public void balanceValues() {
float value2Balance = 0;
if ((-1 * minValue) > maxValue) value2Balance = -1 * minValue;
else value2Balance = -1 * maxValue;
// set zero as base value
bases.add(0, new Integer(1));
values.add(0, new Float(0));
// any negative values? Don't set unless so.
if (minValue < 0) {
bases.add(0, new Integer(0));
values.add(0, new Float(value2Balance));
}
}
/**
* Makes a stair step heat map from an array of windows in bar format. One per chromosome. Don't
* forget to set the barDirectory and score Index!!!!!!!
*/
public void makeStairStepBarFiles() {
// make bar parser
BarParser bp = new BarParser();
bp.setZipCompress(true);
HashMap<String, String> tagVals = new HashMap<String, String>();
tagVals.put(BarParser.GRAPH_TYPE_TAG, BarParser.GRAPH_TYPE_STAIRSTEP);
tagVals.put(BarParser.GRAPH_TYPE_COLOR_TAG, "#FF00FF"); // fusha
tagVals.put(BarParser.SOURCE_TAG, bedFile.toString());
// for each chromosome
System.out.print("Printing... ");
Iterator<String> it = bedLinesHash.keySet().iterator();
while (it.hasNext()) {
chromosome = it.next();
System.out.print(chromosome + " ");
windows = bedLinesHash.get(chromosome);
// add blocks
assembleBlocks();
// balance by adding max or min at zero base
balanceValues();
// write bar file
File barFile = new File(barDirectory, chromosome + ".bar");
bp.writeBarFile(
barFile,
chromosome,
genomeVersion,
'.',
Num.arrayListOfIntegerToInts(bases),
Num.arrayListOfFloatToArray(values),
tagVals);
// clear ArrayLists
bases.clear();
values.clear();
}
System.out.println();
}
/** Adds a gr line to the global ArrayLists for later burning to bar. */
public void add(int base, float value) {
bases.add(new Integer(base));
values.add(new Float(value));
}
