public String calculateExperimentKey(Experiment exp) { return super.createUniquenessString(exp).toString(); } }
/** * Fetches the corresponding CvDatabase for a specific institution. * * @param context The IntactContext to run the queries to the database * @param institution The institution to find a CvDatabase for * @return */ public static CvDatabase retrieveCvDatabase(IntactContext context, Institution institution) { return retrieveCvDatabase(context, institution, null); }
/** * Creates a candiate short label - not taking into account if an interaction with the same name exists in the database * * @param baitShortLabel bait gene name * @param preyShortLabel prey gene name * @return the short label */ protected static String createCandidateShortLabel( String baitShortLabel, String preyShortLabel ) { return createCandidateShortLabel( baitShortLabel, preyShortLabel, null ); }
public static <X extends Xref> X createIdentityXrefEmblGenbankDdbj(AnnotatedObject<X, ?> parent, String emblGenbankDdbjId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.DDBG_MI_REF, CvDatabase.DDBG); return createIdentityXref(parent, emblGenbankDdbjId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
/** * Gets the next available suffix for a provided shortLabel * * @param shortLabel Can already have a suffix or not. * @return The next available shortLabel */ public static String nextAvailableShortlabel( String shortLabel ) { Integer nextSuffix = calculateNextSuffix( shortLabel ); InteractionShortLabel label = new InteractionShortLabel( shortLabel ); if ( nextSuffix != null ) { label.setSuffix( nextSuffix ); } return label.getCompleteLabel(); }
/** * Removes the suffix of a shortLabel * * @param shortLabel a shortLabel with or without suffix * * @return the shortlabel without suffix */ protected static String removeSuffix(String shortLabel) { InteractionShortLabel label = new InteractionShortLabel(shortLabel); return label.getCompleteLabel(false); }
public InteractionShortLabel( String baitLabel, String preyLabel, Integer suffix ) { this.baitLabel = prepareLabel( baitLabel ); this.preyLabel = prepareLabel( preyLabel ); this.suffix = suffix; this.isValid = true; }
/** * Creates a wrapper of experimental role and biological role altogether that have methods to output * the meaningful label for both roles * @param experimentalRole the experimental role to use * @param biologicalRole the biological role to use * @return the object containing both roles */ public static RoleInfo createRoleInfo(CvExperimentalRole experimentalRole, CvBiologicalRole biologicalRole) { return new RoleInfo(biologicalRole, experimentalRole); }
/** * @param rangeAsString : the string containing the range * @return the range instance matching the range described with the String. The feature sequence will be null. * An IllegalRangeException can be thrown if the range is invalid and doesn't fit the protein sequence */ public static Range createRangeFromString(String rangeAsString) { return createRangeFromString(rangeAsString, null, false); }
public static <X extends Xref> X createIdentityXrefEmblGenbankDdbj(AnnotatedObject<X, ?> parent, String emblGenbankDdbjId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.DDBG_MI_REF, CvDatabase.DDBG); return createIdentityXref(parent, emblGenbankDdbjId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public String calculateFeatureKey(Feature feature) { return super.createUniquenessString(feature).toString(); } }
public static <X extends Xref> X createIdentityXrefUniprot(AnnotatedObject<X, ?> parent, String primaryId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.UNIPROT_MI_REF, CvDatabase.UNIPROT); return createIdentityXref(parent, primaryId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public String calculateExperimentKey(Experiment exp) { return super.createUniquenessString(exp).toString(); } }
public static <X extends Xref> X createIdentityXrefIntact(AnnotatedObject<X, ?> parent, String intactId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.INTACT_MI_REF, CvDatabase.INTACT); return createIdentityXref(parent, intactId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public String calculateFeatureKey(Feature feature) { return super.createUniquenessString(feature).toString(); } }
public static <X extends Xref> X createIdentityXrefChebi(AnnotatedObject<X, ?> parent, String chebiId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.CHEBI_MI_REF, CvDatabase.CHEBI); return createIdentityXref(parent, chebiId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefUniprot(AnnotatedObject<X, ?> parent, String primaryId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.UNIPROT_MI_REF, CvDatabase.UNIPROT); return createIdentityXref(parent, primaryId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefUniprot(AnnotatedObject<X,?> parent, String primaryId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.UNIPROT_MI_REF, CvDatabase.UNIPROT); return createIdentityXref(parent, primaryId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefIntact(AnnotatedObject<X, ?> parent, String intactId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.INTACT_MI_REF, CvDatabase.INTACT); return createIdentityXref(parent, intactId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefChebi(AnnotatedObject<X, ?> parent, String chebiId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.CHEBI_MI_REF, CvDatabase.CHEBI); return createIdentityXref(parent, chebiId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }