Changed more concrete DistanceMatrix references to reference interface

[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 20da0c3..cc62751 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
@@ -37,6 +37,7 @@ import org.forester.archaeopteryx.MainFrameApplication;
 import org.forester.evoinference.distance.NeighborJoiningF;
 import org.forester.evoinference.distance.PairwiseDistanceCalculator;
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
+import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.evoinference.tools.BootstrapResampler;
 import org.forester.msa.BasicMsa;
 import org.forester.msa.Mafft;
@@ -47,7 +48,7 @@ import org.forester.msa.MsaMethods;
 import org.forester.msa.ResampleableMsa;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.sequence.Sequence;
+import org.forester.sequence.MolecularSequence;
 import org.forester.tools.ConfidenceAssessor;
 import org.forester.util.ForesterUtil;
 
@@ -56,12 +57,12 @@ public class PhylogeneticInferrer extends RunnableProcess {
     private Msa                                _msa;
     private final MainFrameApplication         _mf;
     private final PhylogeneticInferenceOptions _options;
-    private final List<Sequence>               _seqs;
+    private final List<MolecularSequence>      _seqs;
     private final boolean                      DEBUG           = true;
     public final static String                 MSA_FILE_SUFFIX = ".aln";
     public final static String                 PWD_FILE_SUFFIX = ".pwd";
 
-    public PhylogeneticInferrer( final List<Sequence> seqs,
+    public PhylogeneticInferrer( final List<MolecularSequence> seqs,
                                  final PhylogeneticInferenceOptions options,
                                  final MainFrameApplication mf ) {
         _msa = null;
@@ -116,7 +117,7 @@ public class PhylogeneticInferrer extends RunnableProcess {
     }
 
     private Phylogeny inferPhylogeny( final Msa msa ) {
-        BasicSymmetricalDistanceMatrix m = null;
+        DistanceMatrix m = null;
         switch ( _options.getPwdDistanceMethod() ) {
             case KIMURA_DISTANCE:
                 m = PairwiseDistanceCalculator.calcKimuraDistances( msa );
@@ -144,6 +145,7 @@ public class PhylogeneticInferrer extends RunnableProcess {
         }
         final NeighborJoiningF nj = NeighborJoiningF.createInstance( false, 5 );
         final Phylogeny phy = nj.execute( m );
+        PhylogenyMethods.addMolecularSeqsToTree( phy, msa );
         PhylogenyMethods.extractFastaInformation( phy );
         return phy;
     }
@@ -166,8 +168,8 @@ public class PhylogeneticInferrer extends RunnableProcess {
                                                        + _options.getMsaPrg() + "\" and the following parameters:\n\""
                                                        + _options.getMsaPrgParameters() + "\"\nError: "
                                                        + e.getLocalizedMessage(),
-                                               "Failed to Calculate MSA",
-                                               JOptionPane.ERROR_MESSAGE );
+                                                       "Failed to Calculate MSA",
+                                                       JOptionPane.ERROR_MESSAGE );
                 if ( DEBUG ) {
                     e.printStackTrace();
                 }
@@ -180,8 +182,8 @@ public class PhylogeneticInferrer extends RunnableProcess {
                                                        + _options.getMsaPrg() + "\" and the following parameters:\n\""
                                                        + _options.getMsaPrgParameters() + "\"\nError: "
                                                        + e.getLocalizedMessage(),
-                                               "Unexpected Exception During MSA Calculation",
-                                               JOptionPane.ERROR_MESSAGE );
+                                                       "Unexpected Exception During MSA Calculation",
+                                                       JOptionPane.ERROR_MESSAGE );
                 if ( DEBUG ) {
                     e.printStackTrace();
                 }
@@ -193,8 +195,8 @@ public class PhylogeneticInferrer extends RunnableProcess {
                                                "Could not create multiple sequence alignment with "
                                                        + _options.getMsaPrg() + "\nand the following parameters:\n\""
                                                        + _options.getMsaPrgParameters() + "\"",
-                                               "Failed to Calculate MSA",
-                                               JOptionPane.ERROR_MESSAGE );
+                                                       "Failed to Calculate MSA",
+                                                       JOptionPane.ERROR_MESSAGE );
                 return;
             }
             if ( DEBUG ) {
@@ -203,7 +205,7 @@ public class PhylogeneticInferrer extends RunnableProcess {
             }
             final MsaMethods msa_tools = MsaMethods.createInstance();
             if ( _options.isExecuteMsaProcessing() ) {
-                msa = msa_tools.removeGapColumns( _options.getMsaProcessingMaxAllowedGapRatio(),
+                msa = msa_tools.deleteGapColumns( _options.getMsaProcessingMaxAllowedGapRatio(),
                                                   _options.getMsaProcessingMinAllowedLength(),
                                                   msa );
                 if ( msa == null ) {
@@ -212,8 +214,8 @@ public class PhylogeneticInferrer extends RunnableProcess {
                                                    "Less than two sequences longer than "
                                                            + _options.getMsaProcessingMinAllowedLength()
                                                            + " residues left after MSA processing",
-                                                   "MSA Processing Settings Too Stringent",
-                                                   JOptionPane.ERROR_MESSAGE );
+                                                           "MSA Processing Settings Too Stringent",
+                                                           JOptionPane.ERROR_MESSAGE );
                     return;
                 }
             }
@@ -230,7 +232,7 @@ public class PhylogeneticInferrer extends RunnableProcess {
         if ( _options.isPerformBootstrapResampling() && ( n > 0 ) ) {
             final ResampleableMsa resampleable_msa = new ResampleableMsa( ( BasicMsa ) _msa );
             final int[][] resampled_column_positions = BootstrapResampler.createResampledColumnPositions( _msa
-                    .getLength(), n, seed );
+                                                                                                          .getLength(), n, seed );
             final Phylogeny[] eval_phys = new Phylogeny[ n ];
             for( int i = 0; i < n; ++i ) {
                 resampleable_msa.resample( resampled_column_positions[ i ] );
@@ -259,10 +261,11 @@ public class PhylogeneticInferrer extends RunnableProcess {
         }
     }
 
-    private Msa runMAFFT( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
+    private Msa runMAFFT( final List<MolecularSequence> seqs, final List<String> opts ) throws IOException,
+    InterruptedException {
         Msa msa = null;
         final MsaInferrer mafft = Mafft.createInstance( _mf.getInferenceManager().getPathToLocalMafft()
-                .getCanonicalPath() );
+                                                        .getCanonicalPath() );
         try {
             msa = mafft.infer( seqs, opts );
         }
@@ -272,15 +275,15 @@ public class PhylogeneticInferrer extends RunnableProcess {
         return msa;
     }
 
-    private void writeToFiles( final BasicSymmetricalDistanceMatrix m ) {
+    private void writeToFiles( final DistanceMatrix m ) {
         if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
             try {
                 final BufferedWriter msa_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
-                        + MSA_FILE_SUFFIX ) );
+                                                                                      + MSA_FILE_SUFFIX ) );
                 _msa.write( msa_writer, MSA_FORMAT.PHYLIP );
                 msa_writer.close();
                 final BufferedWriter pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
-                        + PWD_FILE_SUFFIX ) );
+                                                                                      + PWD_FILE_SUFFIX ) );
                 m.write( pwd_writer );
                 pwd_writer.close();
             }