public List<ExperimentListItem> generateAllClassifications() { if ( !experimentsClassified ) { classifyExperiments(); } List<ExperimentListItem> allItems = new ArrayList<ExperimentListItem>(); allItems.addAll( generateClassificationBySpecies() ); allItems.addAll( generateClassificationByPublications() ); return allItems; }
public Set<Experiment> getNegativeExperiments() { if ( negativeExperiments == null ) { classifyNegatives(); } return negativeExperiments; }
public List<ExperimentListItem> generateClassificationByDatasets() { if ( !experimentsClassified ) { classifyExperiments(); } if ( datasetsListItems != null && !datasetsListItems.isEmpty() ) { return datasetsListItems; } createItemClassificationByDataset(); return datasetsListItems; }
public List<ExperimentListItem> generateClassificationByPublications() { if ( !experimentsClassified ) { classifyExperiments(); } if ( publicationsListItems != null && !publicationsListItems.isEmpty() ) { return publicationsListItems; } createItemClassificationByPubmed(); return publicationsListItems; }
public List<ExperimentListItem> generateClassificationBySpecies() { if ( !experimentsClassified ) { classifyExperiments(); } if ( speciesListItems != null && !speciesListItems.isEmpty() ) { return speciesListItems; } createItemClassificationBySpecies(); return speciesListItems; }
private void createExperimentListItems( String name, Collection<SimplifiedAnnotatedObject<Experiment>> exps, Integer chunkNumber, Classification classification, Integer largeScaleChunkSize ) { List<String> labels = new ArrayList<String>(); List<String> labelsNegative = new ArrayList<String>(); for ( SimplifiedAnnotatedObject exp : exps ) { if ( isNegative( exp.getShortLabel() ) ) { labelsNegative.add( exp.getShortLabel() ); } else { labels.add( exp.getShortLabel() ); } } String parentFolders = parentFolders( exps, classification ); if ( !labels.isEmpty() ) { addToList( new ExperimentListItem( labels, name, parentFolders, false, chunkNumber, largeScaleChunkSize ), classification ); } if ( !labelsNegative.isEmpty() ) { addToList( new ExperimentListItem( labelsNegative, name, parentFolders, true, chunkNumber, largeScaleChunkSize ), classification ); } }
final int size = interactionsForExperiment( experiment.getAc() ); createExperimentListItems( largeScalePrefix, largeScale, chunk, classification, largeScaleChunkSize ); chunk++; createExperimentListItems( smallScalePrefix, chunk, index, classification, null );
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 ); } }
public Map<String, String> getExperimentWithErrors() { if ( !experimentsClassified ) { classifyExperiments(); } return experimentsWithErrors; }
private void createExperimentListItems( String name, Collection<SimplifiedAnnotatedObject<Experiment>> exps, Integer chunkNumber, Classification classification, Integer largeScaleChunkSize ) { List<String> labels = new ArrayList<String>(); List<String> labelsNegative = new ArrayList<String>(); for ( SimplifiedAnnotatedObject exp : exps ) { if ( isNegative( exp.getShortLabel() ) ) { labelsNegative.add( exp.getShortLabel() ); } else { labels.add( exp.getShortLabel() ); } } String parentFolders = parentFolders( exps, classification ); if ( !labels.isEmpty() ) { addToList( new ExperimentListItem( labels, name, parentFolders, false, chunkNumber, largeScaleChunkSize ), classification ); } if ( !labelsNegative.isEmpty() ) { addToList( new ExperimentListItem( labelsNegative, name, parentFolders, true, chunkNumber, largeScaleChunkSize ), classification ); } }
public List<ExperimentListItem> generateClassificationByPublications() { if ( !experimentsClassified ) { classifyExperiments(); } if ( publicationsListItems != null && !publicationsListItems.isEmpty() ) { return publicationsListItems; } createItemClassificationByPubmed(); return publicationsListItems; }
public List<ExperimentListItem> generateClassificationBySpecies() { if ( !experimentsClassified ) { classifyExperiments(); } if ( speciesListItems != null && !speciesListItems.isEmpty() ) { return speciesListItems; } createItemClassificationBySpecies(); return speciesListItems; }
final int size = interactionsForExperiment( experiment.getAc() ); createExperimentListItems( largeScalePrefix, largeScale, chunk, classification, largeScaleChunkSize ); chunk++; createExperimentListItems( smallScalePrefix, chunk, index, classification, null );
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 ); } }
public Map<String, String> getExperimentWithErrors() { if ( !experimentsClassified ) { classifyExperiments(); } return experimentsWithErrors; }
public List<ExperimentListItem> generateAllClassifications() { if ( !experimentsClassified ) { classifyExperiments(); } List<ExperimentListItem> allItems = new ArrayList<ExperimentListItem>(); allItems.addAll( generateClassificationBySpecies() ); allItems.addAll( generateClassificationByPublications() ); return allItems; }
private void createExperimentListItems( String name, Collection<SimplifiedAnnotatedObject<Experiment>> exps, Integer chunkNumber, Classification classification, Integer largeScaleChunkSize ) { List<String> labels = new ArrayList<String>(); List<String> labelsNegative = new ArrayList<String>(); for ( SimplifiedAnnotatedObject exp : exps ) { if ( isNegative( exp.getShortLabel() ) ) { labelsNegative.add( exp.getShortLabel() ); } else { labels.add( exp.getShortLabel() ); } } String parentFolders = parentFolders( exps, classification ); if ( !labels.isEmpty() ) { addToList( new ExperimentListItem( labels, name, parentFolders, false, chunkNumber, largeScaleChunkSize ), classification ); } if ( !labelsNegative.isEmpty() ) { addToList( new ExperimentListItem( labelsNegative, name, parentFolders, true, chunkNumber, largeScaleChunkSize ), classification ); } }
public List<ExperimentListItem> generateClassificationByPublications() { if ( !experimentsClassified ) { classifyExperiments(); } if ( publicationsListItems != null && !publicationsListItems.isEmpty() ) { return publicationsListItems; } createItemClassificationByPubmed(); return publicationsListItems; }
public List<ExperimentListItem> generateClassificationByDatasets() { if ( !experimentsClassified ) { classifyExperiments(); } if ( datasetsListItems != null && !datasetsListItems.isEmpty() ) { return datasetsListItems; } createItemClassificationByDataset(); return datasetsListItems; }
public List<ExperimentListItem> generateClassificationBySpecies() { if ( !experimentsClassified ) { classifyExperiments(); } if ( speciesListItems != null && !speciesListItems.isEmpty() ) { return speciesListItems; } createItemClassificationBySpecies(); return speciesListItems; }