From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Tue, 15 Jan 2013 18:41:46 +0000 (+0000)
Subject: removed clustalo
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=56fcc7953ce4896eed89a3129d862e0aaf2d65e1;p=jalview.git

removed clustalo
---

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" );