ubic.BAMSandAllen.adjacency.IdentityAdjacency.java Source code

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Here is the source code for ubic.BAMSandAllen.adjacency.IdentityAdjacency.java

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/*******************************************************************************
 * The ABAMS project
 * 
 * Copyright (c) 2012 University of British Columbia
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *       http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 ******************************************************************************/
package ubic.BAMSandAllen.adjacency;

import java.util.HashSet;
import java.util.Set;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import ubic.BAMSandAllen.Util;
import ubic.basecode.dataStructure.matrix.DenseDoubleMatrix;
import ubic.basecode.dataStructure.matrix.DoubleMatrix;

public class IdentityAdjacency extends AdjacencyComputeSlow {
    private static Log log = LogFactory.getLog(IdentityAdjacency.class.getName());

    public IdentityAdjacency(DoubleMatrix<String, String> matrix) {
        super(matrix);
    }

    @Override
    public AdjacencyCompute clone() {
        // TODO Auto-generated method stub
        return this;
    }

    /**
     * Return the same matrix given.
     */
    public DoubleMatrix<String, String> getAdjacency(DoubleMatrix<String, String> toCompute) {
        Set<String> rowSet = new HashSet<String>(toCompute.getRowNames());
        Set<String> colSet = new HashSet<String>(toCompute.getColNames());
        if (!rowSet.equals(colSet)) {
            throw new RuntimeException("Not a square matrix with matching rows/cols");
        }
        // re-order the rows to be the same as cols
        DoubleMatrix<String, String> result = new DenseDoubleMatrix<String, String>(colSet.size(), colSet.size());
        result.setColumnNames(toCompute.getColNames());
        result.setRowNames(toCompute.getColNames());
        for (String row : colSet) {
            for (String col : colSet) {
                result.setByKeys(row, col, toCompute.getByKeys(row, col));
                result.setByKeys(col, row, toCompute.getByKeys(row, col));
            }
        }
        return result;
    }

}