org.caleydo.view.bicluster.ScanLZTable.java Source code

Introduction

Here is the source code for org.caleydo.view.bicluster.ScanLZTable.java

Source

/*******************************************************************************
 * Caleydo - Visualization for Molecular Biology - http://caleydo.org
 * Copyright (c) The Caleydo Team. All rights reserved.
 * Licensed under the new BSD license, available at http://caleydo.org/license
 *******************************************************************************/
package org.caleydo.view.bicluster;

import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.Callable;

import org.caleydo.core.data.collection.table.Table;
import org.caleydo.view.bicluster.sorting.FuzzyClustering;
import org.caleydo.view.bicluster.sorting.IntFloat;

import com.google.common.collect.ImmutableList;
import com.google.common.collect.ImmutableSortedSet;

/**
 * scan the L or Z table and produce a list of {@link FuzzyClustering} instances
 * 
 * @author Samuel Gratzl
 * 
 */
public class ScanLZTable implements Callable<List<FuzzyClustering>> {
    private final Table lOrZ;

    public ScanLZTable(Table lOrZ) {
        this.lOrZ = lOrZ;
    }

    @Override
    public List<FuzzyClustering> call() throws Exception {
        final int rows = lOrZ.depth();
        final int clusters = lOrZ.size();

        List<FuzzyClustering> l = new ArrayList<>(clusters);
        for (int i = 0; i < clusters; ++i) {
            ImmutableSortedSet.Builder<IntFloat> b = ImmutableSortedSet.orderedBy(IntFloat.BY_MEMBERSHIP);
            for (int j = 0; j < rows; ++j) {
                float p = lOrZ.getRaw(i, j);
                b.add(new IntFloat(j, p));
            }
            l.add(new FuzzyClustering(b.build()));
        }
        return ImmutableList.copyOf(l);
    }
}