From 5e7eafb37727b10c8faa67377e652377e997cb77 Mon Sep 17 00:00:00 2001
From: Frederic Lemoine <fredericlemoine@users.noreply.github.com>
Date: Wed, 9 Nov 2016 11:40:27 +0100
Subject: [PATCH] Added compare edges command to list edges that are found in
 another tree

---
 cmd/compare.go      |  4 +--
 cmd/compareedges.go | 60 +++++++++++++++++++++++++++++++++++++++++++++
 tree/edge.go        |  2 +-
 3 files changed, 63 insertions(+), 3 deletions(-)
 create mode 100644 cmd/compareedges.go

diff --git a/cmd/compare.go b/cmd/compare.go
index 43e6f70..688c780 100644
--- a/cmd/compare.go
+++ b/cmd/compare.go
@@ -122,7 +122,7 @@ between it and the reference tree, as well as the number of specific edges.
 
 func init() {
 	RootCmd.AddCommand(compareCmd)
-	compareCmd.Flags().StringVarP(&compareTree1, "reftree", "i", "stdin", "Reference tree input file")
-	compareCmd.Flags().StringVarP(&compareTree2, "compared", "c", "none", "Compared trees input file")
+	compareCmd.PersistentFlags().StringVarP(&compareTree1, "reftree", "i", "stdin", "Reference tree input file")
+	compareCmd.PersistentFlags().StringVarP(&compareTree2, "compared", "c", "none", "Compared trees input file")
 	compareCmd.Flags().BoolVarP(&compareTips, "tips", "l", false, "Compared trees input file")
 }
diff --git a/cmd/compareedges.go b/cmd/compareedges.go
new file mode 100644
index 0000000..a7e65f3
--- /dev/null
+++ b/cmd/compareedges.go
@@ -0,0 +1,60 @@
+package cmd
+
+import (
+	"fmt"
+	"github.com/fredericlemoine/gotree/io"
+	"github.com/fredericlemoine/gotree/io/utils"
+	"github.com/fredericlemoine/gotree/tree"
+	"github.com/spf13/cobra"
+	"os"
+)
+
+// compareedgesCmd represents the compareedges command
+var compareedgesCmd = &cobra.Command{
+	Use:   "edges",
+	Short: "Compare edges of a reference tree with another tree",
+	Long: `Compare edges of a reference tree with another tree
+
+If the compared tree file contains several trees, it will take the first one only
+`,
+	Run: func(cmd *cobra.Command, args []string) {
+		fmt.Fprintf(os.Stderr, "Reference : %s\n", compareTree1)
+		fmt.Fprintf(os.Stderr, "Compared  : %s\n", compareTree2)
+		var err error
+		var refTree *tree.Tree
+		if refTree, err = utils.ReadRefTree(compareTree1); err != nil {
+			io.ExitWithMessage(err)
+		}
+		refTree.ComputeDepths()
+
+		nbtrees := 0
+		compareChannel := make(chan tree.Trees, 15)
+
+		go func() {
+			if nbtrees, err = utils.ReadCompTrees(compareTree2, compareChannel); err != nil {
+				io.ExitWithMessage(err)
+			}
+		}()
+
+		t2 := <-compareChannel
+
+		edges1 := refTree.Edges()
+		edges2 := t2.Tree.Edges()
+
+		fmt.Printf("brid\tlength\tsupport\tterminal\tdepth\ttopodepth\trightname\tfound\n")
+		for i, e1 := range edges1 {
+			found := false
+			for _, e2 := range edges2 {
+				if e1.SameBipartition(e2) {
+					found = true
+					break
+				}
+			}
+			fmt.Printf("%d\t%s\t%t\n", i, e1.ToStatsString(), found)
+		}
+	},
+}
+
+func init() {
+	compareCmd.AddCommand(compareedgesCmd)
+}
diff --git a/tree/edge.go b/tree/edge.go
index afa5c83..c4da09a 100644
--- a/tree/edge.go
+++ b/tree/edge.go
@@ -118,7 +118,7 @@ func (e *Edge) ToStatsString() string {
 	if err != nil {
 		io.ExitWithMessage(err)
 	}
-	return fmt.Sprintf("%s\t%s\t%t\t%d\t%d\t%s\n",
+	return fmt.Sprintf("%s\t%s\t%t\t%d\t%d\t%s",
 		length, support, e.Right().Tip(),
 		depth, topodepth, e.Right().Name())