_options = options;
}
- private Msa inferMsa() throws IOException {
- final File temp_seqs_file = File.createTempFile( "aptx", ".fasta" );
+ private Msa inferMsa() throws IOException, InterruptedException {
+ final File temp_seqs_file = File.createTempFile( "__msa__temp__", ".fasta" );
+ System.out.println();
System.out.println( "temp file: " + temp_seqs_file );
+ System.out.println();
//final File temp_seqs_file = new File( _options.getTempDir() + ForesterUtil.FILE_SEPARATOR + "s.fasta" );
final BufferedWriter writer = new BufferedWriter( new FileWriter( temp_seqs_file ) );
SequenceWriter.writeSeqs( _seqs, writer, SEQ_FORMAT.FASTA, 100 );
writer.close();
final List<String> opts = processMafftOptions();
- Msa msa = null;
- try {
- msa = runMAFFT( temp_seqs_file, opts );
- }
- catch ( final InterruptedException e ) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- // copy aln file to intermediate dir file
- // delete temp seqs file
- return msa;
+ return runMAFFT( temp_seqs_file, opts );
}
private List<String> processMafftOptions() {
return phy;
}
- private void infer() {
+ private void infer() throws InterruptedException {
//_mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
if ( ( _msa == null ) && ( _seqs == null ) ) {
throw new IllegalArgumentException( "cannot run phylogenetic analysis with null msa and seq array" );
@Override
public void run() {
- infer();
+ try {
+ infer();
+ }
+ catch ( InterruptedException e ) {
+ // TODO need to handle this exception SOMEHOW!
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
}
private Msa runMAFFT( final File input_seqs, final List<String> opts ) throws IOException, InterruptedException {
private int _exit_code;
private final String _path_to_prg;
+ public static MsaInferrer createInstance() {
+ return createInstance( getPathToCmd() );
+ }
+
public static MsaInferrer createInstance( final String path_to_prg ) {
return new Mafft( path_to_prg );
}
private static String getPathToCmd() {
//TODO this needs to come from env variable, etc.
+ //FIXME ..
+ //should not be in this class!
String path = "";
final String os = ForesterUtil.OS_NAME.toLowerCase();
if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
path = "C:\\Program Files\\mafft-win\\mafft.bat";
}
else {
- path = "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-6.832-without-extensions/scripts/mafft";
+ path = "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-6.864-without-extensions/scripts/mafft";
}
return path;
}
return SystemCommandExecutor.isExecuteableFile( new File( getPathToCmd() ) );
}
- public static MsaInferrer createInstance() {
- return createInstance( getPathToCmd() );
- }
-
private Mafft( final String path_to_prg ) {
if ( !SystemCommandExecutor.isExecuteableFile( new File( path_to_prg ) ) ) {
throw new IllegalArgumentException( "cannot execute MAFFT via [" + path_to_prg + "]" );
my_opts.add( opts.get( i ) );
}
my_opts.add( path_to_input_seqs.getAbsolutePath() );
- final SystemCommandExecutor commandExecutor = new SystemCommandExecutor( my_opts );
- final int _exit_code = commandExecutor.executeCommand();
+ final SystemCommandExecutor command_executor = new SystemCommandExecutor( my_opts );
+ final int _exit_code = command_executor.executeCommand();
if ( _exit_code != 0 ) {
- throw new IOException( "MAFFT failed, exit code: " + _exit_code );
+ throw new IOException( "MAFFT program failed, exit code: " + _exit_code + ", command: " + my_opts );
+ }
+ final StringBuilder stdout = command_executor.getStandardOutputFromCommand();
+ final StringBuilder stderr = command_executor.getStandardErrorFromCommand();
+ if ( stdout == null || stdout.length() < 2 ) {
+ throw new IOException( "MAFFT program did not produce any output, command: " + my_opts );
}
- final StringBuilder stdout = commandExecutor.getStandardOutputFromCommand();
- final StringBuilder stderr = commandExecutor.getStandardErrorFromCommand();
- System.out.println( stdout );
- System.out.println();
- System.out.println( stderr );
_error = stderr.toString();
final Msa msa = FastaParser.parseMsa( stdout.toString() );
return msa;
*
* http://devdaily.com/java/java-processbuilder-process-system-exec
*
- *
* Copyright 2010 alvin j. alexander, devdaily.com.
*
* This program is free software: you can redistribute it and/or modify it under
* You should have received a copy of the GNU Lesser Public License along with
* this program. If not, see <http://www.gnu.org/licenses/>.
*
- * Please ee the following page for the LGPL license:
+ * Please see the following page for the LGPL license:
* http://www.gnu.org/licenses/lgpl.txt
*
*/
public class SystemCommandExecutor {
- private final List<String> commandInformation;
- private final String adminPassword;
- private ThreadedStreamHandler inputStreamHandler;
- private ThreadedStreamHandler errorStreamHandler;
+ private final List<String> _command_information;
+ private final String _admin_password;
+ private ThreadedStreamHandler _input_stream_handler;
+ private ThreadedStreamHandler _error_stream_handler;
+ private final static boolean DEBUG = false;
/**
* Pass in the system command you want to run as a List of Strings, as shown here:
* working to the point where it won't hang when the given password is
* wrong.
*
- * @param commandInformation The command you want to run.
+ * @param command_information The command you want to run.
*/
- public SystemCommandExecutor( final List<String> commandInformation ) {
- if ( ( commandInformation == null ) || commandInformation.isEmpty() ) {
+ public SystemCommandExecutor( final List<String> command_information ) {
+ if ( ( command_information == null ) || command_information.isEmpty() ) {
throw new IllegalArgumentException( "The commandInformation is required." );
}
- checkCmdFile( new File( commandInformation.get( 0 ) ) );
- this.commandInformation = commandInformation;
- adminPassword = null;
+ checkCmdFile( new File( command_information.get( 0 ) ) );
+ _command_information = command_information;
+ _admin_password = null;
}
public static boolean isExecuteableFile( final File path_to_cmd_f ) {
return true;
}
- private void checkCmdFile( final File path_to_cmd_f ) {
+ private static void checkCmdFile( final File path_to_cmd_f ) {
if ( !path_to_cmd_f.exists() ) {
throw new IllegalArgumentException( "[" + path_to_cmd_f.getAbsolutePath() + "] does not exist" );
}
}
public int executeCommand() throws IOException, InterruptedException {
- int exitValue = -99;
+ int exit_value = -99;
try {
- final ProcessBuilder pb = new ProcessBuilder( commandInformation );
+ final ProcessBuilder pb = new ProcessBuilder( _command_information );
+ if ( DEBUG ) {
+ System.out.println( "command_information=" + _command_information );
+ }
final Process process = pb.start();
// you need this if you're going to write something to the command's input stream
// (such as when invoking the 'sudo' command, and it prompts you for a password).
// these need to run as java threads to get the standard output and error from the command.
// the inputstream handler gets a reference to our stdOutput in case we need to write
// something to it, such as with the sudo command
- inputStreamHandler = new ThreadedStreamHandler( inputStream, stdOutput, adminPassword );
- errorStreamHandler = new ThreadedStreamHandler( errorStream );
+ _input_stream_handler = new ThreadedStreamHandler( inputStream, stdOutput, _admin_password );
+ _error_stream_handler = new ThreadedStreamHandler( errorStream );
// TODO the inputStreamHandler has a nasty side-effect of hanging if the given password is wrong; fix it
- inputStreamHandler.start();
- errorStreamHandler.start();
+ _input_stream_handler.start();
+ _error_stream_handler.start();
// TODO a better way to do this?
- exitValue = process.waitFor();
+ exit_value = process.waitFor();
// TODO a better way to do this?
- inputStreamHandler.interrupt();
- errorStreamHandler.interrupt();
- inputStreamHandler.join();
- errorStreamHandler.join();
+ _input_stream_handler.interrupt();
+ _error_stream_handler.interrupt();
+ _input_stream_handler.join();
+ _error_stream_handler.join();
}
catch ( final IOException e ) {
- // TODO deal with this here, or just throw it?
throw e;
}
catch ( final InterruptedException e ) {
// generated by process.waitFor() call
- // TODO deal with this here, or just throw it?
throw e;
}
- finally {
- return exitValue;
- }
+ // finally {
+ return exit_value;
+ // }
}
/**
* Get the standard error (stderr) from the command you just exec'd.
*/
public StringBuilder getStandardErrorFromCommand() {
- return errorStreamHandler.getOutputBuffer();
+ return _error_stream_handler.getOutputBuffer();
}
/**
* Get the standard output (stdout) from the command you just exec'd.
*/
public StringBuilder getStandardOutputFromCommand() {
- return inputStreamHandler.getOutputBuffer();
+ return _input_stream_handler.getOutputBuffer();
}
}
git://source.jalview.org / jalview.git / commitdiff