Functions
alignment.c File Reference

Collection of routines for reading alignments. More...

Functions

static pllAlignmentDatapllParsePHYLIP (const char *filename)
 Parse a PHYLIP file. More...
 
static pllAlignmentDatapllParseFASTA (const char *filename)
 Parse a FASTA file. More...
 
static int read_phylip_header (int *inp, int *sequenceCount, int *sequenceLength)
 Parse the PHYLIP file header.
 
static int parsedOk (int *actLen, int sequenceCount, int sequenceLength)
 
static int parse_phylip (pllAlignmentData *alignmentData, int input)
 Parse the PHYLIP file body.
 
static int getFastaAlignmentInfo (int *inp, int *seqCount, int *seqLen)
 Get information about the FASTA alignment. More...
 
static int parseFastaAlignment (pllAlignmentData *alignmentData, int input)
 Check whether the FASTA content is valid.
 
static int printTokens (int input)
 
pllAlignmentDatapllInitAlignmentData (int sequenceCount, int sequenceLength)
 Initialize alignment structure fields. More...
 
void pllAlignmentDataDestroy (pllAlignmentData *alignmentData)
 Deallocates the memory associated with the alignment data structure. More...
 
void pllAlignmentDataDumpConsole (pllAlignmentData *alignmentData)
 Prints the alignment to the console. More...
 
int pllAlignmentDataDumpFile (pllAlignmentData *alignmentData, int fileFormat, const char *filename)
 Dump the alignment to a file of format fileFormat. More...
 
pllAlignmentDatapllParseAlignmentFile (int fileType, const char *filename)
 Parse a file that contains a multiple sequence alignment. More...
 

Detailed Description

Collection of routines for reading alignments.

PLL (version 1.0.0) a software library for phylogenetic inference

Copyright (C) 2013 Tomas Flouri and Alexandros Stamatakis

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

For any other enquiries send an Email to Tomas Flouri Tomas.nosp@m..Flo.nosp@m.uri@h.nosp@m.-its.nosp@m..org

When publishing work that uses PLL please cite PLL

Auxiliary functions for storing alignments read from predefined file formats