Examples with IntegerMatrix ubic.basecode.dataStructure.matrix.IntegerMatrix used on opensource projects

Example 1 with IntegerMatrix

use of ubic.basecode.dataStructure.matrix.IntegerMatrix in project Gemma by PavlidisLab.

the class ExpressionDataIntegerMatrix method createMatrix.

/**
 * Fill in the data
 *
 * @return DoubleMatrixNamed
 */
private IntegerMatrix<CompositeSequence, Integer> createMatrix(Collection<? extends DesignElementDataVector> vectors, int maxSize) {
    int numRows = this.rowDesignElementMapByInteger.keySet().size();
    IntegerMatrix<CompositeSequence, Integer> mat = new IntegerMatrix<>(numRows, maxSize);
    for (int j = 0; j < mat.columns(); j++) {
        mat.addColumnName(j);
    }
    // initialize the matrix to 0
    for (int i = 0; i < mat.rows(); i++) {
        for (int j = 0; j < mat.columns(); j++) {
            mat.set(i, j, 0);
        }
    }
    ByteArrayConverter bac = new ByteArrayConverter();
    Map<Integer, CompositeSequence> rowNames = new TreeMap<>();
    for (DesignElementDataVector vector : vectors) {
        CompositeSequence designElement = vector.getDesignElement();
        assert designElement != null : "No design element for " + vector;
        Integer rowIndex = this.rowElementMap.get(designElement);
        assert rowIndex != null;
        rowNames.put(rowIndex, designElement);
        byte[] bytes = vector.getData();
        int[] vals = bac.byteArrayToInts(bytes);
        BioAssayDimension dimension = vector.getBioAssayDimension();
        Collection<BioAssay> bioAssays = dimension.getBioAssays();
        assert bioAssays.size() == vals.length : "Expected " + vals.length + " got " + bioAssays.size();
        Iterator<BioAssay> it = bioAssays.iterator();
        this.setMatBioAssayValues(mat, rowIndex, ArrayUtils.toObject(vals), bioAssays, it);
    }
    for (int i = 0; i < mat.rows(); i++) {
        mat.addRowName(rowNames.get(i));
    }
    ExpressionDataIntegerMatrix.log.debug("Created a " + mat.rows() + " x " + mat.columns() + " matrix");
    return mat;
}