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_fastme;
private final File _path_to_local_raxml;
public static InferenceManager createInstance( final Configuration c ) {
- return new InferenceManager( c.getpathToLocalMafft(),
- c.getPathToLocalFastme(),
- c.getPathToLocalRaxml(),
- c.getPathToLocalClustalOmega() );
+ return new InferenceManager( c.getPathToLocalMafft(), c.getPathToLocalFastme(), c.getPathToLocalRaxml() );
}
public boolean canDoMsa() {
private InferenceManager( final File path_to_local_mafft,
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_fastme = createLocalPath( path_to_local_fastme, "fastme" );
_path_to_local_raxml = createLocalPath( path_to_local_raxml, "raxml" );