Examples of org.broad.igv.util.collections.FloatArrayList

org.broad.igv.util.collections.FloatArrayList
Author: jrobinso Date: Jul 22, 2010
ArrayList type collection for int types. Purpose is to avoid the need to create an object for each entry in the standard java collections.

            int[] sortedEnds = reorder(indices, endLocationsMap.get(chr));
            float[] sortedData = reorder(indices, dataMap.get(chr));


            startLocationsMap.put(chr, new IntArrayList(sortedStarts));
            endLocationsMap.put(chr, new IntArrayList(sortedEnds));
            dataMap.put(chr, new FloatArrayList(sortedData));
        }


    }

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            } else {
                endLocations.addAll(ends);
            }
        }


        FloatArrayList dataArray = this.dataMap.get(chr);
        if (dataArray == null) {
            this.dataMap.put(chr, data);
        } else {


            dataArray.addAll(data);
        }
        float[] d = data.toArray();
        for (int i = 0; i < d.length; i++) {
            dataMax = Math.max(dataMax, d[i]);
            dataMin = Math.min(dataMin, d[i]);

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            return endLocations.toArray();
        }
    }


    public float[] getData(String heading, String chr) {
        FloatArrayList data = this.dataMap.get(chr);
        if (data == null) {
            return null;
        } else {
            return data.toArray();
        }
    }

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    }


    protected void initializeDataHolders() {
        startLocations = new IntArrayList(estArraySize);
        endLocations = new IntArrayList(estArraySize);
        data = new FloatArrayList(estArraySize);
        lastPosition = -1;
    }

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        dataMap = new HashMap<String, Map<String, FloatArrayList>>();
        for (String chr : chrNames) {
            locationMap.put(chr, new IntArrayList(nPixels / 10));
            dataMap.put(chr, new HashMap<String, FloatArrayList>());
            for (String s : samples) {
                dataMap.get(chr).put(s, new FloatArrayList(nPixels / 10));
            }
        }
    }

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            this.tileEnd = end;
            startArray = new IntArrayList();
            endArray = new IntArrayList();
            dataArray = new FloatArrayList[nTracks];
            for (int i = 0; i < nTracks; i++) {
                dataArray[i] = new FloatArrayList();
            }
        }

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            IntArrayList endLocations = (hasEndLocations ? new IntArrayList(nRowsEst) : null);
            List<String> probes = new ArrayList(nRowsEst);


            Map<String, FloatArrayList> dataMap = new HashMap();
            for (String h : dataHeaders) {
                dataMap.put(h, new FloatArrayList(nRowsEst));
            }


            // Begin loop through rows
            String chromosome = chrSummary.getName();
            boolean chromosomeStarted = false;

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        Map<String, FloatArrayList> data = new HashMap();


        WholeGenomeData(String[] headings) {
            this.headings = headings;
            for (String h : headings) {
                data.put(h, new FloatArrayList(50000));
            }
        }

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        }


        // TODO -- fetch data directly in arrays to avoid creation of multiple "WigItem" objects?
        IntArrayList startsList = new IntArrayList(100000);
        IntArrayList endsList = new IntArrayList(100000);
        FloatArrayList valuesList = new FloatArrayList(100000);


        String chrAlias = chrNameMap.containsKey(chr) ? chrNameMap.get(chr) : chr;
        Iterator<BedFeature> bedIterator = reader.getBigBedIterator(chrAlias, start, chrAlias, end, false);


        while (bedIterator.hasNext()) {
            BedFeature feat = bedIterator.next();


            startsList.add(feat.getStartBase());
            endsList.add(feat.getEndBase());
            //valuesList.add(wi.getWigValue());
        }


        DataTile tile = new DataTile(startsList.toArray(), endsList.toArray(), valuesList.toArray(), null);
        currentInterval = new RawDataInterval(chr, start, end, tile);


        return tile;
    }

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        }


        // TODO -- fetch data directly in arrays to avoid creation of multiple "WigItem" objects?
        IntArrayList startsList = new IntArrayList(100000);
        IntArrayList endsList = new IntArrayList(100000);
        FloatArrayList valuesList = new FloatArrayList(100000);


        String chrAlias = chrNameMap.containsKey(chr) ? chrNameMap.get(chr) : chr;
        Iterator<WigItem> iter = reader.getBigWigIterator(chrAlias, start, chrAlias, end, false);


        while (iter.hasNext()) {
            WigItem wi = iter.next();
            startsList.add(wi.getStartBase());
            endsList.add(wi.getEndBase());
            valuesList.add(wi.getWigValue());
        }


        DataTile tile = new DataTile(startsList.toArray(), endsList.toArray(), valuesList.toArray(), null);
        currentInterval = new RawDataInterval(chr, start, end, tile);


        return tile;


    }

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Related Classes of org.broad.igv.util.collections.FloatArrayList

org.broad.igv.bigwig.BigWigDataSource

org.broad.igv.data.GenomeSummaryData

org.broad.igv.data.IGVDatasetParser

org.broad.igv.data.IGVDatasetParser$WholeGenomeData

org.broad.igv.data.WiggleDataset

org.broad.igv.data.WiggleParser

org.broad.igv.methyl.ZillerDataSource2

org.broad.igv.tools.Preprocessor$RawTile

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