X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2Ftools%2FPhylogeneticInferrer.java;h=10bc95e29947d242587e5ddbc0fc4189efb464ef;hb=ae9764d1d2d667c26a90543b553f2ada548f1bcf;hp=6cf66148e526bc0f97ad1ff2f434e196c3b5eb7d;hpb=6a8e6ec5f2cebcb8ec901add6fb64033fcd572da;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 6cf6614..10bc95e 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;
@@ -35,18 +34,17 @@ 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;
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 import org.forester.evoinference.tools.BootstrapResampler;
 import org.forester.io.parsers.FastaParser;
-import org.forester.io.writers.SequenceWriter;
-import org.forester.io.writers.SequenceWriter.SEQ_FORMAT;
 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;
 import org.forester.msa.MsaInferrer;
 import org.forester.msa.MsaMethods;
 import org.forester.msa.ResampleableMsa;
@@ -86,19 +84,25 @@ public class PhylogeneticInferrer extends RunnableProcess {
         _options = options;
     }
 
-    private Msa inferMsa() throws IOException, InterruptedException {
-        final File temp_seqs_file = File.createTempFile( "__msa__temp__", ".fasta" );
-        if ( DEBUG ) {
-            System.out.println();
-            System.out.println( "temp file: " + temp_seqs_file );
-            System.out.println();
+    private Msa inferMsa( final MSA_PRG msa_prg ) throws IOException, InterruptedException {
+        //        final File temp_seqs_file = File.createTempFile( "__msa__temp__", ".fasta" );
+        //        if ( DEBUG ) {
+        //            System.out.println();
+        //            System.out.println( "temp file: " + temp_seqs_file );
+        //            System.out.println();
+        //        }
+        //        //final File temp_seqs_file = new File( _options.getTempDir() + ForesterUtil.FILE_SEPARATOR + "s.fasta" );
+        //        final BufferedWriter writer = new BufferedWriter( new FileWriter( temp_seqs_file ) );
+        //        SequenceWriter.writeSeqs( _seqs, writer, SEQ_FORMAT.FASTA, 100 );
+        //        writer.close();
+        switch ( msa_prg ) {
+            case MAFFT:
+                return runMAFFT( _seqs, processMafftOptions() );
+            case CLUSTAL_O:
+                return runClustalOmega( _seqs, processMafftOptions() );
+            default:
+                return null;
         }
-        //final File temp_seqs_file = new File( _options.getTempDir() + ForesterUtil.FILE_SEPARATOR + "s.fasta" );
-        final BufferedWriter writer = new BufferedWriter( new FileWriter( temp_seqs_file ) );
-        SequenceWriter.writeSeqs( _seqs, writer, SEQ_FORMAT.FASTA, 100 );
-        writer.close();
-        final List<String> opts = processMafftOptions();
-        return runMAFFT( temp_seqs_file, opts );
     }
 
     private List<String> processMafftOptions() {
@@ -160,7 +164,7 @@ public class PhylogeneticInferrer extends RunnableProcess {
         if ( _msa == null ) {
             Msa msa = null;
             try {
-                msa = inferMsa();
+                msa = inferMsa( MSA_PRG.MAFFT );
             }
             catch ( final IOException e ) {
                 end( _mf );
@@ -202,7 +206,7 @@ public class PhylogeneticInferrer extends RunnableProcess {
             }
             if ( DEBUG ) {
                 System.out.println( msa.toString() );
-                System.out.println( MsaMethods.calcBasicGapinessStatistics( msa ).toString() );
+                System.out.println( MsaMethods.calcGapRatio( msa ) );
             }
             final MsaMethods msa_tools = MsaMethods.createInstance();
             if ( _options.isExecuteMsaProcessing() ) {
@@ -223,7 +227,7 @@ public class PhylogeneticInferrer extends RunnableProcess {
             if ( DEBUG ) {
                 System.out.println( msa_tools.getIgnoredSequenceIds() );
                 System.out.println( msa.toString() );
-                System.out.println( MsaMethods.calcBasicGapinessStatistics( msa ).toString() );
+                System.out.println( MsaMethods.calcGapRatio( msa ) );
             }
             _msa = msa;
         }
@@ -262,11 +266,12 @@ public class PhylogeneticInferrer extends RunnableProcess {
         }
     }
 
-    private Msa runMAFFT( final File input_seqs, final List<String> opts ) throws IOException, InterruptedException {
+    private Msa runMAFFT( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
         Msa msa = null;
-        final MsaInferrer mafft = Mafft.createInstance();
+        final MsaInferrer mafft = Mafft.createInstance( _mf.getInferenceManager().getPathToLocalMafft()
+                .getCanonicalPath() );
         try {
-            msa = mafft.infer( input_seqs, opts );
+            msa = mafft.infer( seqs, opts );
         }
         catch ( final IOException e ) {
             System.out.println( mafft.getErrorDescription() );
@@ -274,12 +279,26 @@ 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 {
                 final BufferedWriter msa_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
                         + MSA_FILE_SUFFIX ) );
-                _msa.write( msa_writer );
+                _msa.write( msa_writer, MSA_FORMAT.PHYLIP );
                 msa_writer.close();
                 final BufferedWriter pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
                         + PWD_FILE_SUFFIX ) );
@@ -308,19 +327,23 @@ 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;
+    }
 }