public final class InferenceManager {
- private final static String DEFAULT_PATHS[] = { "C:\\Program Files\\", "C:\\Program Files (x86)\\", "/bin/",
- "/usr/local/bin/", "/usr/bin/" };
+ private final static String DEFAULT_PATHS[] = {"C:\\Program Files\\mafft-win\\", "C:\\Program Files\\", "C:\\Program Files (x86)\\", "/bin/",
+ "/usr/local/bin/", "/usr/bin/" };
private final File _path_to_local_mafft;
- private final File _path_to_local_kalign;
private final File _path_to_local_fastme;
private final File _path_to_local_raxml;
- private final File _path_to_local_clustalo;
public static InferenceManager createInstance( final Configuration c ) {
- return new InferenceManager( c.getpathToLocalMafft(),
- c.getPathToLocalKalign(),
- c.getPathToLocalFastme(),
- c.getPathToLocalRaxml(),
- c.getPathToLocalClustalOmega() );
+ return new InferenceManager( c.getPathToLocalMafft(), c.getPathToLocalFastme(), c.getPathToLocalRaxml() );
}
public boolean canDoMsa() {
- return ( getPathToLocalMafft() != null ) || ( getPathToLocalKalign() != null )
- || ( getPathToLocalClustalo() != null );
+ return ( getPathToLocalMafft() != null );
}
public File getPathToLocalMafft() {
return _path_to_local_mafft;
}
- public File getPathToLocalKalign() {
- return _path_to_local_kalign;
- }
-
public File getPathToLocalFastme() {
return _path_to_local_fastme;
}
return _path_to_local_raxml;
}
- public File getPathToLocalClustalo() {
- return _path_to_local_clustalo;
- }
-
private final static File createLocalPath( final File path, final String name ) {
if ( ( path != null ) && path.canExecute() && !path.isDirectory() ) {
return path;
}
private InferenceManager( final File path_to_local_mafft,
- final File path_to_local_kalign,
final File path_to_local_fastme,
- final File path_to_local_raxml,
- final File path_to_local_clustalo ) {
+ final File path_to_local_raxml ) {
_path_to_local_mafft = createLocalPath( path_to_local_mafft, "mafft" );
- _path_to_local_kalign = createLocalPath( path_to_local_kalign, "kalign" );
_path_to_local_fastme = createLocalPath( path_to_local_fastme, "fastme" );
_path_to_local_raxml = createLocalPath( path_to_local_raxml, "raxml" );
- _path_to_local_clustalo = createLocalPath( path_to_local_clustalo, "clustalo" );
}
}