cleanup

[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 4cac659..9e651fb 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
@@ -26,7 +26,6 @@
 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;
@@ -42,12 +41,11 @@ 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;
@@ -87,19 +85,25 @@ 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() {
@@ -161,7 +165,7 @@ 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 );
@@ -203,7 +207,7 @@ 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() ) {
@@ -224,7 +228,7 @@ 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;
         }
@@ -263,23 +267,26 @@ 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( _mf.getInferenceManager().getPathToLocalMafft().getCanonicalPath());
+        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() );
         }
         return msa;
     }
-    
-    private Msa runClustalOmega( final File input_seqs, final List<String> opts ) throws IOException, InterruptedException {
+
+    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());
+        final MsaInferrer clustalo = ClustalOmega.createInstance( _mf.getInferenceManager().getPathToLocalClustalo()
+                .getCanonicalPath() );
         try {
-            msa = clustalo.infer( input_seqs, opts );
+            msa = clustalo.infer( seqs, opts );
         }
         catch ( final IOException e ) {
             System.out.println( clustalo.getErrorDescription() );
@@ -292,7 +299,7 @@ public class PhylogeneticInferrer extends RunnableProcess {
             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 ) );
@@ -336,4 +343,8 @@ public class PhylogeneticInferrer extends RunnableProcess {
             }
         }
     }
+
+    public enum MSA_PRG {
+        MAFFT, CLUSTAL_O;
+    }
 }