com.hfg.bio.seq.format.ReadableSeqFormat Maven / Gradle / Ivy

Go to download

Show more of this group Show more artifacts with this name
Show all versions of com_hfg Show documentation

com.hfg xml, html, svg, and bioinformatics utility library

There is a newer version: 20240423

package com.hfg.bio.seq.format;

import com.hfg.bio.seq.BioSequence;

import java.io.BufferedReader;
import java.io.File;
import java.util.List;


//------------------------------------------------------------------------------
/**
 Interface for readable sequence formats.
 
   @author J. Alex Taylor, hairyfatguy.com
 
 */
//------------------------------------------------------------------------------
// com.hfg Library
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library 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
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
//
// J. Alex Taylor, President, Founder, CEO, COO, CFO, OOPS hairyfatguy.com
// [email protected]
//------------------------------------------------------------------------------

public interface ReadableSeqFormat
{
   public List read(File inFile) throws SeqIOException;

   public List read(BufferedReader inFile) throws SeqIOException;

   public T readRecord(CharSequence inString) throws SeqIOException;

   public T readRecord(BufferedReader inReader) throws SeqIOException;

   public boolean isEndOfRecord(String inLine);

   /**
    A format has a Janus delimiter if the line that indicates that the previous record is over is also part of the
    next record. Will return true for formats like FASTA.
    @return whether or not this format's record delimiter is also part of the next record
    */
   public boolean hasJanusDelimiter();
}