analyze pplacer output...

diff --git a/forester/java/src/org/forester/application/pplacer_summary.java b/forester/java/src/org/forester/application/pplacer_summary.java
new file mode 100644 (file)
index 0000000..91a488a
--- /dev/null
+++ b/forester/java/src/org/forester/application/pplacer_summary.java
@@ -0,0 +1,147 @@
+
+package org.forester.application;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.util.BasicDescriptiveStatistics;
+
+public class pplacer_summary {
+
+    public static void main( final String args[] ) {
+        final File indir = new File( "." );
+        final File[] list_of_files = indir.listFiles();
+        final List<File> infiles = new ArrayList<>();
+        for( final File file : list_of_files ) {
+            if ( file.isFile() && file.canRead() && file.toString().endsWith( ".sing.tre" ) ) {
+                infiles.add( file );
+            }
+        }
+        Collections.sort( infiles );
+        final BasicDescriptiveStatistics non_unique_placements_stats = new BasicDescriptiveStatistics();
+        final BasicDescriptiveStatistics unexpected_top_placements_stats = new BasicDescriptiveStatistics();
+        final BasicDescriptiveStatistics unexpected_unique_top_placements_stats = new BasicDescriptiveStatistics();
+        for( final File infile : infiles ) {
+            Phylogeny phys[] = null;
+            try {
+                final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+                phys = factory.create( infile,
+                                       org.forester.io.parsers.util.ParserUtils
+                                               .createParserDependingOnFileType( infile, true ) );
+            }
+            catch ( final Exception e ) {
+                System.out.println( "Could not read " + infile + ":" + e );
+                System.exit( -1 );
+            }
+            final Pattern p = Pattern.compile( "_Q_#\\d+_M=(.+)" );
+            int total_trees = 0;
+            int total_placements = 0;
+            int total_expected_top_placements = 0;
+            int total_unexpected_top_placements = 0;
+            int total_unexpected_unique_top_placements = 0;
+            int unique_placements = 0;
+            int non_unique_placements = 0;
+            int m1_placements = 0;
+            int non_m1_placements = 0;
+            for( final Phylogeny phy : phys ) {
+                ++total_trees;
+                final List<PhylogenyNode> nodes = phy.getNodes( p );
+                if ( nodes.isEmpty() ) {
+                    System.out.println();
+                    System.out.println( "not found!" );
+                    System.exit( -1 );
+                }
+                else {
+                    total_placements++;
+                    if ( nodes.size() == 1 ) {
+                        unique_placements++;
+                    }
+                    else {
+                        non_unique_placements++;
+                    }
+                    final PhylogenyNode n = nodes.get( 0 );
+                    if ( n.isExternal() && !n.isRoot() ) {
+                        final Matcher m = p.matcher( n.getName() );
+                        if ( m.find() ) {
+                            final double M = Double.parseDouble( m.group( 1 ) );
+                            if ( M > 0.999999 ) {
+                                m1_placements++;
+                            }
+                            else {
+                                non_m1_placements++;
+                            }
+                        }
+                        else {
+                            System.out.println();
+                            System.out.println( "no match!" );
+                            System.exit( -1 );
+                        }
+                        String sib = null;
+                        if ( n.getChildNodeIndex() == 0 ) {
+                            sib = n.getParent().getChildNode2().getName();
+                        }
+                        else if ( n.getChildNodeIndex() == 1 ) {
+                            sib = n.getParent().getChildNode1().getName();
+                        }
+                        else {
+                            System.out.println();
+                            System.out.println( "more than two children!" );
+                            System.exit( -1 );
+                        }
+                        //  System.out.println( n.getName() + "->" + sib );
+                        if ( n.getName().startsWith( sib ) ) {
+                            total_expected_top_placements++;
+                        }
+                        else {
+                            total_unexpected_top_placements++;
+                            if ( nodes.size() == 1 ) {
+                                total_unexpected_unique_top_placements++;
+                            }
+                        }
+                    }
+                }
+            }
+            System.out.println();
+            System.out.println( infile.getName() );
+            final Pattern pa = Pattern.compile( "(\\d+)-\\d+" );
+            final Matcher m = pa.matcher( infile.getName() );
+            if ( m.find() ) {
+                final int start = Integer.parseInt( m.group( 1 ) );
+                //      System.out.println( start + "\t"
+                //              + ( ( ( double ) total_unexpected_top_placements ) / total_placements ) );
+            }
+            System.out.println( "total trees" + "\t" + total_trees );
+            System.out.println( "total placements" + "\t" + total_placements );
+            System.out.println( "total expected top placements" + "\t" + total_expected_top_placements );
+            System.out.println( "total un-expected top placements" + "\t" + total_unexpected_top_placements );
+            System.out.println( "total un-expected unique placements" + "\t" + total_unexpected_unique_top_placements );
+            System.out.println( "unique placements" + "\t" + unique_placements );
+            System.out.println( "non unique placements" + "\t" + non_unique_placements );
+            System.out.println( "m1 placements" + "\t" + m1_placements );
+            System.out.println( "non m1 placements" + "\t" + non_m1_placements );
+            non_unique_placements_stats.addValue( ( ( double ) non_unique_placements ) / total_placements );
+            unexpected_top_placements_stats
+                    .addValue( ( ( double ) total_unexpected_top_placements ) / total_placements );
+            unexpected_unique_top_placements_stats
+                    .addValue( ( ( double ) total_unexpected_unique_top_placements ) / total_placements );
+        }
+        System.out.println( "Non-unique placements: Mean\t" + non_unique_placements_stats.arithmeticMean() );
+        System.out.println( "Non-unique placements: Min\t" + non_unique_placements_stats.getMin() );
+        System.out.println( "Non-unique placements: Max\t" + non_unique_placements_stats.getMax() );
+        System.out.println( "Unexpected top-placements: Mean\t" + unexpected_top_placements_stats.arithmeticMean() );
+        System.out.println( "Unexpected top-placements: Min\t" + unexpected_top_placements_stats.getMin() );
+        System.out.println( "Unexpected top-placements: Max\t" + unexpected_top_placements_stats.getMax() );
+        System.out.println( "Unexpected unique placements: Mean\t"
+                + unexpected_unique_top_placements_stats.arithmeticMean() );
+        System.out.println( "Unexpected unique placements: Min\t" + unexpected_unique_top_placements_stats.getMin() );
+        System.out.println( "Unexpected unique placements: Max\t" + unexpected_unique_top_placements_stats.getMax() );
+    }
+}