woring on subsetting

README.textile

@@ -162,15 +162,18 @@ h3. BAYES FACTORS
 
 h3. PARSING
 
-* -parse -locations /home/filip/Dropbox/JavaProjects/Spread2/data/discrete/H5N1/locationCoordinates_H5N1 -log /home/filip/Dropbox/JavaProjects/Spread2/data/discrete/H5N1/H5N1_HA_discrete_rateMatrix.log -output test_discrete.json
+-parse -locations /home/filip/Dropbox/JavaProjects/Spread2/data/discrete/H5N1/locationCoordinates_H5N1 -log /home/filip/Dropbox/JavaProjects/Spread2/data/discrete/H5N1/H5N1_HA_discrete_rateMatrix.log -burnin 10 -output test_discrete.json
 
 h3. RENDERING
 
-* TODO
+* use all default settings
+-render -json /home/filip/Dropbox/JavaProjects/Spread2/test_discrete.json -output test.kml
 
 h4. LINES
 
-* TODO
+* TODO: attribute cutoff [bayes factor values]
+-render -json /home/filip/Dropbox/JavaProjects/Spread2/test_discrete.json -linesSubset bayesFactor -linesCutoff 10 -output test.kml
+
 
 
 h1. LICENSE
@@ -188,7 +191,7 @@ h1. LICENSE
 h1. TODO
 
 * Renderers
-  - alpha channel mapping for lines
+  - subsetting numerical and factor values
   - control arc curvature [0 - 1]
   - D3 renderer tool
 * Two data modes. dd/mm/yyyy and old origin dates.

src/app/Spread2ConsoleApp.java

@@ -50,13 +50,21 @@ public class Spread2ConsoleApp {
 	private static final String TREES = "trees";
 	private static final String LOCATIONS = "locations";
 	private static final String LOG = "log";
+	private static final String BURNIN = "burnin";
 	private static final String LOCATION_TRAIT = "locationTrait";
 	private static final String TRAITS = "traits";
 	private static final String HPD = "hpd";
 	private static final String INTERVALS = "intervals";
 	private static final String OUTPUT = "output";
 	private static final String JSON = "json";
 
+	private static final String LINES_SUBSET = "linesSubset";
+	private static final String LINES_CUTOFF = "linesCutoff";
+	private static final String LINES_VALUE = "linesValue";
+
+   //	TODO: polygon cutoffs
+
+
 	private static final String POLYGON_COLOR_MAPPING = "polygoncolormapping";
 	private static final String POLYGON_COLORS = "polygoncolors";
 	private static final String POLYGON_COLOR = "polygoncolor";
@@ -122,6 +130,8 @@ public Spread2ConsoleApp() {
 
 		new Arguments.StringOption(LOG, "", "tree file name"),
 
+		new Arguments.RealOption(BURNIN, "log file burning in %"),
+
 		new Arguments.StringOption(OUTPUT, "", "json output file name")
 
 		});
@@ -217,6 +227,12 @@ public Spread2ConsoleApp() {
 
 			    new Arguments.StringOption(POLYGON_RADIUS_MAPPING, "" ,"attribute to map radius aesthetic. Only makes sense for polygons with locations."),
 
+			    new Arguments.StringOption(LINES_SUBSET, "" ,"attribute to select a subset of values above the certain cutoff."),
+
+			    new Arguments.RealOption(LINES_CUTOFF, "specify cutoff value to create a subset"),
+
+			    new Arguments.StringOption(LINES_VALUE, "", "specify fixed value to create a subset"),
+
 				});
 
 	}// END: Constructor
@@ -475,7 +491,26 @@ public void run(String[] args) {
 								.getStringOption(OUTPUT);
 					} // END: option check
 
+					if (args2.hasOption(BURNIN)) {
+
+						Double burnin = args2
+								.getRealOption(BURNIN);
+
+						if (burnin < 0.0 || burnin > 100.0) {
+
+							throw new ArgumentException(
+									"Burnin outside of [0,100].");
+
+						} else {
+							settings.bayesFactorsSettings.burnin = burnin;
+						}
+
+					} // END: option check
 
+//					if (args2.hasOption(BF_CUTOFF)) {
+//						settings.bayesFactorsSettings.bfcutoff = args2
+//								.getRealOption(BF_CUTOFF);
+//					} // END: option check
 
 
 
@@ -787,6 +822,31 @@ public void run(String[] args) {
 
 			}
 
+			//---LINES SUBSET---//	
+
+			if(renderArguments.hasOption(LINES_SUBSET)) {
+
+				settings.kmlRendererSettings.linesSubset = renderArguments.getStringOption(LINES_SUBSET);
+
+				if(renderArguments.hasOption(LINES_CUTOFF)) {
+
+					settings.kmlRendererSettings.linesCutoff = renderArguments.getRealOption(LINES_CUTOFF);
+
+				} else if(renderArguments.hasOption(LINES_VALUE)) {
+
+                     //TODO: this should work for both real value and a factor
+					settings.kmlRendererSettings.linesValue = renderArguments.getStringOption(LINES_VALUE);
+
+				} else {
+
+					gracefullyExit("Can't create a subset from these options!", renderArguments, null);
+
+				}
+
+			}
+
+
+
 
 		} catch (ArgumentException e) {
 			gracefullyExit(e.getMessage(), renderArguments, e);

src/data/structure/Layer.java

@@ -8,8 +8,8 @@ public class Layer {
 	private final String id;
 	private final String description;
 	private final List<Polygon> polygons;
-
 	private final List<Line> lines;
+	private boolean hasPolygons;
 
 	public Layer(String id, //
 			String description, //
@@ -19,14 +19,19 @@ public Layer(String id, //
 
 		super();
 
+
+		this.hasPolygons = true;
 		this.polygons = new ArrayList<Polygon>();
 		this.lines = new ArrayList<Line>();
 
 		this.lines.addAll(lines);
-		if(polygons != null) {
-		this.polygons.addAll(polygons);
-		}
 
+		if (polygons != null) {
+			this.polygons.addAll(polygons);
+		} else {
+			this.hasPolygons = false;
+		}
+
 		this.id = id;
 		this.description = description;
 
@@ -36,6 +41,10 @@ public List<Line> getLines() {
 		return lines;
 	}
 
+	public boolean hasPolygons() {
+		return hasPolygons;
+	}
+
 	public List<Polygon> getPolygons() {
 		return polygons;
 	}

src/parsers/BayesFactorLinesParser.java

@@ -6,7 +6,6 @@
 
 import utils.Trait;
 import utils.Utils;
-
 import data.structure.Coordinate;
 import data.structure.Line;
 import data.structure.Location;
@@ -16,79 +15,76 @@ public class BayesFactorLinesParser {
 
 	private static final String BAYES_FACTOR = "bayesFactor";
 	private static final String POSTERIOR_PROBABILITY = "posteriorProbability";
-
-	private LinkedList<Location> locationsList;
 
+	private LinkedList<Location> locationsList;
 	private LinkedList<String> from;
 	private LinkedList<String> to;
-	LinkedList<Double> bayesFactors;
-	LinkedList<Double> posteriorProbabilities;
-
-
-
+	private LinkedList<Double> bayesFactors;
+	private LinkedList<Double> posteriorProbabilities;
+
 	public BayesFactorLinesParser(LinkedList<Location> locationsList, //
 			LinkedList<String> from, //
 			LinkedList<String> to, //
 			LinkedList<Double> bayesFactors, //
 			LinkedList<Double> posteriorProbabilities //
-			) {
-		
+	) {
+
 		this.locationsList = locationsList;
 		this.from = from;
 		this.to = to;
 		this.bayesFactors = bayesFactors;
 		this.posteriorProbabilities = posteriorProbabilities;
-		
-	}//END: Constructor
+
+	}// END: Constructor
 
 	public LinkedList<Line> parseLines() throws LocationNotFoundException {
-		
+
 		LinkedList<Line> linesList = new LinkedList<Line>();
 		Location dummy;
-		
-		int n = from.size();
-		for(int i = 0; i < n; i++) {
-			
-
-			dummy = new Location(from.get(i), "", new Coordinate(0.0, 0.0), null);
+
+		int n = bayesFactors.size();
+		for (int i = 0; i < n; i++) {
+
+			dummy = new Location(from.get(i), "", new Coordinate(0.0, 0.0),
+					null);
 			int fromLocationIndex = Integer.MAX_VALUE;
-			if(locationsList.contains(dummy)) {
+			if (locationsList.contains(dummy)) {
 				fromLocationIndex = locationsList.indexOf(dummy);
 			} else {
 				throw new LocationNotFoundException(dummy);
 			}
-
-
-
+
 			dummy = new Location(to.get(i), "", new Coordinate(0.0, 0.0), null);
 			int toLocationIndex = Integer.MAX_VALUE;
-			if(locationsList.contains(dummy)) {
+			if (locationsList.contains(dummy)) {
 				toLocationIndex = locationsList.indexOf(dummy);
 			} else {
 				throw new LocationNotFoundException(dummy);
 			}
-
-
+
 			Location fromLocation = locationsList.get(fromLocationIndex);
 			Location toLocation = locationsList.get(toLocationIndex);
-			
+
 			Map<String, Trait> attributes = new LinkedHashMap<String, Trait>();
-		
+
 			Double bayesFactor = bayesFactors.get(i);
 			Trait bayesFactorTrait = new Trait(bayesFactor);
 			attributes.put(BAYES_FACTOR, bayesFactorTrait);
-			
+
 			Double posteriorProbability = posteriorProbabilities.get(i);
 			Trait posteriorProbabilityTrait = new Trait(posteriorProbability);
 			attributes.put(POSTERIOR_PROBABILITY, posteriorProbabilityTrait);
+
+			Double distance = Utils.rhumbDistance(fromLocation.getCoordinate(), toLocation.getCoordinate());
+			Trait distanceTrait = new Trait(distance);
+			attributes.put(Utils.DISTANCE, distanceTrait);
 
 			Line line = new Line(fromLocation, toLocation, 0.0, 0.0, attributes);
 			linesList.add(line);
-
-		}//END: i loop
-
-
+
+		}// END: i loop
+
 		return linesList;
-	}//END: parseLines
+	}// END: parseLines
 
-}//END: class
+}// END: class