phylotastic hackathon at NESCENT 120607

[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 a44fe96..6cf6614 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
@@ -48,7 +48,7 @@ import org.forester.msa.BasicMsa;
 import org.forester.msa.Mafft;
 import org.forester.msa.Msa;
 import org.forester.msa.MsaInferrer;
-import org.forester.msa.MsaTools;
+import org.forester.msa.MsaMethods;
 import org.forester.msa.ResampleableMsa;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
@@ -58,12 +58,13 @@ import org.forester.sequence.Sequence;
 import org.forester.tools.ConfidenceAssessor;
 import org.forester.util.ForesterUtil;
 
-public class PhylogeneticInferrer implements Runnable {
+public class PhylogeneticInferrer extends RunnableProcess {
 
     private Msa                                _msa;
     private final MainFrameApplication         _mf;
     private final PhylogeneticInferenceOptions _options;
     private final List<Sequence>               _seqs;
+    private final boolean                      DEBUG           = true;
     public final static String                 MSA_FILE_SUFFIX = ".aln";
     public final static String                 PWD_FILE_SUFFIX = ".pwd";
 
@@ -85,25 +86,19 @@ public class PhylogeneticInferrer implements Runnable {
         _options = options;
     }
 
-    private Msa inferMsa() throws IOException {
-        final File temp_seqs_file = File.createTempFile( "aptx", ".fasta" );
-        System.out.println( "temp file: " + temp_seqs_file );
+    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();
+        }
         //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();
-        Msa msa = null;
-        try {
-            msa = runMAFFT( temp_seqs_file, opts );
-        }
-        catch ( final InterruptedException e ) {
-            // TODO Auto-generated catch block
-            e.printStackTrace();
-        }
-        // copy aln file to intermediate dir file
-        // delete temp seqs file
-        return msa;
+        return runMAFFT( temp_seqs_file, opts );
     }
 
     private List<String> processMafftOptions() {
@@ -150,33 +145,53 @@ public class PhylogeneticInferrer implements Runnable {
                 e.printStackTrace();
             }
         }
-        final NeighborJoining nj = new NeighborJoining();
+        final NeighborJoining nj = NeighborJoining.createInstance();
         final Phylogeny phy = nj.execute( m );
         PhylogeneticInferrer.extractFastaInformation( phy );
         return phy;
     }
 
-    private void infer() {
+    private void infer() throws InterruptedException {
         //_mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
         if ( ( _msa == null ) && ( _seqs == null ) ) {
             throw new IllegalArgumentException( "cannot run phylogenetic analysis with null msa and seq array" );
         }
+        start( _mf, "phylogenetic inference" );
         if ( _msa == null ) {
             Msa msa = null;
             try {
                 msa = inferMsa();
             }
             catch ( final IOException e ) {
+                end( _mf );
                 JOptionPane.showMessageDialog( _mf,
-                                               "Could not create multiple sequence alignment with "
-                                                       + _options.getMsaPrg() + "\nand the following parameters:\n\""
-                                                       + _options.getMsaPrgParameters() + "\"\nError:"
+                                               "Could not create multiple sequence alignment with \""
+                                                       + _options.getMsaPrg() + "\" and the following parameters:\n\""
+                                                       + _options.getMsaPrgParameters() + "\"\nError: "
                                                        + e.getLocalizedMessage(),
                                                "Failed to Calculate MSA",
                                                JOptionPane.ERROR_MESSAGE );
+                if ( DEBUG ) {
+                    e.printStackTrace();
+                }
+                return;
+            }
+            catch ( final Exception e ) {
+                end( _mf );
+                JOptionPane.showMessageDialog( _mf,
+                                               "Could not create multiple sequence alignment with \""
+                                                       + _options.getMsaPrg() + "\" and the following parameters:\n\""
+                                                       + _options.getMsaPrgParameters() + "\"\nError: "
+                                                       + e.getLocalizedMessage(),
+                                               "Unexpected Exception During MSA Calculation",
+                                               JOptionPane.ERROR_MESSAGE );
+                if ( DEBUG ) {
+                    e.printStackTrace();
+                }
                 return;
             }
             if ( msa == null ) {
+                end( _mf );
                 JOptionPane.showMessageDialog( _mf,
                                                "Could not create multiple sequence alignment with "
                                                        + _options.getMsaPrg() + "\nand the following parameters:\n\""
@@ -185,14 +200,17 @@ public class PhylogeneticInferrer implements Runnable {
                                                JOptionPane.ERROR_MESSAGE );
                 return;
             }
-            System.out.println( msa.toString() );
-            System.out.println( MsaTools.calcBasicGapinessStatistics( msa ).toString() );
-            final MsaTools msa_tools = MsaTools.createInstance();
+            if ( DEBUG ) {
+                System.out.println( msa.toString() );
+                System.out.println( MsaMethods.calcBasicGapinessStatistics( msa ).toString() );
+            }
+            final MsaMethods msa_tools = MsaMethods.createInstance();
             if ( _options.isExecuteMsaProcessing() ) {
                 msa = msa_tools.removeGapColumns( _options.getMsaProcessingMaxAllowedGapRatio(),
                                                   _options.getMsaProcessingMinAllowedLength(),
                                                   msa );
                 if ( msa == null ) {
+                    end( _mf );
                     JOptionPane.showMessageDialog( _mf,
                                                    "Less than two sequences longer than "
                                                            + _options.getMsaProcessingMinAllowedLength()
@@ -202,9 +220,11 @@ public class PhylogeneticInferrer implements Runnable {
                     return;
                 }
             }
-            System.out.println( msa_tools.getIgnoredSequenceIds() );
-            System.out.println( msa.toString() );
-            System.out.println( MsaTools.calcBasicGapinessStatistics( msa ).toString() );
+            if ( DEBUG ) {
+                System.out.println( msa_tools.getIgnoredSequenceIds() );
+                System.out.println( msa.toString() );
+                System.out.println( MsaMethods.calcBasicGapinessStatistics( msa ).toString() );
+            }
             _msa = msa;
         }
         final int n = _options.getBootstrapSamples();
@@ -222,7 +242,8 @@ public class PhylogeneticInferrer implements Runnable {
             ConfidenceAssessor.evaluate( "bootstrap", eval_phys, master_phy, true, 1 );
         }
         _mf.getMainPanel().addPhylogenyInNewTab( master_phy, _mf.getConfiguration(), "nj", "njpath" );
-        _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
+        //  _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
+        end( _mf );
         JOptionPane.showMessageDialog( _mf,
                                        "Inference successfully completed",
                                        "Inference Completed",
@@ -231,7 +252,14 @@ public class PhylogeneticInferrer implements Runnable {
 
     @Override
     public void run() {
-        infer();
+        try {
+            infer();
+        }
+        catch ( final InterruptedException e ) {
+            // TODO need to handle this exception SOMEHOW!
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+        }
     }
 
     private Msa runMAFFT( final File input_seqs, final List<String> opts ) throws IOException, InterruptedException {