public Map<String, String> getExperimentWithErrors() { if ( !experimentsClassified ) { classifyExperiments(); } return experimentsWithErrors; }
public ExperimentListItem(Collection<String> experimentLabels, String name, String parentFolders, boolean negative, Integer chunkNumber, Integer largeScaleSize) { this.experimentLabels = experimentLabels; this.name = name; this.negative = negative; this.chunkNumber = chunkNumber; this.largeScaleChunkSize = largeScaleSize; this.parentFolders = removeTrailingSlash(parentFolders); }
public Set<Experiment> getNegativeExperiments() { if ( negativeExperiments == null ) { classifyNegatives(); } return negativeExperiments; }
@Override public void error( SAXParseException e ) throws SAXException { log.error(e.getMessage()); report.setValid(false); PsiValidatorMessage msg = new PsiValidatorMessage(PsiValidatorMessage.Level.ERROR, e); report.addMessage(msg); }
@Override public String toString() { return getAc() + " " + getShortLabel(); }
public void createItemClassificationBySpecies() { for ( SimplifiedAnnotatedObject<BioSource> bioSource : species2experimentSet.keySet() ) { Collection<SimplifiedAnnotatedObject<Experiment>> smallScaleExp = species2experimentSet.get( bioSource ); // split the set into subset of size under SMALL_SCALE_LIMIT String filePrefixGlobal = bioSource.getShortLabel().replace( ' ', '-' ); createExpListItems( smallScaleExp, filePrefixGlobal + "_" + SMALL, // small scale filePrefixGlobal, // large scale Classification.SPECIES ); } }
@Override public void warning( SAXParseException e ) throws SAXException { log.warn(e.getMessage()); PsiValidatorMessage msg = new PsiValidatorMessage(PsiValidatorMessage.Level.WARN, e); report.addMessage(msg); }
@Override public void error( SAXParseException e ) throws SAXException { log.error(e.getMessage()); report.setValid(false); PsiValidatorMessage msg = new PsiValidatorMessage(PsiValidatorMessage.Level.ERROR, e); report.addMessage(msg); }
@Override public String toString() { return getAc() + " " + getShortLabel(); }
public void createItemClassificationBySpecies() { for ( SimplifiedAnnotatedObject<BioSource> bioSource : species2experimentSet.keySet() ) { Collection<SimplifiedAnnotatedObject<Experiment>> smallScaleExp = species2experimentSet.get( bioSource ); // split the set into subset of size under SMALL_SCALE_LIMIT String filePrefixGlobal = bioSource.getShortLabel().replace( ' ', '-' ); createExpListItems( smallScaleExp, filePrefixGlobal + "_" + SMALL, // small scale filePrefixGlobal, // large scale Classification.SPECIES ); } }
@Override public void warning( SAXParseException e ) throws SAXException { log.warn(e.getMessage()); PsiValidatorMessage msg = new PsiValidatorMessage(PsiValidatorMessage.Level.WARN, e); report.addMessage(msg); }
public Map<String, String> getExperimentWithErrors() { if ( !experimentsClassified ) { classifyExperiments(); } return experimentsWithErrors; }
public ExperimentListItem(Collection<String> experimentLabels, String name, String parentFolders, boolean negative, Integer chunkNumber, Integer largeScaleSize) { this.experimentLabels = experimentLabels; this.name = name; this.negative = negative; this.chunkNumber = chunkNumber; this.largeScaleChunkSize = largeScaleSize; this.parentFolders = removeTrailingSlash(parentFolders); }
public Set<Experiment> getNegativeExperiments() { if ( negativeExperiments == null ) { classifyNegatives(); } return negativeExperiments; }
@Override public String toString() { return getAc() + " " + getShortLabel(); }
public void createItemClassificationBySpecies() { for ( SimplifiedAnnotatedObject<BioSource> bioSource : species2experimentSet.keySet() ) { Collection<SimplifiedAnnotatedObject<Experiment>> smallScaleExp = species2experimentSet.get( bioSource ); // split the set into subset of size under SMALL_SCALE_LIMIT String filePrefixGlobal = bioSource.getShortLabel().replace( ' ', '-' ); createExpListItems( smallScaleExp, filePrefixGlobal + "_" + SMALL, // small scale filePrefixGlobal, // large scale Classification.SPECIES ); } }
@Override public void warning( SAXParseException e ) throws SAXException { log.warn(e.getMessage()); PsiValidatorMessage msg = new PsiValidatorMessage(PsiValidatorMessage.Level.WARN, e); report.addMessage(msg); }
public Map<String, String> getExperimentWithErrors() { if ( !experimentsClassified ) { classifyExperiments(); } return experimentsWithErrors; }
public ExperimentListItem(Collection<String> experimentLabels, String name, String parentFolders, boolean negative, Integer chunkNumber, Integer largeScaleSize) { this.experimentLabels = experimentLabels; this.name = name; this.negative = negative; this.chunkNumber = chunkNumber; this.largeScaleChunkSize = largeScaleSize; this.parentFolders = removeTrailingSlash(parentFolders); }
public Set<Experiment> getNegativeExperiments() { if ( negativeExperiments == null ) { classifyNegatives(); } return negativeExperiments; }