in progress

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index d81100a..e45dfc8 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -97,7 +97,6 @@ public final class Configuration {
     private boolean                         _taxonomy_colorize_node_shapes                         = false;
     private int                             _default_bootstrap_samples                             = -1;
     private File                            _path_to_local_mafft                                   = null;
-    private File                            _path_to_local_kalign                                  = null;
     private File                            _path_to_local_fastme                                  = null;
     private File                            _path_to_local_raxml                                   = null;
     private File                            _path_to_local_clustalo                                = null;
@@ -440,9 +439,7 @@ public final class Configuration {
         return _path_to_local_mafft;
     }
 
-    public File getPathToLocalKalign() {
-        return _path_to_local_kalign;
-    }
+  
 
     public File getPathToLocalFastme() {
         return _path_to_local_fastme;
@@ -826,9 +823,7 @@ public final class Configuration {
         _path_to_local_mafft = path_to_local_mafft;
     }
 
-    private void setPathToLocalKalign( final File path_to_local_kalign ) {
-        _path_to_local_kalign = path_to_local_kalign;
-    }
+   
 
     private void setPathToLocalFastme( final File path_to_local_fastme ) {
         _path_to_local_fastme = path_to_local_fastme;
@@ -1068,12 +1063,7 @@ public final class Configuration {
                 setPathToLocalMafft( new File( str ) );
             }
         }
-        else if ( key.equals( "kalign_local" ) ) {
-            final String str = ( ( String ) st.nextElement() ).trim();
-            if ( !ForesterUtil.isEmpty( str ) ) {
-                setPathToLocalKalign( new File( str ) );
-            }
-        }
+       
         else if ( key.equals( "fastme_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 f472ff0..2c416b9 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
@@ -10,21 +10,19 @@ public final class InferenceManager {
     private final static String DEFAULT_PATHS[] = { "C:\\Program Files\\", "C:\\Program Files (x86)\\", "/bin/",
             "/usr/local/bin/", "/usr/bin/"     };
     private final File          _path_to_local_mafft;
-    private final File          _path_to_local_kalign;
     private final File          _path_to_local_fastme;
     private final File          _path_to_local_raxml;
     private final File          _path_to_local_clustalo;
 
     public static InferenceManager createInstance( final Configuration c ) {
         return new InferenceManager( c.getpathToLocalMafft(),
-                                     c.getPathToLocalKalign(),
                                      c.getPathToLocalFastme(),
                                      c.getPathToLocalRaxml(),
                                      c.getPathToLocalClustalOmega() );
     }
 
     public boolean canDoMsa() {
-        return ( getPathToLocalMafft() != null ) || ( getPathToLocalKalign() != null )
+        return ( getPathToLocalMafft() != null ) 
                 || ( getPathToLocalClustalo() != null );
     }
 
@@ -32,9 +30,7 @@ public final class InferenceManager {
         return _path_to_local_mafft;
     }
 
-    public File getPathToLocalKalign() {
-        return _path_to_local_kalign;
-    }
+    
 
     public File getPathToLocalFastme() {
         return _path_to_local_fastme;
@@ -78,12 +74,11 @@ public final class InferenceManager {
     }
 
     private InferenceManager( final File path_to_local_mafft,
-                              final File path_to_local_kalign,
                               final File path_to_local_fastme,
                               final File path_to_local_raxml,
                               final File path_to_local_clustalo ) {
         _path_to_local_mafft = createLocalPath( path_to_local_mafft, "mafft" );
-        _path_to_local_kalign = createLocalPath( path_to_local_kalign, "kalign" );
+      
         _path_to_local_fastme = createLocalPath( path_to_local_fastme, "fastme" );
         _path_to_local_raxml = createLocalPath( path_to_local_raxml, "raxml" );
         _path_to_local_clustalo = createLocalPath( path_to_local_clustalo, "clustalo" );

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java b/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java
index fbfd4c2..399c521 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java
@@ -78,13 +78,16 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
     private JTextField                         _input_seqs_min_length_tf;
     private JTextField                         _input_seqs_max_length_tf;
     private JTextField                         _input_seqs_type_tf;
-    private JTextField                         _input_seqs_msa_program_name_tf;
-    private JTextField                         _input_seqs_msa_paramenters_tf;
+  
+    private JTextField                         _mafft_paramenters_tf;
+    private JTextField                         _clustalo_paramenters_tf;
     private JTextField                         _msa_processing_max_allowed_gap_ratio_tf;
     private JTextField                         _msa_processing_min_allowed_length_tf;
     private JTextField                         _random_seed_tf;
     private JCheckBox                          _execute_msa_processing_cb;
     private JCheckBox                          _msa_processing_remove_all_gap_columns_cb;
+    private JCheckBox                          _mafft_cb;
+    private JCheckBox                          _clustalo_cb;
     private JCheckBox                          _save_pwd_file_cb;
     private JCheckBox                          _save_processed_msa_cb;
     private JCheckBox                          _save_original_msa_cb;
@@ -108,9 +111,11 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
             final JPanel inputfile_pnl_1 = new JPanel();
             final JPanel inputfile_pnl_2 = new JPanel();
             final JPanel inputfile_pnl_3 = new JPanel();
+            final JPanel inputfile_pnl_4 = new JPanel();
             inputfile_pnl_1.setLayout( new FlowLayout() );
             inputfile_pnl_2.setLayout( new FlowLayout() );
             inputfile_pnl_3.setLayout( new FlowLayout() );
+            inputfile_pnl_4.setLayout( new FlowLayout() );
             inputfile_pnl_1.add( new JLabel( "Input Sequence File:" ) );
             inputfile_pnl_1.add( _input_seqs_tf = new JTextField() );
             inputfile_pnl_1.add( _select_input_seqs_btn = new JButton( "Select Input File" ) );
@@ -125,11 +130,15 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
             inputfile_pnl_2.add( _input_seqs_max_length_tf = new JTextField() );
             inputfile_pnl_2.add( new JLabel( "Type:" ) );
             inputfile_pnl_2.add( _input_seqs_type_tf = new JTextField() );
-            inputfile_pnl_3.add( new JLabel( "Mutiple Sequence Alignment: " ) );
-            inputfile_pnl_3.add( new JLabel( "Program: " ) );
-            inputfile_pnl_3.add( _input_seqs_msa_program_name_tf = new JTextField() );
+           
+            
+            inputfile_pnl_3.add( _mafft_cb = new JCheckBox( "MAFFT") );
             inputfile_pnl_3.add( new JLabel( "Parameters: " ) );
-            inputfile_pnl_3.add( _input_seqs_msa_paramenters_tf = new JTextField() );
+            inputfile_pnl_3.add( _mafft_paramenters_tf = new JTextField() );
+           
+            inputfile_pnl_4.add( _clustalo_cb = new  JCheckBox( "ClustalO") );
+            inputfile_pnl_4.add( new JLabel( "Parameters: " ) );
+            inputfile_pnl_4.add( _clustalo_paramenters_tf = new JTextField() );
             _input_seqs_median_length_tf.setColumns( 4 );
             _input_seqs_min_length_tf.setColumns( 4 );
             _input_seqs_max_length_tf.setColumns( 4 );
@@ -142,12 +151,16 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
             _input_seqs_max_length_tf.setEditable( false );
             _input_seqs_number_tf.setEditable( false );
             _input_seqs_type_tf.setEditable( false );
-            _input_seqs_msa_program_name_tf.setEditable( false );
-            _input_seqs_msa_paramenters_tf.setColumns( 26 );
+           
+            _mafft_paramenters_tf.setColumns( 26 );
+            _mafft_paramenters_tf.setText( "--maxiterate 1000 --localpair" );
+            _clustalo_paramenters_tf.setColumns( 26 );
+            _clustalo_paramenters_tf.setText( "clustalo options" );
             _select_input_seqs_btn.addActionListener( this );
             _pnl.add( inputfile_pnl_1 );
             _pnl.add( inputfile_pnl_2 );
             _pnl.add( inputfile_pnl_3 );
+            _pnl.add( inputfile_pnl_4 );
         }
         else {
             setTitle( "Phylogenetic Inference (from already aligned sequences) " );
@@ -273,9 +286,7 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
         _value = JOptionPane.CANCEL_OPTION;
         if ( from_unaligned_seqs ) {
             updateSeqsItems();
-            _input_seqs_msa_program_name_tf.setText( getPhylogeneticInferenceOptions().getMsaPrg() );
-            _input_seqs_msa_paramenters_tf.setText( getPhylogeneticInferenceOptions().getMsaPrgParameters() );
-        }
+              }
         else {
             updateMsaItems();
         }
@@ -376,8 +387,8 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
     }
 
     private void processMsaPrgParameters() {
-        if ( _input_seqs_msa_paramenters_tf != null ) {
-            getPhylogeneticInferenceOptions().setMsaPrgParameters( _input_seqs_msa_paramenters_tf.getText() );
+        if ( _mafft_paramenters_tf != null ) {
+            getPhylogeneticInferenceOptions().setMsaPrgParameters( _mafft_paramenters_tf.getText() );
         }
     }
 

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
index c1aefc5..66fbdbc 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
@@ -86,7 +86,7 @@ public class PhylogeneticInferrer extends RunnableProcess {
         _options = options;
     }
 
-    private Msa inferMsa() throws IOException, InterruptedException {
+    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();
@@ -97,8 +97,17 @@ public class PhylogeneticInferrer extends RunnableProcess {
         //        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( _seqs, opts );
+        switch ( msa_prg ) {
+            case MAFFT: 
+                return runMAFFT( _seqs, processMafftOptions() );
+                
+            case CLUSTAL_O:
+                return runClustalOmega( _seqs, processMafftOptions() );
+            default:
+                return null;
+        }
+        
+       
     }
 
     private List<String> processMafftOptions() {
@@ -160,7 +169,7 @@ 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 );
@@ -275,13 +284,13 @@ public class PhylogeneticInferrer extends RunnableProcess {
         return msa;
     }
 
-    private Msa runClustalOmega( final File input_seqs, final List<String> opts ) throws IOException,
+    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( input_seqs, opts );
+            msa = clustalo.infer( seqs, opts );
         }
         catch ( final IOException e ) {
             System.out.println( clustalo.getErrorDescription() );
@@ -338,4 +347,8 @@ public class PhylogeneticInferrer extends RunnableProcess {
             }
         }
     }
+    
+    public enum MSA_PRG {
+        MAFFT, CLUSTAL_O;
+    }
 }

diff --git a/forester/java/src/org/forester/msa/ClustalOmega.java b/forester/java/src/org/forester/msa/ClustalOmega.java
index 72db9d3..f6d4f65 100644 (file)
--- a/forester/java/src/org/forester/msa/ClustalOmega.java
+++ b/forester/java/src/org/forester/msa/ClustalOmega.java
@@ -25,12 +25,16 @@
 
 package org.forester.msa;
 
+import java.io.BufferedWriter;
 import java.io.File;
+import java.io.FileWriter;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
 import org.forester.io.parsers.FastaParser;
+import org.forester.io.writers.SequenceWriter;
+import org.forester.io.writers.SequenceWriter.SEQ_FORMAT;
 import org.forester.sequence.Sequence;
 import org.forester.util.SystemCommandExecutor;
 
@@ -67,6 +71,19 @@ public final class ClustalOmega extends MsaInferrer {
         return _exit_code;
     }
 
+    
+    public Msa infer( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
+        final File file = File.createTempFile( "__clustalo_input_", ".fasta" );
+        file.deleteOnExit();
+        final BufferedWriter writer = new BufferedWriter( new FileWriter( file ) );
+        SequenceWriter.writeSeqs( seqs, writer, SEQ_FORMAT.FASTA, 100 );
+        writer.close();
+        final Msa msa = infer( file, opts );
+        file.delete();
+        return msa;
+    }
+    
+    
     @Override
     public Msa infer( final File path_to_input_seqs, final List<String> opts ) throws IOException, InterruptedException {
         init();
@@ -98,9 +115,5 @@ public final class ClustalOmega extends MsaInferrer {
         _exit_code = -100;
     }
 
-    @Override
-    public Msa infer( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
-        // TODO Auto-generated method stub
-        return null;
-    }
+  
 }