Ass missing report class

src/main/java/genepi/mut/tasks/ReportTask.java

@@ -0,0 +1,72 @@
+package genepi.mut.tasks;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
+import genepi.mut.App;
+import genepi.mut.objects.ReportObject;
+import genepi.mut.objects.Sample;
+import genepi.mut.objects.Variant;
+import genepi.mut.util.MutationServerReader;
+import lukfor.reports.HtmlReport;
+
+public class ReportTask {
+
+	private String input;
+	private String output;
+
+	public String getInput() {
+		return input;
+	}
+
+	public void setInput(String input) {
+		this.input = input;
+	}
+
+	public String getOutput() {
+		return output;
+	}
+
+	public void setOutput(String output) {
+		this.output = output;
+	}
+
+	public void createReport() throws IOException {
+
+		HtmlReport report = new HtmlReport("/report");
+		report.setSelfContained(true);
+		report.set("title", "mtDNA Server Report - ("+App.VERSION+")");
+
+		List<ReportObject> variants = new ArrayList<ReportObject>();
+		MutationServerReader reader = new MutationServerReader(input);
+		HashMap<String, Sample> samples = reader.parse();
+
+		for (Sample sample : samples.values()) {
+
+			for (ArrayList<Variant> a : sample.getVariants()) {
+
+				for (Variant variant : a) {
+					ReportObject reportObject = new ReportObject();
+					reportObject.setCoverage(variant.getCoverage());
+					reportObject.setId(sample.getId());
+					reportObject.setPos(variant.getPos());
+					reportObject.setFilter(variant.getFilter().name());
+					reportObject.setRef(variant.getRef());
+					reportObject.setVar(variant.getVariant());
+					reportObject.setLevel(variant.getLevel());
+					reportObject.setType(variant.getType());
+					variants.add(reportObject);
+
+				}
+			}
+		}
+
+		report.set("variants", variants);
+		report.generate(new File(output));
+
+	}
+
+}