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

Example 1 with StringMatrix

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

the class ExpressionDataStringMatrix method createMatrix.

private StringMatrix<Integer, Integer> createMatrix(Collection<? extends DesignElementDataVector> vectors, int maxSize) {
    int numRows = this.rowDesignElementMapByInteger.keySet().size();
    StringMatrix<Integer, Integer> mat = new StringMatrix<>(numRows, maxSize);
    for (int j = 0; j < mat.columns(); j++) {
        mat.addColumnName(j);
    }
    // initialize the matrix to "";
    for (int i = 0; i < mat.rows(); i++) {
        for (int j = 0; j < mat.columns(); j++) {
            mat.set(i, j, "");
        }
    }
    ByteArrayConverter bac = new ByteArrayConverter();
    for (DesignElementDataVector vector : vectors) {
        CompositeSequence designElement = vector.getDesignElement();
        assert designElement != null : "No designelement for " + vector;
        Integer rowIndex = this.rowElementMap.get(designElement);
        assert rowIndex != null;
        mat.addRowName(rowIndex);
        byte[] bytes = vector.getData();
        String[] vals = bac.byteArrayToStrings(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();
        for (int j = 0; j < bioAssays.size(); j++) {
            BioAssay bioAssay = it.next();
            Integer column = this.columnAssayMap.get(bioAssay);
            assert column != null;
            mat.setByKeys(rowIndex, column, vals[j]);
        }
    }
    ExpressionDataStringMatrix.log.debug("Created a " + mat.rows() + " x " + mat.columns() + " matrix");
    return mat;
}