utils

Documentation

Index

• Constants
• func GetReader(inputfile string) (io.Closer, *bufio.Reader, error)
• func OpenFile(inputfile string) (*os.File, error)
• func ReadMultiTrees(reader *bufio.Reader, format int) <-chan tree.Trees
• func ReadTree(inputfile string, format int) (*tree.Tree, error)
• func ReadTreeReader(reader *bufio.Reader, format int) (*tree.Tree, error)

Constants

const (
	FORMAT_NEWICK = iota
	FORMAT_NEXUS
	FORMAT_PHYLOXML
)

Functions

func GetReader

func GetReader(inputfile string) (io.Closer, *bufio.Reader, error)

Returns the opened file and a buffered reader (gzip or not) for the file

The file may be a remote file:

• http://
• itol://<itol id>

Or a local file

func OpenFile

func OpenFile(inputfile string) (*os.File, error)

func ReadMultiTrees

func ReadMultiTrees(reader *bufio.Reader, format int) <-chan tree.Trees

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 ReadTree

func ReadTree(inputfile string, format int) (*tree.Tree, error)

func ReadTreeReader

func ReadTreeReader(reader *bufio.Reader, format int) (*tree.Tree, error)

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.