consistency in mapping values

README.textile

@@ -36,7 +36,7 @@ h3. RENDERING
 h4. POLYGONS
 
 * override default polygon color settings:
--render kml -json /home/filip/Dropbox/JavaProjects/Spread2/test_host.json -polygoncolor 0 0 255 -output test.kml
+-render kml -json /home/filip/Dropbox/JavaProjects/Spread2/test_host.json -polygoncolor 255 255 0 -output test.kml
 
 * map polygon colors to host attribute values, use built-in color schemes
 -render kml -json /home/filip/Dropbox/JavaProjects/Spread2/test_host.json -polygoncolormapping host -output test.kml
@@ -45,7 +45,7 @@ h4. POLYGONS
 -render kml -json /home/filip/Dropbox/JavaProjects/Spread2/test_host.json -polygoncolormapping host -polygoncolors /home/filip/Dropbox/JavaProjects/Spread2/data/3colors -output test.kml
 
 * specify alpha channel for polygons, this option overwrites all previous settings, including those in color sheet:
--render kml -json /home/filip/Dropbox/JavaProjects/Spread2/test_host.json -polygoncolormapping host -polygoncolors /home/filip/Dropbox/JavaProjects/Spread2/data/3colors -polygonalpha 255 -output test.kml
+-render kml -json /home/filip/Dropbox/JavaProjects/Spread2/test_host.json -polygoncolormapping host -polygoncolors /home/filip/Dropbox/JavaProjects/Spread2/data/3colors -polygonalpha 100 -output test.kml
 
 * map alpha channel for polygons, this option overwrites all previous settings, including those in color sheet:
 -render kml -json /home/filip/Dropbox/JavaProjects/Spread2/test_host.json -polygoncolormapping host -polygoncolors /home/filip/Dropbox/JavaProjects/Spread2/data/3colors2 -polygonalphamapping modality -output test.kml
@@ -83,7 +83,7 @@ h4. LINES
 -render kml -json /home/filip/Dropbox/JavaProjects/Spread2/test_host.json -polygoncolormapping host -polygoncolors /home/filip/Dropbox/JavaProjects/Spread2/data/3colors2 -polygonalphamapping modality -linecolormapping host -linecolors /home/filip/Dropbox/JavaProjects/Spread2/data/3colors -linealphamapping host -linewidth 2 -linealtitude 50000 -output test.kml
 
 * map lines altitude to distance attribute values. Altitude can only be mapped to attributes which apply to a whole branch.
--render kml -json /home/filip/Dropbox/JavaProjects/Spread2/test_host.json -polygoncolormapping host -polygoncolors /home/filip/Dropbox/JavaProjects/Spread2/data/3colors2 -polygonalphamapping modality -linecolormapping host -linecolors /home/filip/Dropbox/JavaProjects/Spread2/data/3colors -linealphamapping host -linewidthmapping duration -linealtitudemapping distance -output test.kml
+-render kml -json /home/filip/Dropbox/JavaProjects/Spread2/test_host.json -polygoncolormapping host -polygoncolors /home/filip/Dropbox/JavaProjects/Spread2/data/3colors2 -polygonalphamapping modality -linecolormapping host -linecolors /home/filip/Dropbox/JavaProjects/Spread2/data/3colors -linealpha 255 -linewidthmapping duration -linealtitudemapping distance -output test.kml
 
 
 h3. DISCRETE TREE
@@ -240,7 +240,10 @@ h1. TODO
   - D3 renderer
   - GeoJSON renderer
   - KML renderer
+    - node support threshold for polygons (parse posterior support and use polygon cutoffs [TODO] )
+    - Show node ages in the kml
     - control arc curvature [0 - 1]
+* Write tests    
 * Non-geographic locations (e.g. antigenic locations)
 * parsing BEAST2 and MrBayes output
 * Restrict visual summaries or rate statistics to a particular set of nodes, like a clade or a trunk/backbone

data/3colors

@@ -1,3 +1,3 @@
-Gal	255	0	0
-Ans	255	128	0
-Neo	255	255	0
+Gal	127	0	255
+Ans	255	255	0
+Neo	255	0	0

src/data/structure/Line.java

@@ -3,23 +3,24 @@
 import java.util.LinkedHashMap;
 import java.util.Map;
 
+import exceptions.MissingAttributeException;
 import utils.Trait;
 
 public class Line {
 
 	// Traits which have start and end values go here:
 	private final Map<String, Trait> attributes = new LinkedHashMap<String, Trait>();
-	
+
 	private final Coordinate startCoordinate;
 	private final Coordinate endCoordinate;
 
 	private final Location startLocation;
 	private final Location endLocation;
 	private final boolean connectsLocations;
-	
+
 	private final String startTime;
 	private final String endTime;
-	
+
 	public Line(Location startLocation, //
 			Location endLocation, //
 			String startTime, //
@@ -30,7 +31,7 @@ public Line(Location startLocation, //
 		this.startLocation = startLocation;
 		this.endLocation = endLocation;
 		this.connectsLocations = true;
-		
+
 		this.startTime = startTime;
 		this.endTime = endTime;
 
@@ -40,19 +41,18 @@ public Line(Location startLocation, //
 		if (attributes != null) {
 			this.attributes.putAll(attributes);
 		}
-		
+
 	}// END: Constructor
 
-
 	public Line(Location startLocation, //
 			Location endLocation, //
-			Map<String, Trait> nodeAttributes //
-			) {
-		
+			Map<String, Trait> attributes //
+	) {
+
 		this.startLocation = startLocation;
 		this.endLocation = endLocation;
 		this.connectsLocations = true;
-		
+
 		this.startTime = null;
 		this.endTime = null;
 
@@ -62,9 +62,9 @@ public Line(Location startLocation, //
 		if (attributes != null) {
 			this.attributes.putAll(attributes);
 		}
-		
+
 	}
-	
+
 	public Line(Coordinate startCoordinate, //
 			Coordinate endCoordinate, //
 			String startTime, //
@@ -80,7 +80,7 @@ public Line(Coordinate startCoordinate, //
 		this.startLocation = null;
 		this.endLocation = null;
 		this.connectsLocations = false;
-		
+
 		if (attributes != null) {
 			this.attributes.putAll(attributes);
 		}
@@ -111,12 +111,12 @@ public Location getEndLocation() {
 		return endLocation;
 	}
 
-	public boolean connectsLocations(){
+	public boolean connectsLocations() {
 		return connectsLocations;
 	}
-	
+
 	public Map<String, Trait> getAttributes() {
 		return attributes;
 	}
-	
+
 }// END: class

src/parsers/BayesFactorLinesParser.java

@@ -79,6 +79,9 @@ public LinkedList<Line> parseLines() throws LocationNotFoundException {
 			Trait distanceTrait = new Trait(distance);
 			attributes.put(Utils.DISTANCE, distanceTrait);
 
+
+//			Utils.printMap(attributes);
+
 			Line line = new Line(fromLocation, toLocation, attributes);
 			linesList.add(line);
 

src/parsers/DiscretePolygonsParser.java

@@ -18,7 +18,7 @@
 public class DiscretePolygonsParser {
 
 	public static final String COUNT = "count";
-	public static final String LOCATION = "location";
+//	public static final String LOCATION = "location";
 
 	private RootedTree rootedTree;
 	private String locationTrait;
@@ -142,8 +142,9 @@ public  LinkedList<Polygon> parseDiscretePolygons() throws LocationNotFoundExcep
 						}// END: traits loop
 					}// END: null check
 
+					// it's just easier to add them here as well, we avoid convoluted logic in renderers 
 					Trait locationTrait = new Trait(location.getId());
-					attributes.put(LOCATION, locationTrait);
+					attributes.put(Utils.LOCATION, locationTrait);
 
 					Trait countTrait = new Trait(locationCount);
 					attributes.put(COUNT, countTrait);

src/parsers/DiscreteTreeLinesParser.java

@@ -131,6 +131,13 @@ public LinkedList<Line> parseLines() throws IOException, ImportException,
 					Trait distanceTrait = new Trait(distance);
 					attributes.put(Utils.DISTANCE, distanceTrait);
 
+					// it's just easier to add them here as well, we avoid convoluted logic in renderers 
+					Trait startLocationTrait = new Trait(parentLocation.getId());
+					attributes.put(Utils.START+Utils.LOCATION, startLocationTrait);
+
+					Trait endLocationTrait = new Trait(nodeLocation.getId());
+					attributes.put(Utils.END+Utils.LOCATION, endLocationTrait);
+
 					Line line = new Line(parentLocation, nodeLocation,
 							startTime, endTime, attributes);
 					linesList.add(line);

src/parsers/TimeParser.java

@@ -32,7 +32,7 @@ public void parseTime() throws AnalysisException {
 			month = Integer.valueOf(endDateFields[Utils.MONTH_INDEX]);
 			day = Integer.valueOf(endDateFields[Utils.DAY_INDEX]);
 
-			System.out.println("MRSD in a decimal date format and corresponds to: " + year +"-" + month + "-" + day);
+			System.out.println("MRSD in a decimal date format corresponds to: " + year +"-" + month + "-" + day);
 
 		} else if(mrsd.contains("-")) {