/**
* 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();
}
@Override
protected void updateText(final int pre, final byte[] value, final int kind) {
final boolean text = kind != ATTR;
if (meta.updindex) {
// update indexes
final int id = id(pre);
final byte[] oldval = text(pre, text);
final DiskValues index = (DiskValues) (text ? textIndex : attrIndex);
// don't index document names
if (index != null && kind != DOC) index.replace(oldval, value, id);
}
// reference to text store
final DataAccess store = text ? texts : values;
// file length
final long len = store.length();
// new entry (offset or value)
final long v = toSimpleInt(value);
if (v != Integer.MIN_VALUE) {
// inline integer value
textOff(pre, v | IO.OFFNUM);
} else {
// text to be stored (possibly packed)
final byte[] val = COMP.get().pack(value);
// old entry (offset or value)
final long old = textOff(pre);
// find text store offset
final long off;
if (number(old)) {
// numeric entry: append new entry at the end
off = len;
} else {
// text size (0 if value will be inlined)
final int vl = val.length;
off = store.free(old & IO.OFFCOMP - 1, vl + Num.length(vl));
}
store.writeToken(off, val);
textOff(pre, val == value ? off : off | IO.OFFCOMP);
}
}
