public HeatMapData(ProteinGroupComparisonDataset grpComparison) {
datasetLabels = new ArrayList<String>(grpComparison.getDatasetCount() + 1);
for (Dataset ds : grpComparison.getDatasets()) {
if (ds.getDatasetName() != null && ds.getDatasetName().length() > 0) {
datasetLabels.add((ds.getDatasetName() + "(ID" + ds.getDatasetId()) + ")");
} else {
datasetLabels.add(("ID_" + ds.getDatasetId()));
}
}
rows = new ArrayList<HeatMapRow>(grpComparison.getTotalProteinGroupCount() + 1);
int index = 0;
for (ComparisonProteinGroup grp : grpComparison.getProteinsGroups()) {
HeatMapRow row = new HeatMapRow();
row.setIndexInList(index);
index += grp.getProteins().size();
rows.add(row);
ComparisonProtein protein = grp.getProteins().get(0);
List<HeatMapCell> cells = new ArrayList<HeatMapCell>();
// add cell for molecular wt.
String molWtCellColor = getColorForMolWt(protein.getMolecularWeight());
HeatMapCell cell1 = new HeatMapCell();
cell1.setLabel("");
cell1.setHexColor(molWtCellColor);
cells.add(cell1);
row.setRowName(protein.getProteinListing().getFastaReferences().get(0).getShortAccession());
List<String> allNames = new ArrayList<String>();
for (ComparisonProtein prot : grp.getProteins()) {
allNames.add(prot.getProteinListing().getFastaReferences().get(0).getShortAccession());
}
row.setRowAllNames(allNames);
for (Dataset ds : grpComparison.getDatasets()) {
HeatMapCell cell = new HeatMapCell();
cells.add(cell);
cell.setLabel("");
DatasetProteinInformation dpi = protein.getDatasetProteinInformation(ds);
if (dpi == null || !dpi.isPresent()) {
cell.setHexColor("#FFFFFF");
} else {
float heatMapSpectrumCount = dpi.getHeatMapSpectrumCount();
cell.setHexColor(grpComparison.getHeatMapColor(heatMapSpectrumCount));
}
}
// http://chart.apis.google.com/chart?chs=320x200&cht=bvs&chd=t:1,19,27,53,61&chds=0,61&chco=FFCC33&chxt=x,y&chxr=1,0,61,10&chxl=0:|Jan|Feb|Mar|Apr|May
String plotUrl = getPlotUrl(protein, grpComparison.getDatasets());
row.setPlotUrl(plotUrl);
row.setCells(cells);
}
}
private String getColorForMolWt(float molecularWeight) {
// int r = 255;
// int g = 255;
// int b = 0;
//
// int bin = (int) (molecularWeight / 10000);
// //r += 25 * bin;
// g -= 25 * bin;
// //b -= 25 * bin;
// r = Math.min(255, r);
// g = Math.max(0, g);
// //b = Math.max(0, bin);
if (molecularWeight > 0 && molecularWeight <= 12000)
return ProteinGroupComparisonDataset.hexValue(255, 255, 0); // 0 to 12000; yellow
else if (molecularWeight > 12000 && molecularWeight <= 18000)
return ProteinGroupComparisonDataset.hexValue(255, 180, 0); // 12000 to 18000; orange
else if (molecularWeight > 18000 && molecularWeight <= 22000)
return ProteinGroupComparisonDataset.hexValue(255, 0, 0); // 18000 to 22000; red
else if (molecularWeight > 22000 && molecularWeight <= 25000)
return ProteinGroupComparisonDataset.hexValue(255, 0, 180); // 22000 to 25000;
else if (molecularWeight > 25000 && molecularWeight <= 35000)
return ProteinGroupComparisonDataset.hexValue(255, 0, 255); // 25000 to 35000; magenta
else if (molecularWeight > 35000 && molecularWeight <= 40000)
return ProteinGroupComparisonDataset.hexValue(180, 0, 255); // 35000 to 40000
else if (molecularWeight > 40000 && molecularWeight <= 50000)
return ProteinGroupComparisonDataset.hexValue(0, 0, 255); // 40000 to 50000; blue
else if (molecularWeight > 50000 && molecularWeight <= 60000)
return ProteinGroupComparisonDataset.hexValue(0, 180, 255); // 50000 to 60000;
else if (molecularWeight > 60000 && molecularWeight <= 70000)
return ProteinGroupComparisonDataset.hexValue(0, 255, 255); // 60000 to 70000; cyan
else if (molecularWeight > 70000 && molecularWeight <= 80000)
return ProteinGroupComparisonDataset.hexValue(0, 255, 180); // 70000 to 80000;
else if (molecularWeight > 80000 && molecularWeight <= 90000)
return ProteinGroupComparisonDataset.hexValue(0, 255, 0); // 80000 to 90000; green
else return ProteinGroupComparisonDataset.hexValue(0, 0, 0); // 90000 to 100000; black
// return ProteinGroupComparisonDataset.hexValue(r, g, b);
}
