X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2Ftools%2FPhylogeneticInferrer.java;h=1144fcbf9e90f8d5f23472e135a14fb0f5d166a5;hb=a9cc2cc5c9cda0ab49f26ccfb7a1aa30531e6ecf;hp=66fbdbc843b1d10684902c833d85556413125114;hpb=def5f3c9ca461176f1188d0adfd744726a56e6ed;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
index 66fbdbc..1144fcb 100644
--- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
@@ -21,12 +21,11 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.archaeopteryx.tools;
 
 import java.io.BufferedWriter;
-import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -35,7 +34,6 @@ import java.util.regex.Matcher;
 
 import javax.swing.JOptionPane;
 
-import org.forester.archaeopteryx.AptxUtil;
 import org.forester.archaeopteryx.MainFrameApplication;
 import org.forester.evoinference.distance.NeighborJoining;
 import org.forester.evoinference.distance.PairwiseDistanceCalculator;
@@ -43,7 +41,6 @@ import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 import org.forester.evoinference.tools.BootstrapResampler;
 import org.forester.io.parsers.FastaParser;
 import org.forester.msa.BasicMsa;
-import org.forester.msa.ClustalOmega;
 import org.forester.msa.Mafft;
 import org.forester.msa.Msa;
 import org.forester.msa.Msa.MSA_FORMAT;
@@ -98,16 +95,11 @@ public class PhylogeneticInferrer extends RunnableProcess {
         //        SequenceWriter.writeSeqs( _seqs, writer, SEQ_FORMAT.FASTA, 100 );
         //        writer.close();
         switch ( msa_prg ) {
-            case MAFFT: 
+            case MAFFT:
                 return runMAFFT( _seqs, processMafftOptions() );
-                
-            case CLUSTAL_O:
-                return runClustalOmega( _seqs, processMafftOptions() );
             default:
                 return null;
         }
-        
-       
     }
 
     private List<String> processMafftOptions() {
@@ -284,20 +276,6 @@ public class PhylogeneticInferrer extends RunnableProcess {
         return msa;
     }
 
-    private Msa runClustalOmega( final List<Sequence> seqs, final List<String> opts ) throws IOException,
-            InterruptedException {
-        Msa msa = null;
-        final MsaInferrer clustalo = ClustalOmega.createInstance( _mf.getInferenceManager().getPathToLocalClustalo()
-                .getCanonicalPath() );
-        try {
-            msa = clustalo.infer( seqs, opts );
-        }
-        catch ( final IOException e ) {
-            System.out.println( clustalo.getErrorDescription() );
-        }
-        return msa;
-    }
-
     private void writeToFiles( final BasicSymmetricalDistanceMatrix m ) {
         if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
             try {
@@ -332,23 +310,23 @@ public class PhylogeneticInferrer extends RunnableProcess {
                     final String seq_name = name_m.group( 3 );
                     final String tax_sn = name_m.group( 4 );
                     if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) {
-                        AptxUtil.ensurePresenceOfSequence( node );
+                        ForesterUtil.ensurePresenceOfSequence( node );
                         node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) );
                     }
                     if ( !ForesterUtil.isEmpty( seq_name ) ) {
-                        AptxUtil.ensurePresenceOfSequence( node );
+                        ForesterUtil.ensurePresenceOfSequence( node );
                         node.getNodeData().getSequence( 0 ).setName( seq_name );
                     }
                     if ( !ForesterUtil.isEmpty( tax_sn ) ) {
-                        AptxUtil.ensurePresenceOfTaxonomy( node );
+                        ForesterUtil.ensurePresenceOfTaxonomy( node );
                         node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn );
                     }
                 }
             }
         }
     }
-    
+
     public enum MSA_PRG {
-        MAFFT, CLUSTAL_O;
+        MAFFT;
     }
 }