionId != null && accessionId.startsWith(CHROMOSOME + ":"); + public String getCanonicalSourceName() { + 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 + * @param canonical + */ + public void setCanonical(boolean canonical) + { + isCanonicalAccession = canonical; + } + /** * - * @return + * @return true if this is the primary canonical accession for the database source */ - public Object getCanonicalSourceName() { - return canonicalSourceName; + public boolean isCanonical() + { + // TODO Auto-generated method stub + return isCanonicalAccession; } - - }