Package org.broad.igv.data

Examples of org.broad.igv.data.DataTile

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        Iterator<Feature> features = featureSource.getFeatures(chr, start, end);
        int count = countNonNullFeatures(features);
        assertTrue("No features read" , count > 0);

        assertTrue("No longest feature", geneTrackingSource.getLongestFeature(chr) > 0);
        DataTile dataTile = geneTrackingSource.getRawData(chr, start, end);
        assertNotNull("No fpkm data returned", dataTile);
        assertFalse(dataTile.isEmpty());

    }
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                }
            }
        }

        coverageData.dataCache.put(Globals.CHR_ALL, new DataTile(starts, ends, values, null));
    }
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        }

        protected DataTile getRawData(String chr, int startLocation, int endLocation) {


            DataTile coverageData = dataCache.get(chr);
            if (coverageData == null) {
                coverageData = computeCoverage(chr, startLocation, endLocation);
                dataCache.put(chr, coverageData);
            }
            return coverageData;
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                        values[i] = values[i] + 1;
                        dataMax = Math.max(dataMax, values[i]);
                    }
                }
            }
            return new DataTile(starts, ends, values, null);

        }
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                    }
                }
            }

            dataCache.put(Globals.CHR_ALL, new DataTile(starts, ends, values, null));
        }
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            }

            protected DataTile getRawData(String chr, int startLocation, int endLocation) {


                DataTile coverageData = dataCache.get(chr);
                if (coverageData == null) {
                    coverageData = computeCoverage(chr, startLocation, endLocation);
                    dataCache.put(chr, coverageData);
                }
                return coverageData;
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                            values[i] = values[i] + 1;
                            dataMax = Math.max(dataMax, values[i]);
                        }
                    }
                }
                return new DataTile(starts, ends, values, null);

            }
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                        }
                    }
                }

                dataCache.put(Globals.CHR_ALL, new DataTile(starts, ends, values, null));
            }
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                endLocations[idx] = locusScore.getEnd();
                scores[idx] = locusScore.getScore();
                names[idx] = Locus.getFormattedLocusString(locusScore.getChr(), locusScore.getStart(), locusScore.getEnd());
                idx++;
            }
            return new DataTile(startLocations, endLocations, scores, names);

        } catch (IOException e) {
            log.error(e.getMessage(), e);
            throw new RuntimeException(e);
        }
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            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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Related Classes of org.broad.igv.data.DataTile

  • org.broad.igv.bigwig.BigWigDataSource
  • org.broad.igv.cli_plugin.CufflinksPluginTest
  • org.broad.igv.cli_plugin.PluginDataSource
  • org.broad.igv.methyl.ZillerDataSource2
  • org.broad.igv.track.FeatureCollectionSource
  • org.broad.igv.track.FeatureCollectionSource$CoverageDataSource
  • org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource$CoverageDataSource
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