X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;fp=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=aedfd3b793adb47e468834fa9755a5f0bb5127ba;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=93a54607c88dfc8521ce3b8187d87919f1d13ab7;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java index 93a5460..aedfd3b 100755 --- a/src/jalview/datamodel/DBRefEntry.java +++ b/src/jalview/datamodel/DBRefEntry.java @@ -33,16 +33,16 @@ public class DBRefEntry implements DBRefEntryI String source = ""; private String version = ""; - + private String ucversion; private String accessionId = ""; - + int sourceKey = Integer.MIN_VALUE; String canonicalSourceName; - - boolean isCanonicalAccession=false; + + boolean isCanonicalAccession = false; /* * maps from associated sequence to the database sequence's coordinate system @@ -57,30 +57,32 @@ public class DBRefEntry implements DBRefEntryI /** * * @param source - * may not be null + * may not be null * @param version - * may be null + * may be null * @param accessionId - * may be null + * may be null */ public DBRefEntry(String source, String version, String accessionId) { - this(source, version, accessionId, null,false); + this(source, version, accessionId, null, false); } /** * * @param source - * may not be null + * may not be null * @param version - * may be null + * may be null * @param accessionId - * may be null + * may be null */ - public DBRefEntry(String source, String version, String accessionId, Mapping map) + public DBRefEntry(String source, String version, String accessionId, + Mapping map) { - this(source, version, accessionId, map,false); + this(source, version, accessionId, map, false); } + /** * * @param source @@ -94,14 +96,14 @@ public class DBRefEntry implements DBRefEntryI * numbering or null) */ public DBRefEntry(String source, String version, String accessionId, - Mapping map,boolean isCanonical) + Mapping map, boolean isCanonical) { - + this.source = source.toUpperCase(Locale.ROOT); setVersion(version); this.accessionId = accessionId; this.map = map; - this.isCanonicalAccession=isCanonical; + this.isCanonicalAccession = isCanonical; } /** @@ -115,7 +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.isCanonical()); + (entry.getMap() == null ? null : new Mapping(entry.getMap())), + entry.isCanonical()); } @Override @@ -123,28 +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; } /** @@ -174,7 +175,7 @@ public class DBRefEntry implements DBRefEntryI return true; } - boolean improved=false; + boolean improved = false; /* * source must either match or be both null */ @@ -262,10 +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())) @@ -281,9 +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); } /** @@ -307,8 +311,9 @@ public class DBRefEntry implements DBRefEntryI @Override public void setAccessionId(String accessionId) { - this.accessionId = accessionId; -// this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase(Locale.ROOT); + this.accessionId = accessionId; + // this.accessionId = (accessionId == null ? "" : + // accessionId).toUpperCase(Locale.ROOT); } /** @@ -317,18 +322,19 @@ public class DBRefEntry implements DBRefEntryI @Override public void setSource(String source) { - this.source = source; - -// this.source = (source == null ? "" : source).toUpperCase(Locale.ROOT); -// 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(Locale.ROOT)); + this.ucversion = (version == null ? null + : version.toUpperCase(Locale.ROOT)); } @Override @@ -381,14 +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; } @@ -403,7 +409,7 @@ public class DBRefEntry implements DBRefEntryI // no version string implies the reference has not been verified at all. return false; } - + return DBRefSource.isPrimaryCandidate(ucversion); } @@ -415,8 +421,12 @@ public class DBRefEntry implements DBRefEntryI * * @return */ - public String getCanonicalSourceName() { - return (canonicalSourceName == null ? (canonicalSourceName = DBRefUtils.getCanonicalName(this.source)) : canonicalSourceName); + public String getCanonicalSourceName() + { + return (canonicalSourceName == null + ? (canonicalSourceName = DBRefUtils + .getCanonicalName(this.source)) + : canonicalSourceName); } /** @@ -427,9 +437,11 @@ public class DBRefEntry implements DBRefEntryI { isCanonicalAccession = canonical; } + /** * - * @return true if this is the primary canonical accession for the database source + * @return true if this is the primary canonical accession for the database + * source */ public boolean isCanonical() {