@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(); } }
@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(); } }
@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(); }
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 ");
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 ");
public static void check( final InteractionDetectionTag interactionDetection ) { final XrefTag psiDef = interactionDetection.getPsiDefinition(); XrefChecker.check( psiDef ); final String id = psiDef.getId(); if ( !cache.keySet().contains( id ) ) { CvInteraction cvInteraction = null; try { cvInteraction = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvInteraction.class,id); if ( cvInteraction == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvInteraction by PSI definition: " + id ) ); } else { System.out.println( "Found CvInteraction " + id + " as " + cvInteraction.getShortLabel() ); } } catch ( IntactException e ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while searching for CvInteraction " + "having the PSI definition: " + id ) ); e.printStackTrace(); } cache.put( id, cvInteraction ); } } }
public static void check( final InteractionDetectionTag interactionDetection ) { final XrefTag psiDef = interactionDetection.getPsiDefinition(); XrefChecker.check( psiDef ); final String id = psiDef.getId(); if ( !cache.keySet().contains( id ) ) { CvInteraction cvInteraction = null; try { cvInteraction = IntactContext.getCurrentInstance().getCvContext().getByMiRef(CvInteraction.class,id); if ( cvInteraction == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvInteraction by PSI definition: " + id ) ); } else { System.out.println( "Found CvInteraction " + id + " as " + cvInteraction.getShortLabel() ); } } catch ( IntactException e ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while searching for CvInteraction " + "having the PSI definition: " + id ) ); e.printStackTrace(); } cache.put( id, cvInteraction ); } } }
public static void check( final InteractionDetectionTag interactionDetection ) { final XrefTag psiDef = interactionDetection.getPsiDefinition(); XrefChecker.check( psiDef ); final String id = psiDef.getId(); if ( !cache.keySet().contains( id ) ) { CvInteraction cvInteraction = null; try { cvInteraction = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getCvObjectDao(CvInteraction.class).getByXref(id); if ( cvInteraction == null ) { MessageHolder.getInstance().addCheckerMessage( new Message( "Could not find CvInteraction by PSI definition: " + id ) ); } else { System.out.println( "Found CvInteraction " + id + " as " + cvInteraction.getShortLabel() ); } } catch ( IntactException e ) { MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while searching for CvInteraction " + "having the PSI definition: " + id ) ); e.printStackTrace(); } cache.put( id, cvInteraction ); } } }
getOut().println("\t\t\t That experiment add an other evidence with that same CvInteraction( " + cvInteraction.getShortLabel() + " )."); 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()));
getOut().println("\t\t\t That experiment add an other evidence with that same CvInteraction( " + cvInteraction.getShortLabel() + " )."); 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()));
getOut().println("\t\t\t\t " + cvInteraction.getShortLabel() + ", threshold: " + threshold + " #experiment: " + (experimentAcs == null ? "none" : "" + experimentAcs.size()));
getOut().println("\t\t\t " + cvInteraction.getShortLabel() + ", threshold: " + threshold + " #experiment: " + (experimentAcs == null ? "none" : "" + experimentAcs.size()));
getOut().println("\t\t\t\t " + cvInteraction.getShortLabel() + ", threshold: " + threshold + " #experiment: " + (experimentAcs == null ? "none" : "" + experimentAcs.size()));