in progress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / tools / PhylogeneticInferrer.java

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
index 9e651fb..1144fcb 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
@@ -21,7 +21,7 @@
 // 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;
 
@@ -34,7 +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;
@@ -42,7 +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;
@@ -99,8 +97,6 @@ public class PhylogeneticInferrer extends RunnableProcess {
         switch ( msa_prg ) {
             case MAFFT:
                 return runMAFFT( _seqs, processMafftOptions() );
-            case CLUSTAL_O:
-                return runClustalOmega( _seqs, processMafftOptions() );
             default:
                 return null;
         }
@@ -280,20 +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 {
@@ -328,15 +310,15 @@ 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 );
                     }
                 }
@@ -345,6 +327,6 @@ public class PhylogeneticInferrer extends RunnableProcess {
     }
 
     public enum MSA_PRG {
-        MAFFT, CLUSTAL_O;
+        MAFFT;
     }
 }