this marks a first release

phylogeography · Jun 25, 2015 · 0671522 · 0671522
1 parent 5adc21d
commit 0671522
Show file tree

Hide file tree

Showing 5 changed files with 9 additions and 19 deletions.
diff --git a/README.textile b/README.textile
@@ -2,7 +2,7 @@
 .:: SPREAD 2::.
 ===================
 *Spatial Phylogenetic Reconstruction of EvolutionAry Dynamics 2*
-Version: 2.0.0 alpha, 2015
+Version: 0.0.1, 2015
 Authors: Filip Bielejec, Andrew Rambaut, Marc A. Suchard & Philippe 'The Wise' Lemey
 Homepage: http://rega.kuleuven.be/cev/ecv/software/spread
 License: LGPL

diff --git a/src/app/Spread2App.java b/src/app/Spread2App.java
@@ -2,8 +2,6 @@
 
 import java.util.Locale;
 
-import exceptions.ArgumentException;
-
 /**
  * @author Andrew Rambaut
  * @author Filip Bielejec

diff --git a/src/data/SpreadData.java b/src/data/SpreadData.java
@@ -5,7 +5,6 @@
 
 import data.structure.Layer;
 import data.structure.Location;
-import data.structure.TimeLine;
 
 /**
  * @author Andrew Rambaut
@@ -14,13 +13,13 @@
  */
 public class SpreadData {
 
-	private final TimeLine timeLine;
+//	private final TimeLine timeLine;
 	private final LinkedList<Location> locations;
 	private final LinkedList<Layer> layers;
 
 	public SpreadData(LinkedList<Location> locations, LinkedList<Layer> layers) {
 
-		this.timeLine = null; // TODO
+//		this.timeLine = null; // TODO
 		this.locations = locations;
 		this.layers = layers;
 

diff --git a/src/renderers/kml/KmlRenderer.java b/src/renderers/kml/KmlRenderer.java
@@ -12,12 +12,6 @@
 import java.util.Map;
 import java.util.Map.Entry;
 
-import org.joda.time.DateTime;
-import org.joda.time.Duration;
-import org.joda.time.Interval;
-import org.joda.time.LocalDate;
-import org.joda.time.Period;
-
 import kmlframework.kml.AltitudeModeEnum;
 import kmlframework.kml.Document;
 import kmlframework.kml.Feature;
@@ -31,10 +25,14 @@
 import kmlframework.kml.Point;
 import kmlframework.kml.PolyStyle;
 import kmlframework.kml.StyleSelector;
-import kmlframework.kml.TimePrimitive;
 import kmlframework.kml.TimeSpan;
+
+import org.joda.time.DateTime;
+import org.joda.time.Duration;
+import org.joda.time.Interval;
+import org.joda.time.LocalDate;
+
 import parsers.DiscreteColorsParser;
-import parsers.TimeParser;
 import renderers.Renderer;
 import settings.rendering.KmlRendererSettings;
 import utils.Trait;
@@ -647,10 +645,6 @@ private Feature generateLine(
 
 		LinkedList<Coordinate> coords = getIntermediateCoords(startCoordinate, endCoordinate, sliceCount);
 
-
-		// TODO time intervals
-
-
 		String startTime = line.getStartTime();
 		DateTime startDate = new DateTime(startTime);
 

diff --git a/src/utils/Utils.java b/src/utils/Utils.java
@@ -17,7 +17,6 @@
 import jebl.evolution.trees.RootedTree;
 import data.structure.Coordinate;
 import exceptions.AnalysisException;
-import exceptions.ArgumentException;
 
 public class Utils {