com.hfg.bio.seq.alignment.muscle.Muscle Maven / Gradle / Ivy

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com.hfg xml, html, svg, and bioinformatics utility library
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package com.hfg.bio.seq.alignment.muscle;

import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.Collection;
import java.util.List;

import com.hfg.bio.seq.BioSequence;
import com.hfg.bio.seq.format.FASTA;
import com.hfg.util.Executor;
import com.hfg.util.StringBuilderPlus;
import com.hfg.util.StringUtil;

//==============================================================================
/**
 Wrapper for a Muscle multiple sequence alignment.
 
 Command-line executable is downloadable from https://www.drive5.com/muscle
 
 @author J. Alex Taylor, hairyfatguy.com
 */
//==============================================================================
// com.hfg XML/HTML Coding 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 class Muscle
{
   private MuscleSettings mSettings;

   private static MuscleSettings sDefaultSettings;

   //###########################################################################
   // CONSTRUCTORS
   //###########################################################################

   //---------------------------------------------------------------------------
   public Muscle()
   {
      this(null);
   }

   //---------------------------------------------------------------------------
   public Muscle(MuscleSettings inSettings)
   {
      mSettings = inSettings != null ? inSettings : getDefaultSettings();
   }

   //###########################################################################
   // PUBLIC METHODS
   //###########################################################################

   //---------------------------------------------------------------------------
   public MuscleSettings getSettings()
   {
      return mSettings;
   }

   //---------------------------------------------------------------------------
   public MuscleOutput run(List inQueries)
      throws IOException
   {
      preflight();

      String cmd = generateCmd();

      Executor executor = new Executor();
      executor.setSTDIN(generateSTDIN(inQueries));
      executor.setCommand(cmd);

      int exitStatus = executor.exec();

      MuscleOutput output = new MuscleOutput()
            .setExitStatus(exitStatus)
            .setStdErr(executor.getSTDERR())
            .setStdOut(executor.getSTDOUT())
            .setExecutedCmd(cmd)
            .setMuscleVersion(getVersion());

      return output;
   }

   //###########################################################################
   // PRIVATE METHODS
   //###########################################################################

   //---------------------------------------------------------------------------
   public static void setDefaultSettings(MuscleSettings inValue)
   {
      sDefaultSettings = inValue;
   }

   //---------------------------------------------------------------------------
   public static MuscleSettings getDefaultSettings()
   {
      return (sDefaultSettings != null ? sDefaultSettings : new MuscleSettings());
   }

   //---------------------------------------------------------------------------
   private File getExecutable()
   {
      return (getSettings().getExecutable() != null ? new File(getSettings().getExecutableDir(), getSettings().getExecutable()) : null);
   }

   //---------------------------------------------------------------------------
   private void preflight()
      throws IOException
   {
      File exe = getExecutable();
      if (null == exe)
      {
         throw new IOException("No Muscle executable was specified!");
      }
      else if (! exe.exists())
      {
         File exeDir = exe.getParentFile();
         if (exeDir != null
               && !exeDir.exists())
         {
            throw new IOException("The Muscle executable directory " + StringUtil.singleQuote(exeDir.getPath()) + " doesn't exist!");
         }

         throw new IOException("The Muscle executable " + StringUtil.singleQuote(exe.getPath()) + " doesn't exist!");
      }
   }


   //---------------------------------------------------------------------------
   private String generateCmd()
   {
      StringBuilderPlus cmd = new StringBuilderPlus(getExecutable().getPath()).setDelimiter(" ");

      if (getSettings().getOutputFormat() != null)
      {
         cmd.delimitedAppend("-" + getSettings().getOutputFormat().name());
      }

      if (getSettings().getCommandLineParams() != null)
      {
         cmd.delimitedAppend(getSettings().getCommandLineParams());
      }

      return cmd.toString();
   }

   //---------------------------------------------------------------------------
   private InputStream generateSTDIN(Collection inQuery)
   {
      FASTA fasta = new FASTA();
      // TODO
      return new ByteArrayInputStream(fasta.write(inQuery).getBytes());
   }

   //---------------------------------------------------------------------------
   private String getVersion()
   {
      String version = null;

      Executor executor = new Executor();
      executor.setCommand(getExecutable() + " -version");

      int exitStatus = executor.exec();
      if (0 == exitStatus)
      {
         // MUSCLE v3.8.31 by Robert C. Edgar
         version = executor.getSTDOUT().split("\\s+")[1];
      }

      return version;
   }
}