@Override public String toString() { String result; Iterator i; result = "AC: " + this.getAc() + " Owner: " + this.getOwner().getShortLabel() + " Label: " + this.getShortLabel() + "["; if ( null != this.getXrefs() ) { i = this.getXrefs().iterator(); while ( i.hasNext() ) { result = result + i.next(); } } return result + "]"; }
/** * Equality for Interactions is currently based on equality for <code>Interactors</code>, CvInteractionType, kD and * Components. * * @param o The object to check * * @return true if the parameter equals this object, false otherwise * * @see InteractorImpl * @see Component * @see CvInteractionType */ @Override public boolean equals( Object o ) { if ( this == o ) { return true; } if ( !( o instanceof Interaction ) ) { return false; } if ( !super.equals( o ) ) { return false; } return equals(o, true); }
@Override public boolean equals( Object o ) { if ( this == o ) { return true; } if( !( o instanceof Interactor ) ) { return false; } final Interactor other = ( Interactor ) o; if (!getObjClass().equals(other.getObjClass())) { return false; } // if ( !super.equals( o ) ) { // return false; // } return equals(o, true); }
if( interactor.getBioSource() != null && interactorCandidate.getBioSource() != null ) { final String t = interactor.getBioSource().getTaxId(); final String tc = interactorCandidate.getBioSource().getTaxId(); if( t != null && !t.equals(tc) ) { log.warn( "Interactors with the same identity xref(s) but with different BioSource: " + "["+ interactor.getShortLabel() +" / "+ interactor.getAc() +" / taxid:"+ t +"] and " + "["+ interactorCandidate.getShortLabel() +" / "+ interactorCandidate.getAc() +" / taxid:"+ tc +"]" ); Interactor existingObject = interactorDao.getByShortLabel(interactor.getShortLabel()); if (existingObject != null) { ac = existingObject.getAc();
BioSource interactorBiosource = interactor.getBioSource(); report.addWarning("The interactor " + interactor.getAc() + " was matching the name " + name + ". As the organism of the matching protein is null we cannot take into account this protein."); interactorsAc.add(interactor.getAc()); report.addWarning("The interactor " + interactor.getAc() + " was matching the name " + name + " but its organism " + interactorBiosource.getAc() + " is not matching " + organism); report.addWarning("The interactor " + interactor.getAc() + " was matching the name " + name + " but its organism ("+interactorBiosource.getAc()+") doesn't have a valid taxId and is not matching " + organism); interactorsAc.add(interactor.getAc()); report.addWarning("The interactor " + interactor.getAc() + " was matching the name " + name + " but its organism is null and is not matching " + organism);
@Override public String toString() { return super.toString() + " [ CRC64: " + getCrc64() + " Sequence: " + getSequence() + "]"; } }
/** * Constructor for subclass use only. Ensures that Interactors cannot be created without at least a shortLabel, an * owner and type specified. NOTE: It is assumed that subclasses of Interactor will supply a valid BioSource; this * is initially set to null but <b>other classes may expect it to be non-null</b>. * * @param shortLabel The memorable label to identify this Interactor * @param owner The Institution which owns this Interactor * @param type The Interactor type * * @throws NullPointerException thrown if either parameters are not specified */ public InteractorImpl( String shortLabel, Institution owner, CvInteractorType type ) { super( shortLabel, owner ); setCvInteractorType( type ); }
InteractionImpl copy = ( InteractionImpl ) super.clone();
if( interactor.getBioSource() != null && interactorCandidate.getBioSource() != null ) { final String t = interactor.getBioSource().getTaxId(); final String tc = interactorCandidate.getBioSource().getTaxId(); if( t != null && !t.equals(tc) ) { log.warn( "Interactors with the same identity xref(s) but with different BioSource: " + "["+ interactor.getShortLabel() +" / "+ interactor.getAc() +" / taxid:"+ t +"] and " + "["+ interactorCandidate.getShortLabel() +" / "+ interactorCandidate.getAc() +" / taxid:"+ tc +"]" ); Interactor existingObject = interactorDao.getByShortLabel(interactor.getShortLabel()); if (existingObject != null) { ac = existingObject.getAc();
@Override public boolean equals( Object o ) { if ( this == o ) { return true; } if( !( o instanceof Interactor ) ) { return false; } final Interactor other = ( Interactor ) o; if (!getObjClass().equals(other.getObjClass())) { return false; } // if ( !super.equals( o ) ) { // return false; // } return equals(o, true); }
@Override public String toString() { return super.toString() + " [ CRC64: " + getCrc64() + " Sequence: " + getSequence() + "]"; } }
/** * Constructor for subclass use only. Ensures that Interactors cannot be created without at least a shortLabel, an * owner and type specified. NOTE: It is assumed that subclasses of Interactor will supply a valid BioSource; this * is initially set to null but <b>other classes may expect it to be non-null</b>. * * @param shortLabel The memorable label to identify this Interactor * @param owner The Institution which owns this Interactor * @param type The Interactor type * * @throws NullPointerException thrown if either parameters are not specified */ protected InteractorImpl( String shortLabel, Institution owner, CvInteractorType type ) { super( shortLabel, owner ); setCvInteractorType( type ); }
InteractionImpl copy = ( InteractionImpl ) super.clone();
@Override public String toString() { String result; Iterator i; result = "AC: " + this.getAc() + " Owner: " + this.getOwner().getShortLabel() + " Label: " + this.getShortLabel() + "["; if ( null != this.getXrefs() ) { i = this.getXrefs().iterator(); while ( i.hasNext() ) { result = result + i.next(); } } return result + "]"; }
/** * Equality for Interactions is currently based on equality for <code>Interactors</code>, CvInteractionType, kD and * Components. * * @param o The object to check * * @return true if the parameter equals this object, false otherwise * * @see InteractorImpl * @see Component * @see CvInteractionType */ @Override public boolean equals( Object o ) { if ( this == o ) { return true; } if ( !( o instanceof Interaction ) ) { return false; } if ( !super.equals( o ) ) { return false; } return equals(o, true); }
@Override public String toString() { return super.toString() + " [ CRC64: " + getCrc64() + " Sequence: " + getSequence() + "]"; } }
/** * Constructor for subclass use only. Ensures that Interactors cannot be created without at least a shortLabel, an * owner and type specified. NOTE: It is assumed that subclasses of Interactor will supply a valid BioSource; this * is initially set to null but <b>other classes may expect it to be non-null</b>. * * @param shortLabel The memorable label to identify this Interactor * @param owner The Institution which owns this Interactor * @param type The Interactor type * * @throws NullPointerException thrown if either parameters are not specified */ public InteractorImpl( String shortLabel, Institution owner, CvInteractorType type ) { super( shortLabel, owner ); setCvInteractorType( type ); }
InteractionImpl copy = ( InteractionImpl ) super.clone();