public HeatMapData(ProteinComparisonDataset comparison) {
datasetLabels = new ArrayList<String>(comparison.getDatasetCount() + 1);
for (Dataset ds : comparison.getDatasets()) {
datasetLabels.add(("ID_" + ds.getDatasetId()));
}
rows = new ArrayList<HeatMapRow>(comparison.getTotalProteinCount() + 1);
int index = 0;
for (ComparisonProtein protein : comparison.getProteins()) {
HeatMapRow row = new HeatMapRow();
row.setIndexInList(index++);
rows.add(row);
List<HeatMapCell> cells = new ArrayList<HeatMapCell>();
row.setRowName(protein.getProteinListing().getFastaReferences().get(0).getShortAccession());
List<String> allNames = new ArrayList<String>(1);
allNames.add(row.getRowName());
row.setRowAllNames(allNames);
// add cell for molecular wt.
String molWtCellColor = getColorForMolWt(protein.getMolecularWeight());
HeatMapCell cell1 = new HeatMapCell();
cell1.setLabel("");
cell1.setHexColor(molWtCellColor);
cells.add(cell1);
for (Dataset ds : comparison.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(comparison.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, comparison.getDatasets());
row.setPlotUrl(plotUrl);
}
row.setCells(cells);
}
}
private String getPlotUrl(ComparisonProtein protein, List<? extends Dataset> datasets) {
String plotUrl = "http://chart.apis.google.com/chart?cht=bhg&chxt=x,y";
String data1 = "";
String data2 = "";
// String colors = "";
String xrange = "";
String scale = "";
String xlabel = "";
String chartSize = "chs=";
// chart title
// String title =
// "&chtt="+protein.getProteinListing().getFastaReferences().get(0).getShortAccession();
// plotUrl += title;
int idx = 0;
int maxSc = 0;
int maxLabel = 0;
boolean allDatasetsHaveNames = true;
for (Dataset ds : datasets) {
if (ds.getDatasetName() == null || ds.getDatasetName().length() == 0) {
allDatasetsHaveNames = false;
break;
}
}
for (Dataset ds : datasets) {
DatasetProteinInformation dpi = protein.getDatasetProteinInformation(ds);
if (allDatasetsHaveNames) {
xlabel = "|" + ds.getDatasetName() + xlabel;
} else {
xlabel = "|" + ds.getDatasetId() + xlabel;
}
// colors += "|"+DatasetColor.get(idx).hexValue();
idx++;
maxLabel = (int) Math.max(maxLabel, ("" + ds.getDatasetId()).length());
if (dpi == null || !dpi.isPresent()) {
data1 += ",0";
data2 += ",0";
} else {
data1 += "," + dpi.getNormalizedSpectrumCountRounded();
data2 += "," + dpi.getSpectrumCount();
maxSc = (int) Math.max(maxSc, dpi.getNormalizedSpectrumCount());
}
}
int barWidth = (maxLabel * 6) / 2;
if (barWidth < 12) barWidth = 12;
String barSpacing = barWidth + ",1,10";
int chartHeight = ((barWidth * 2 + 1 + 10) * datasets.size()) + 50;
chartSize += "250x" + chartHeight;
plotUrl += "&" + chartSize;
plotUrl += "&chbh=" + barSpacing;
// colors = colors.substring(1);
plotUrl += "&chco=C6D9FD,4D89F9";
data1 = data1.substring(1);
data1 = "t:" + data1;
data2 = data2.substring(1);
data2 = "|" + data2;
plotUrl += "&chd=" + data1 + data2;
int div = (int) Math.ceil((double) maxSc / 10.0);
if (div > 5) {
div = Math.round((float) div / 5.0f) * 5;
}
xrange = "0,0," + maxSc + "," + div;
plotUrl += "&chxr=" + xrange;
scale = "0," + maxSc;
plotUrl += "&chds=" + scale;
// x-axis labels
plotUrl += "&chxl=1:" + xlabel + "|";
// bar labels
plotUrl += "&chm=N,000000,0,,10|N,000000,1,,10";
// legend
plotUrl += "&chdl=Norm.+Spectrum+Count|Spectrum+Count&chdlp=b";
return plotUrl;
}