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readtrees.go
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readtrees.go
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package utils
import (
"bufio"
"fmt"
"strings"
"github.com/fredericlemoine/gotree/io/newick"
"github.com/fredericlemoine/gotree/io/nexus"
"github.com/fredericlemoine/gotree/io/phyloxml"
"github.com/fredericlemoine/gotree/tree"
)
const (
FORMAT_NEWICK = iota
FORMAT_NEXUS
FORMAT_PHYLOXML
)
func ReadTree(inputfile string, format int) (*tree.Tree, error) {
if f, r, err := GetReader(inputfile); err != nil {
return nil, err
} else {
if t, err2 := ReadTreeReader(r, format); err2 != nil {
return nil, err2
} else {
if err = f.Close(); err != nil {
return nil, err
}
return t, nil
}
}
}
// Reads one tree from the input reader
// this function does not close the reader
// May take several formats: newick or nexus
// In both case, takes the first tree in the file.
func ReadTreeReader(reader *bufio.Reader, format int) (*tree.Tree, error) {
var reftree *tree.Tree
var err error
switch format {
case FORMAT_NEWICK:
if reftree, err = newick.NewParser(reader).Parse(); err != nil {
return nil, err
}
case FORMAT_NEXUS:
if n, err2 := nexus.NewParser(reader).Parse(); err2 != nil {
return nil, err2
} else {
if n.HasTrees {
reftree = n.FirstTree()
} else {
return nil, fmt.Errorf("No tree in the input Nexus file")
}
}
case FORMAT_PHYLOXML:
if p, err3 := phyloxml.NewParser(reader).Parse(); err3 != nil {
return nil, err3
} else {
reftree, err = p.FirstTree()
if err != nil {
return nil, err
}
if reftree == nil {
return nil, fmt.Errorf("No tree in the input PhyloXML file")
}
}
default:
return nil, fmt.Errorf("Unsupported tree format: %q", format)
}
return reftree, nil
}
// Read a bunch of trees from the input reader and send each of them to the output channel
// this function does not close the reader, but closes the channel at the end of the reading.
// It returns almost immediately because parsing is performed in a go routine. Iterating over
// the tree channel will synchronize computations.
// If an error occures while parsing, it stops parsing and sends a nil tree with the error in
// the channel
// Different parsing formats: utils.FORMAT_NEWICK or utils.FORMAT_NEXUS
func ReadMultiTrees(reader *bufio.Reader, format int) <-chan tree.Trees {
var compTrees chan tree.Trees = make(chan tree.Trees, 10)
go func() {
var err error
var id int = 0
var compTree *tree.Tree
switch format {
case FORMAT_NEWICK:
line, e := ReadUntilSemiColon(reader)
if e != nil {
compTrees <- tree.Trees{
nil,
id,
e,
}
}
for e == nil {
parser := newick.NewParser(strings.NewReader(line))
if compTree, err = parser.Parse(); err != nil {
compTrees <- tree.Trees{
nil,
id,
err,
}
break
} else {
compTrees <- tree.Trees{
compTree,
id,
nil,
}
}
id++
line, e = ReadUntilSemiColon(reader)
}
case FORMAT_NEXUS:
if n, err := nexus.NewParser(reader).Parse(); err != nil {
compTrees <- tree.Trees{
nil,
id,
err,
}
} else {
n.IterateTrees(func(name string, t *tree.Tree) {
compTrees <- tree.Trees{
t,
id,
nil,
}
id++
})
}
case FORMAT_PHYLOXML:
if p, err2 := phyloxml.NewParser(reader).Parse(); err2 != nil {
compTrees <- tree.Trees{
nil,
id,
err2,
}
} else {
p.IterateTrees(func(t *tree.Tree, err error) {
compTrees <- tree.Trees{
t,
id,
err,
}
id++
})
}
default:
compTrees <- tree.Trees{
nil,
id,
fmt.Errorf("Unsupported tree format: %q", format),
}
}
close(compTrees)
}()
return compTrees
}