Description: various fields in libjung-free-java have a type that now extends
 Function, so that they use apply() instead of transform().
Author: Pierre Gruet <pgt@debian.org>
Forwarded: not-needed
Last-Update: 2021-11-15

--- trinityrnaseq.orig/Butterfly/Butterfly/src/src/TransAssembly_allProbPaths.java
+++ trinityrnaseq/Butterfly/Butterfly/src/src/TransAssembly_allProbPaths.java
@@ -9211,7 +9211,7 @@
 		HashMap<List<Integer>, Integer> gene_grouping = new HashMap<List<Integer>, Integer>();
 		
 		WeakComponentClusterer<List<Integer>, String> compClus = new WeakComponentClusterer<List<Integer>,String>();
-		Set<Set<List<Integer>>> comps = compClus.transform(sparseGraph);
+		Set<Set<List<Integer>>> comps = compClus.apply(sparseGraph);
 		
 		debugMes("IsoformClustering, number of clusters = " + comps.size(), 10);
 		
@@ -13378,7 +13378,7 @@
 	{
 
 		WeakComponentClusterer<SeqVertex, SimpleEdge> compClus = new WeakComponentClusterer<SeqVertex, SimpleEdge>();
-		Set<Set<SeqVertex>> comps = compClus.transform(graph);
+		Set<Set<SeqVertex>> comps = compClus.apply(graph);
 		
 		int comp_counter = 0;
 		for (Set<SeqVertex> s : comps) {
--- trinityrnaseq.orig/Butterfly/Butterfly/src/src/edu/uci/ics/jung/algorithms/shortestpath/DijkstraDistanceWoVer.java
+++ trinityrnaseq/Butterfly/Butterfly/src/src/edu/uci/ics/jung/algorithms/shortestpath/DijkstraDistanceWoVer.java
@@ -97,7 +97,7 @@
 				{
 					if (!w.equals(verToExclude) && !sd.distances.containsKey(w))
 					{
-						double edge_weight = ((Number) nev.transform(e)).doubleValue();
+						double edge_weight = ((Number) nev.apply(e)).doubleValue();
 						if (edge_weight < 0)
 							throw new IllegalArgumentException("Edges weights must be non-negative");
 						double new_dist = v_dist + edge_weight;