@Override public String toString() { StringBuffer result = new StringBuffer( 512 ); result.append( "Experiment [AC: " + this.getAc() + " Shortlabel: " + getShortLabel() ); result.append( " BioSource: " + ( getBioSource() == null ? "-" : getBioSource().getShortLabel() ) ); result.append( NEW_LINE ); result.append( "CvIdentification: " + ( cvIdentification == null ? "-" : cvIdentification.getShortLabel() ) ); result.append( NEW_LINE ); result.append( "CvInteraction: " + ( cvInteraction == null ? "NOT SPECIFIED" : cvInteraction.getShortLabel() ) ); result.append( NEW_LINE ); result.append( ']' ); return result.toString(); } }
return false; if ( detectionMethod != null ? !detectionMethod.equals( that.detectionMethod ) : that.detectionMethod != null ) { return false;
CvInteractionStatus cache = cvInteractionExportStatusCache.get(cvInteraction.getAc()); if (null != cache) { final Collection<Annotation> annotations = cvInteraction.getAnnotations(); multipleAnnotationFound = true; out.println("ERROR: There are multiple annotation having Topic:" + CvTopic.UNIPROT_DR_EXPORT + " in CvInteraction: " + cvInteraction.getShortLabel() + ". \nWe do not export."); } else { String err = cvInteraction.getShortLabel() + " having annotation (" + CvTopic.UNIPROT_DR_EXPORT + ") has an annotationText like <integer value>. Value was: " + i + ", We consider it as to be exported."; String err = cvInteraction.getShortLabel() + " having annotation (" + CvTopic.UNIPROT_DR_EXPORT + ") has an annotationText like <integer value>. Value was: " + i + " However, having a value < 1 is not valid, We consider it as to be NOT exported."; out.println("ERROR: " + cvInteraction.getShortLabel() + " having annotation (" + CvTopic.UNIPROT_DR_EXPORT + ") has an annotationText different from yes/no/<integer value> !!!" + " value was: '" + text + "'."); out.println("ERROR: " + cvInteraction.getShortLabel() + " doesn't have an annotation: " + CvTopic.UNIPROT_DR_EXPORT); out.println(logPrefix + "\t\t\t not annotation found: do not export "); cvInteractionExportStatusCache.put(cvInteraction.getAc(), status);
if (cvInteraction.equals(method) && false == experimentAcs.contains(experiment1.getAc())) { experimentAcs.add(experiment1.getAc()); getOut().println("\t\t\t That experiment add an other evidence with that same CvInteraction( " + cvInteraction.getShortLabel() + " )."); if (cvInteraction.equals(method) && false == experimentAcs.contains(experiment2.getAc())) { experimentAcs.add(experiment2.getAc()); getOut().println("\t\t\t\t That experiment add an other evidence with that same CvInteraction( " + cvInteraction.getShortLabel() + " )."); getOut().println("\t\t\t " + cvInteraction.getShortLabel() + ", threshold: " + threshold + " #experiment: " + (experimentAcs == null ? "none" : "" + experimentAcs.size()));
canBeProcessed = true; String detectionMI = detectionMethod.getIdentifier();
@Override public int hashCode() { int result; long temp; result = ( pk != null ? pk.hashCode() : 0 ); result = 31 * result + ( shortLabel1 != null ? shortLabel1.hashCode() : 0 ); result = 31 * result + ( shortLabel2 != null ? shortLabel2.hashCode() : 0 ); result = 31 * result + ( taxid != null ? taxid.hashCode() : 0 ); temp = weight != +0.0d ? Double.doubleToLongBits( weight ) : 0L; result = 31 * result + ( int ) ( temp ^ ( temp >>> 32 ) ); result = 31 * result + graphId; result = 31 * result + ( experiment != null ? experiment.hashCode() : 0 ); result = 31 * result + ( detectionMethod != null ? detectionMethod.hashCode() : 0 ); result = 31 * result + ( pubmedId != null ? pubmedId.hashCode() : 0 ); return result; } }
if (cvInteraction.equals(method) && false == experimentAcs.contains(experiment1.getAc())) { experimentAcs.add(experiment1.getAc()); getOut().println("\t\t\t That experiment add an other evidence with that same CvInteraction( " + cvInteraction.getShortLabel() + " )."); if (cvInteraction.equals(method) && false == experimentAcs.contains(experiment2.getAc())) { experimentAcs.add(experiment2.getAc()); getOut().println("\t\t\t\t That experiment add an other evidence with that same CvInteraction( " + cvInteraction.getShortLabel() + " )."); getOut().println("\t\t\t " + cvInteraction.getShortLabel() + ", threshold: " + threshold + " #experiment: " + (experimentAcs == null ? "none" : "" + experimentAcs.size()));
CvInteractionType interactionType = interaction.getCvInteractionType(); String detectionMI = detectionMethod.getIdentifier();
@Override public int hashCode() { int result; long temp; result = ( pk != null ? pk.hashCode() : 0 ); result = 31 * result + ( shortLabel1 != null ? shortLabel1.hashCode() : 0 ); result = 31 * result + ( shortLabel2 != null ? shortLabel2.hashCode() : 0 ); result = 31 * result + ( taxid != null ? taxid.hashCode() : 0 ); temp = weight != +0.0d ? Double.doubleToLongBits( weight ) : 0L; result = 31 * result + ( int ) ( temp ^ ( temp >>> 32 ) ); result = 31 * result + graphId; result = 31 * result + ( experiment != null ? experiment.hashCode() : 0 ); result = 31 * result + ( detectionMethod != null ? detectionMethod.hashCode() : 0 ); result = 31 * result + ( pubmedId != null ? pubmedId.hashCode() : 0 ); return result; } }
if (cvInteraction.equals(method)) { experimentAcs.add(experiment1.getAc()); if (cvInteraction.equals(method)) { experimentAcs.add(experiment2.getAc()); getOut().println("\t\t\t\t " + cvInteraction.getShortLabel() + ", threshold: " + threshold + " #experiment: " + (experimentAcs == null ? "none" : "" + experimentAcs.size()));
@Override public String toString() { StringBuffer result = new StringBuffer( 512 ); result.append( "Experiment [AC: " + this.getAc() + " Shortlabel: " + getShortLabel() ); result.append( " BioSource: " + ( getBioSource() == null ? "-" : getBioSource().getShortLabel() ) ); result.append( NEW_LINE ); result.append( "CvIdentification: " + ( cvIdentification == null ? "-" : cvIdentification.getShortLabel() ) ); result.append( NEW_LINE ); result.append( "CvInteraction: " + ( cvInteraction == null ? "NOT SPECIFIED" : cvInteraction.getShortLabel() ) ); result.append( NEW_LINE ); result.append( ']' ); return result.toString(); } }
CvInteractionStatus cache = cvInteractionExportStatusCache.get(cvInteraction.getAc()); if (null != cache) { annotations = cvInteraction.getAnnotations(); multipleAnnotationFound = true; out.println("ERROR: There are multiple annotation having Topic:" + CvTopic.UNIPROT_DR_EXPORT + " in CvInteraction: " + cvInteraction.getShortLabel() + ". \nWe do not export."); } else { String err = cvInteraction.getShortLabel() + " having annotation (" + CvTopic.UNIPROT_DR_EXPORT + ") has an annotationText like <integer value>. Value was: " + i + ", We consider it as to be exported."; String err = cvInteraction.getShortLabel() + " having annotation (" + CvTopic.UNIPROT_DR_EXPORT + ") has an annotationText like <integer value>. Value was: " + i + " However, having a value < 1 is not valid, We consider it as to be NOT exported."; out.println("ERROR: " + cvInteraction.getShortLabel() + " having annotation (" + CvTopic.UNIPROT_DR_EXPORT + ") has an annotationText different from yes/no/<integer value> !!!" + " value was: '" + text + "'."); out.println("ERROR: " + cvInteraction.getShortLabel() + " doesn't have an annotation: " + CvTopic.UNIPROT_DR_EXPORT); out.println(logPrefix + "\t\t\t not annotation found: do not export "); cvInteractionExportStatusCache.put(cvInteraction.getAc(), status);
return false; if ( detectionMethod != null ? !detectionMethod.equals( that.detectionMethod ) : that.detectionMethod != null ) { return false;
query.setParameter("interactionDetectionMethodMi", experiment.getCvInteraction().getIdentifier());
@Override public int hashCode() { int result = super.hashCode(); // result = 29 * result + bioSource.hashCode(); result = 29 * result + ( bioSource != null ? bioSource.hashCode() : 0 ); result = 29 * result + ( publication != null ? publication.hashCode() : 0 ); result = 29 * result + ( cvIdentification != null ? cvIdentification.hashCode() : 0 ); result = 29 * result + ( cvInteraction != null ? cvInteraction.hashCode() : 0 ); return result; }
if (cvInteraction.equals(method)) { experimentAcs.add(experiment1.getAc()); if (cvInteraction.equals(method)) { experimentAcs.add(experiment2.getAc()); getOut().println("\t\t\t\t " + cvInteraction.getShortLabel() + ", threshold: " + threshold + " #experiment: " + (experimentAcs == null ? "none" : "" + experimentAcs.size()));
@Override public String toString() { StringBuffer result = new StringBuffer( 128 ); result.append( "Experiment [AC: " + this.getAc() + " Shortlabel: " + getShortLabel() ); result.append( " BioSource: " + ( getBioSource() == null ? "-" : getBioSource().getShortLabel() ) ); result.append( NEW_LINE ); result.append( "CvIdentification: " + ( cvIdentification == null ? "-" : cvIdentification.getShortLabel() ) ); result.append( NEW_LINE ); result.append( "CvInteraction: " + ( cvInteraction == null ? "NOT SPECIFIED" : cvInteraction.getShortLabel() ) ); result.append( NEW_LINE ); // TODO in experiments with many interactions this can throw OutOfMemoryErrors // result.append( "Interactions (" ); // if( null != getInteractions() ) { // for( Iterator iterator = interactions.iterator(); iterator.hasNext(); ) { // Interaction interaction = (Interaction) iterator.next(); // result.append( interaction.getShortLabel() ).append( ", " ); // } // } // result.append( ')' ); // result.append( NEW_LINE ); result.append( ']' ); return result.toString(); }
return false; if ( cvInteraction != null ? !cvInteraction.equals( that.cvInteraction ) : that.cvInteraction != null ) { return false;
query.setParameter("interactionDetectionMethodMi", experiment.getCvInteraction().getIdentifier());
@Override public int hashCode() { int result = super.hashCode(); // result = 29 * result + bioSource.hashCode(); result = 29 * result + ( bioSource != null ? bioSource.hashCode() : 0 ); result = 29 * result + ( publication != null ? publication.hashCode() : 0 ); result = 29 * result + ( cvIdentification != null ? cvIdentification.hashCode() : 0 ); result = 29 * result + ( cvInteraction != null ? cvInteraction.hashCode() : 0 ); return result; }