@Override public boolean equals( Object obj ) { SimplifiedAnnotatedObject o = (SimplifiedAnnotatedObject) obj; return ac.equals( o.getAc() ) && shortLabel.equals( o.getShortLabel() ); }
/** * Given a set of Experiments, it returns the year of the date of creation of the oldest experiment. * * @param experiments experiments * * @return an int corresponding to the year. */ private static String getCreatedYear( Collection<SimplifiedAnnotatedObject<Experiment>> experiments ) { if ( experiments.isEmpty() ) { throw new IllegalArgumentException( "The given Set of Experiments is empty" ); } int year = Integer.MAX_VALUE; for ( SimplifiedAnnotatedObject<Experiment> exp : experiments ) { Date created = exp.getCreated(); java.sql.Date d = new java.sql.Date( created.getTime() ); Calendar c = new GregorianCalendar(); c.setTime( d ); if ( year > c.get( Calendar.YEAR ) ) { year = c.get( Calendar.YEAR ); } } return String.valueOf( year ); }
experimentSet.add( new SimplifiedAnnotatedObject<Experiment>( experiment ) ); } else { log.debug( "ERROR: Could not find a pubmed ID for experiment: " + experiment.getShortLabel() + "(" + experiment.getAc() + ")" ); SimplifiedAnnotatedObject<BioSource> source = new SimplifiedAnnotatedObject<BioSource>( bioSource ); experiments.add( new SimplifiedAnnotatedObject<Experiment>( experiment ) ); experimentList.add( new SimplifiedAnnotatedObject<Experiment>( experiment ) );
experimentSet.add( new SimplifiedAnnotatedObject<Experiment>( experiment ) ); } else { output.println( "ERROR: Could not find a pubmed ID for experiment: " + experiment.getShortLabel() + "(" + experiment.getAc() + ")" ); SimplifiedAnnotatedObject<BioSource> source = new SimplifiedAnnotatedObject<BioSource>( bioSource ); experiments.add( new SimplifiedAnnotatedObject<Experiment>( experiment ) ); experimentList.add( new SimplifiedAnnotatedObject<Experiment>( experiment ) );
experimentSet.add( new SimplifiedAnnotatedObject<Experiment>( experiment ) ); } else { output.println( "ERROR: Could not find a pubmed ID for experiment: " + experiment.getShortLabel() + "(" + experiment.getAc() + ")" ); SimplifiedAnnotatedObject<BioSource> source = new SimplifiedAnnotatedObject<BioSource>( bioSource ); experiments.add( new SimplifiedAnnotatedObject<Experiment>( experiment ) ); experimentList.add( new SimplifiedAnnotatedObject<Experiment>( experiment ) );
final int size = interactionsForExperiment( experiment.getAc() );
final int size = interactionsForExperiment( experiment.getAc() );
final int size = interactionsForExperiment( experiment.getAc() );
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 ); } }
/** * Given a set of Experiments, it returns the year of the date of creation of the oldest experiment. * * @param experiments experiments * * @return an int corresponding to the year. */ private static String getCreatedYear( Collection<SimplifiedAnnotatedObject<Experiment>> experiments ) { if ( experiments.isEmpty() ) { throw new IllegalArgumentException( "The given Set of Experiments is empty" ); } int year = Integer.MAX_VALUE; for ( SimplifiedAnnotatedObject<Experiment> exp : experiments ) { Date created = exp.getCreated(); java.sql.Date d = new java.sql.Date( created.getTime() ); Calendar c = new GregorianCalendar(); c.setTime( d ); if ( year > c.get( Calendar.YEAR ) ) { year = c.get( Calendar.YEAR ); } } return String.valueOf( year ); }
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 ); } }
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 ); } }
/** * Given a set of Experiments, it returns the year of the date of creation of the oldest experiment. * * @param experiments experiments * * @return an int corresponding to the year. */ private static String getCreatedYear( Collection<SimplifiedAnnotatedObject<Experiment>> experiments ) { if ( experiments.isEmpty() ) { throw new IllegalArgumentException( "The given Set of Experiments is empty" ); } int year = Integer.MAX_VALUE; for ( SimplifiedAnnotatedObject<Experiment> exp : experiments ) { Date created = exp.getCreated(); java.sql.Date d = new java.sql.Date( created.getTime() ); Calendar c = new GregorianCalendar(); c.setTime( d ); if ( year > c.get( Calendar.YEAR ) ) { year = c.get( Calendar.YEAR ); } } return String.valueOf( year ); }
/** * Sort a collection of String (shorltabel). The given collection is not modified, a new one is returned. * * @param experiments collection to sort. * * @return the sorted collection. */ private static List<String> getSortedShortlabel( Collection<SimplifiedAnnotatedObject<Experiment>> experiments ) { List<String> sorted = new ArrayList<String>( experiments.size() ); for ( SimplifiedAnnotatedObject<Experiment> experiment : experiments ) { sorted.add( experiment.getShortLabel() ); } Collections.sort( sorted ); return sorted; }
/** * Sort a collection of String (shorltabel). The given collection is not modified, a new one is returned. * * @param experiments collection to sort. * * @return the sorted collection. */ private static List<String> getSortedShortlabel( Collection<SimplifiedAnnotatedObject<Experiment>> experiments ) { List<String> sorted = new ArrayList<String>( experiments.size() ); for ( SimplifiedAnnotatedObject<Experiment> experiment : experiments ) { sorted.add( experiment.getShortLabel() ); } Collections.sort( sorted ); return sorted; }
/** * Sort a collection of String (shorltabel). The given collection is not modified, a new one is returned. * * @param experiments collection to sort. * * @return the sorted collection. */ private static List<String> getSortedShortlabel( Collection<SimplifiedAnnotatedObject<Experiment>> experiments ) { List<String> sorted = new ArrayList<String>( experiments.size() ); for ( SimplifiedAnnotatedObject<Experiment> experiment : experiments ) { sorted.add( experiment.getShortLabel() ); } Collections.sort( sorted ); return sorted; }
@Override public String toString() { return getAc() + " " + getShortLabel(); }
@Override public String toString() { return getAc() + " " + getShortLabel(); }
@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 ); } }