Rename LineageTreeUtils to GraphUtils

Author: maarzt

…neage_registration/LineageTreeUtils.java …cak/lineage_registration/GraphUtils.javasrc/main/java/org/mastodon/mamut/tomancak/lineage_registration/LineageTreeUtils.java renamed to src/main/java/org/mastodon/mamut/tomancak/lineage_registration/GraphUtils.java src/main/java/org/mastodon/mamut/tomancak/lineage_registration/LineageTreeUtils.java renamed to src/main/java/org/mastodon/mamut/tomancak/lineage_registration/GraphUtils.java

@@ -8,7 +8,7 @@
 import org.mastodon.graph.Vertex;
 import org.mastodon.spatial.HasTimepoint;
 
-public class LineageTreeUtils
+public class GraphUtils
 {
 	/**
 	 * @return the set of root nodes of the given graph.

src/main/java/org/mastodon/mamut/tomancak/trackmatching/BranchGraphUtils.java

@@ -137,7 +137,7 @@ public static < V extends Vertex< E >, E extends Edge< V > > boolean doesBranchD
 	}
 
 	/**
-	 * Returns the first vertex of the specified branch with {@code vertex.getTimepoint() > timepoint.}
+	 * Returns the first vertex of the specified branch with {@code vertex.getTimepoint() >= timepoint.}
 	 *
 	 * @param branchStart The first vertex of the branch.
 	 * @param timepoint   The time point.

src/main/java/org/mastodon/mamut/tomancak/trackmatching/RootsPairing.java

@@ -41,6 +41,7 @@
 import org.mastodon.collection.ref.RefRefHashMap;
 import org.mastodon.mamut.model.ModelGraph;
 import org.mastodon.mamut.model.Spot;
+import org.mastodon.mamut.tomancak.lineage_registration.GraphUtils;
 
 /**
  * Pair the root spots in two ModelGraphs based on their label.
@@ -72,7 +73,7 @@ static RefRefMap< Spot, Spot > pairDividingRoots( ModelGraph graphA, int timepoi
 
 	private static RefSet< Spot > getRoots( ModelGraph graph, int timepoint )
 	{
-		return getBranchStarts( filterDividingSpots( LineageTreeUtils.getRoots( graph, timepoint ) ) );
+		return getBranchStarts( filterDividingSpots( GraphUtils.getRoots( graph, timepoint ) ) );
 	}
 
 	private static RefRefMap< Spot, Spot > pairSpotsBasedOnLabel( RefSet< Spot > spotsA, RefSet< Spot > spotsB )
@@ -99,6 +100,10 @@ private static RefSet< Spot > filterDividingSpots( RefSet< Spot > spots )
 		}
 	}
 
+	/**
+	 * Returns the set that contains the first vertices of all branches, that
+	 * contain a vertex in the given set ({@code spots}).
+	 */
 	private static RefSet< Spot > getBranchStarts( RefSet< Spot > spots )
 	{
 		Spot ref = spots.createRef();