uk.ac.ebi.intact.application.dataConversion.ExperimentListGenerator$SimplifiedAnnotatedObject.getShortLabel java code examples

Add the Codota plugin to your IDE and get smart completions

private void myMethod () {
 OutputStreamWriter o =OutputStream out;new OutputStreamWriter(out)
OutputStream out;String charsetName;new OutputStreamWriter(out, charsetName)
HttpURLConnection connection;new OutputStreamWriter(connection.getOutputStream())
Smart code suggestions by Codota
}

/**
 * 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;
}

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 boolean equals( Object obj ) {
  SimplifiedAnnotatedObject o = (SimplifiedAnnotatedObject) obj;
  return ac.equals( o.getAc() ) && shortLabel.equals( o.getShortLabel() );
}

@Override
public boolean equals( Object obj ) {
  SimplifiedAnnotatedObject o = (SimplifiedAnnotatedObject) obj;
  return ac.equals( o.getAc() ) && shortLabel.equals( o.getShortLabel() );
}

@Override
public String toString() {
  return getAc() + " " + getShortLabel();
}

@Override
public boolean equals( Object obj ) {
  SimplifiedAnnotatedObject o = (SimplifiedAnnotatedObject) obj;
  return ac.equals( o.getAc() ) && shortLabel.equals( o.getShortLabel() );
}

@Override
public String toString() {
  return getAc() + " " + getShortLabel();
}

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 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 );
  }
}

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 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 );
  }
}

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 );
  }
}

@Override
public String toString() {
  return getAc() + " " + getShortLabel();
}

Popular methods of ExperimentListGenerator$SimplifiedAnnotatedObject

Popular in Java

Running tasks concurrently on multiple threads
getSupportFragmentManager (FragmentActivity)
setContentView (Activity)
getSharedPreferences (Context)
GridLayout (java.awt)
The GridLayout class is a layout manager that lays out a container's components in a rectangular gri
ResultSet (java.sql)
An interface for an object which represents a database table entry, returned as the result of the qu
Timestamp (java.sql)
A Java representation of the SQL TIMESTAMP type. It provides the capability of representing the SQL
DataSource (javax.sql)
A factory for connections to the physical data source that this DataSource object represents. An alt
JButton (javax.swing)
JPanel (javax.swing)

How to use getShortLabelmethodin uk.ac.ebi.intact.application.dataConversion.ExperimentListGenerator$SimplifiedAnnotatedObject

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.ExperimentListGenerator$SimplifiedAnnotatedObject.getShortLabel (Showing top 15 results out of 315)

How to use
getShortLabel
method
in
uk.ac.ebi.intact.application.dataConversion.ExperimentListGenerator$SimplifiedAnnotatedObject