From 56fcc7953ce4896eed89a3129d862e0aaf2d65e1 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 15 Jan 2013 18:41:46 +0000 Subject: [PATCH] removed clustalo --- .../src/org/forester/archaeopteryx/Configuration.java | 15 --------------- .../forester/archaeopteryx/tools/InferenceManager.java | 8 ++------ 2 files changed, 2 insertions(+), 21 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index e647804..5d354cc 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -104,7 +104,6 @@ public final class Configuration { private File _path_to_local_mafft = null; private File _path_to_local_fastme = null; private File _path_to_local_raxml = null; - private File _path_to_local_clustalo = null; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; @@ -347,10 +346,6 @@ public final class Configuration { return _label_for_get_ext_descendents_data; } - public File getPathToLocalClustalOmega() { - return _path_to_local_clustalo; - } - public File getPathToLocalFastme() { return _path_to_local_fastme; } @@ -523,10 +518,6 @@ public final class Configuration { _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values; } - public void setPathToLocalClustalOmega( final File path_to_local_clustalo ) { - _path_to_local_clustalo = path_to_local_clustalo; - } - public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) { _phylogeny_graphics_type = phylogeny_graphics_type; } @@ -1200,12 +1191,6 @@ public final class Configuration { "value for [default_number_of_bootstrap_resamples] cannot be negative" ); } } - else if ( key.equals( "clustalo_local" ) ) { - final String str = ( ( String ) st.nextElement() ).trim(); - if ( !ForesterUtil.isEmpty( str ) ) { - setPathToLocalClustalOmega( new File( str ) ); - } - } else if ( key.equals( "mafft_local" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); if ( !ForesterUtil.isEmpty( str ) ) { diff --git a/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java b/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java index 30db176..e3e5e65 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java @@ -14,10 +14,7 @@ public final class InferenceManager { 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() { @@ -67,8 +64,7 @@ public final class InferenceManager { 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" ); -- 1.7.10.2