Reorganized commands : difftips and compare

cmd/compare.go

@@ -1,112 +1,19 @@
 package cmd
 
 import (
-	"errors"
-	"fmt"
-	"github.com/fredericlemoine/gotree/io"
-	"github.com/fredericlemoine/gotree/tree"
 	"github.com/spf13/cobra"
-	"os"
-	"runtime"
-	"sync"
 )
 
-// Type for channel of tree stats
-type stats struct {
-	id     int
-	tree1  int
-	common int
-}
-
-func compare(tree1 string, tree2 string, tips bool, cpus int) {
-	maxcpus := runtime.NumCPU()
-	var edges []*tree.Edge
-
-	statsChannel := make(chan stats, 15)
-
-	if tree2 == "none" {
-		io.ExitWithMessage(errors.New("You must provide a file containing compared trees"))
-	}
-	if cpus > maxcpus {
-		cpus = maxcpus
-	}
-
-	fmt.Fprintf(os.Stderr, "Reference : %s\n", tree1)
-	fmt.Fprintf(os.Stderr, "Compared  : %s\n", tree2)
-	fmt.Fprintf(os.Stderr, "With tips : %t\n", tips)
-	fmt.Fprintf(os.Stderr, "Threads   : %d\n", cpus)
-
-	refTree := readTree(intreefile)
-	compareChannel := readTrees(intree2file)
-
-	edges = refTree.Edges()
-	index := tree.NewEdgeIndex(int64(len(edges)*2), 0.75)
-	total := 0
-	for i, e := range edges {
-		index.PutEdgeValue(e, i, e.Length())
-		if tips || !e.Right().Tip() {
-			total++
-		}
-	}
-	var wg sync.WaitGroup
-	for cpu := 0; cpu < cpus; cpu++ {
-		wg.Add(1)
-		go func(cpu int) {
-			for treeV := range compareChannel {
-				common := 0
-				var err error
-
-				edges2 := treeV.Tree.Edges()
-				// Check wether the 2 trees have the same set of tip names
-				if err = refTree.CompareTipIndexes(treeV.Tree); err != nil {
-					io.ExitWithMessage(err)
-				}
-
-				for _, e2 := range edges2 {
-					_, ok := index.Value(e2)
-					if ok && (tips || !e2.Right().Tip()) {
-						common++
-					}
-				}
-
-				statsChannel <- stats{
-					treeV.Id,
-					total - common,
-					common,
-				}
-			}
-			wg.Done()
-		}(cpu)
-	}
-
-	go func() {
-		wg.Wait()
-		close(statsChannel)
-	}()
-
-	fmt.Printf("Tree\tspecref\tcommon\n")
-	for stats := range statsChannel {
-		fmt.Printf("%d\t%d\t%d\n", stats.id, stats.tree1, stats.common)
-	}
-}
-
 // compareCmd represents the compare command
 var compareCmd = &cobra.Command{
 	Use:   "compare",
-	Short: "Compare a reference tree with a set of trees",
-	Long: `Compare a reference tree with a set of trees.
-
-for each trees in the compared tree file, prints the number of common edges
-between it and the reference tree, as well as the number of specific edges.
+	Short: "Compare full trees, edges, or tips",
+	Long: `Compare full trees, edges, or tips.
 `,
-	Run: func(cmd *cobra.Command, args []string) {
-		compare(intreefile, intree2file, compareTips, rootCpus)
-	},
 }
 
 func init() {
 	RootCmd.AddCommand(compareCmd)
 	compareCmd.PersistentFlags().StringVarP(&intreefile, "reftree", "i", "stdin", "Reference tree input file")
 	compareCmd.PersistentFlags().StringVarP(&intree2file, "compared", "c", "none", "Compared trees input file")
-	compareCmd.Flags().BoolVarP(&compareTips, "tips", "l", false, "Compared trees input file")
 }

cmd/difftips.go → cmd/comparetips.go

@@ -10,7 +10,7 @@ import (
 
 // difftipsCmd represents the difftips command
 var difftipsCmd = &cobra.Command{
-	Use:   "difftips",
+	Use:   "tips",
 	Short: "Print diff between tip names of two trees",
 	Long: `Print diff between tip names of two trees.
 
@@ -60,7 +60,5 @@ should produce the following output:
 }
 
 func init() {
-	RootCmd.AddCommand(difftipsCmd)
-	difftipsCmd.Flags().StringVarP(&intreefile, "reftree", "i", "stdin", "Reference tree input file")
-	difftipsCmd.Flags().StringVarP(&intree2file, "compared", "c", "none", "Other tree file to compare with")
+	compareCmd.AddCommand(difftipsCmd)
 }

cmd/comparetrees.go

@@ -0,0 +1,110 @@
+package cmd
+
+import (
+	"errors"
+	"fmt"
+	"github.com/fredericlemoine/gotree/io"
+	"github.com/fredericlemoine/gotree/tree"
+	"github.com/spf13/cobra"
+	"os"
+	"runtime"
+	"sync"
+)
+
+// Type for channel of tree stats
+type stats struct {
+	id     int
+	tree1  int
+	common int
+}
+
+func compare(tree1 string, tree2 string, tips bool, cpus int) {
+	maxcpus := runtime.NumCPU()
+	var edges []*tree.Edge
+
+	statsChannel := make(chan stats, 15)
+
+	if tree2 == "none" {
+		io.ExitWithMessage(errors.New("You must provide a file containing compared trees"))
+	}
+	if cpus > maxcpus {
+		cpus = maxcpus
+	}
+
+	fmt.Fprintf(os.Stderr, "Reference : %s\n", tree1)
+	fmt.Fprintf(os.Stderr, "Compared  : %s\n", tree2)
+	fmt.Fprintf(os.Stderr, "With tips : %t\n", tips)
+	fmt.Fprintf(os.Stderr, "Threads   : %d\n", cpus)
+
+	refTree := readTree(intreefile)
+	compareChannel := readTrees(intree2file)
+
+	edges = refTree.Edges()
+	index := tree.NewEdgeIndex(int64(len(edges)*2), 0.75)
+	total := 0
+	for i, e := range edges {
+		index.PutEdgeValue(e, i, e.Length())
+		if tips || !e.Right().Tip() {
+			total++
+		}
+	}
+	var wg sync.WaitGroup
+	for cpu := 0; cpu < cpus; cpu++ {
+		wg.Add(1)
+		go func(cpu int) {
+			for treeV := range compareChannel {
+				common := 0
+				var err error
+
+				edges2 := treeV.Tree.Edges()
+				// Check wether the 2 trees have the same set of tip names
+				if err = refTree.CompareTipIndexes(treeV.Tree); err != nil {
+					io.ExitWithMessage(err)
+				}
+
+				for _, e2 := range edges2 {
+					_, ok := index.Value(e2)
+					if ok && (tips || !e2.Right().Tip()) {
+						common++
+					}
+				}
+
+				statsChannel <- stats{
+					treeV.Id,
+					total - common,
+					common,
+				}
+			}
+			wg.Done()
+		}(cpu)
+	}
+
+	go func() {
+		wg.Wait()
+		close(statsChannel)
+	}()
+
+	fmt.Printf("Tree\tspecref\tcommon\n")
+	for stats := range statsChannel {
+		fmt.Printf("%d\t%d\t%d\n", stats.id, stats.tree1, stats.common)
+	}
+}
+
+// compareCmd represents the compare command
+var compareTreesCmd = &cobra.Command{
+	Use:   "trees",
+	Short: "Compare a reference tree with a set of trees",
+	Long: `Compare a reference tree with a set of trees.
+
+for each trees in the compared tree file, prints the number of common edges
+between it and the reference tree, as well as the number of specific edges.
+`,
+	Run: func(cmd *cobra.Command, args []string) {
+		compare(intreefile, intree2file, compareTips, rootCpus)
+	},
+}
+
+func init() {
+	compareCmd.AddCommand(compareTreesCmd)
+	compareTreesCmd.Flags().BoolVarP(&compareTips, "tips", "l", false, "Include tips in the comparison")
+}