From 4ec226ac591d8c9e3837e4c096b2d3cdafd3a3a7 Mon Sep 17 00:00:00 2001
From: cmzmasek <chris.zma@outlook.com>
Date: Wed, 10 May 2017 17:30:14 -0700
Subject: [PATCH] in progress...

---
 .../org/forester/phylogeny/PhylogenyMethods.java   |   26 ++++++-
 .../surfacing/MinimalDomainomeCalculator.java      |   71 ++++++++++++--------
 2 files changed, 67 insertions(+), 30 deletions(-)

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index 9f73532..42fde76 100644
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -261,8 +261,6 @@ public class PhylogenyMethods {
         return node1;
     }
 
-   
-
     public static int calculateMaxDepth( final Phylogeny phy ) {
         int max = 0;
         for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
@@ -548,6 +546,30 @@ public class PhylogenyMethods {
         return descs;
     }
 
+    public static List<PhylogenyNode> getAllDescendantsOfGivenLevel( final PhylogenyNode node, final int level ) {
+        final List<PhylogenyNode> descs = new ArrayList<PhylogenyNode>();
+        final Set<Long> encountered = new HashSet<Long>();
+        if ( !node.isExternal() ) {
+            final List<PhylogenyNode> exts = node.getAllExternalDescendants();
+            for( PhylogenyNode current : exts ) {
+                if ( calculateLevel( current ) == level ) {
+                    descs.add( current );
+                }
+                while ( current != node ) {
+                    current = current.getParent();
+                    if ( encountered.contains( current.getId() ) ) {
+                        continue;
+                    }
+                    if ( calculateLevel( current ) == level ) {
+                        descs.add( current );
+                    }
+                    encountered.add( current.getId() );
+                }
+            }
+        }
+        return descs;
+    }
+
     /**
      *
      * Convenience method
diff --git a/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java b/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java
index 8c25cd3..1fa7929 100644
--- a/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java
+++ b/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java
@@ -313,42 +313,57 @@ public final class MinimalDomainomeCalculator {
             }
             final List<Set<String>> features_per_genome_list = new ArrayList<Set<String>>();
             boolean first = true;
-            for( final PhylogenyNode external_desc : external_descs ) {
-                final String code = external_desc.getNodeData().getTaxonomy().getTaxonomyCode();
-                if ( node.isInternal() ) {
-                    if ( first ) {
-                        first = false;
-                    }
-                    else {
-                        out.write( ", " );
+            if ( level >= 1 ) {
+                ////////////
+                ////////////
+                final int node_level = PhylogenyMethods.calculateLevel( node );
+                if ( node_level >= level ) {
+                    final List<PhylogenyNode> given_level_descs = PhylogenyMethods
+                            .getAllDescendantsOfGivenLevel( node, level );
+                    for( final PhylogenyNode given_level_desc : given_level_descs ) {
+                        final String spec_name = given_level_desc.getNodeData().isHasTaxonomy()
+                                ? given_level_desc.getNodeData().getTaxonomy().getScientificName() : given_level_desc.getName();
                     }
-                    out.write( code );
                 }
-                final List<Protein> proteins_per_species = protein_lists_per_species.get( new BasicSpecies( code ) );
-                final int node_level = PhylogenyMethods.calculateLevel( node );
-                final List<Protein> proteins_per_quasi_species = protein_lists_per_species
-                        .get( new BasicSpecies( code ) );
-                if ( proteins_per_species != null ) {
-                    final SortedSet<String> features_per_genome = new TreeSet<String>();
-                    for( final Protein protein : proteins_per_species ) {
-                        if ( use_domain_architectures ) {
-                            final String da = protein.toDomainArchitectureString( separator, ie_cutoff );
-                            features_per_genome.add( da );
+                ///////////
+                ///////////
+            }
+            else {
+                for( final PhylogenyNode external_desc : external_descs ) {
+                    final String code = external_desc.getNodeData().getTaxonomy().getTaxonomyCode();
+                    if ( node.isInternal() ) {
+                        if ( first ) {
+                            first = false;
                         }
                         else {
-                            List<Domain> domains = protein.getProteinDomains();
-                            for( final Domain domain : domains ) {
-                                if ( ( ie_cutoff <= -1 ) || ( domain.getPerDomainEvalue() <= ie_cutoff ) ) {
-                                    features_per_genome.add( domain.getDomainId() );
+                            out.write( ", " );
+                        }
+                        out.write( code );
+                    }
+                    final List<Protein> proteins_per_species = protein_lists_per_species
+                            .get( new BasicSpecies( code ) );
+                    if ( proteins_per_species != null ) {
+                        final SortedSet<String> features_per_genome = new TreeSet<String>();
+                        for( final Protein protein : proteins_per_species ) {
+                            if ( use_domain_architectures ) {
+                                final String da = protein.toDomainArchitectureString( separator, ie_cutoff );
+                                features_per_genome.add( da );
+                            }
+                            else {
+                                List<Domain> domains = protein.getProteinDomains();
+                                for( final Domain domain : domains ) {
+                                    if ( ( ie_cutoff <= -1 ) || ( domain.getPerDomainEvalue() <= ie_cutoff ) ) {
+                                        features_per_genome.add( domain.getDomainId() );
+                                    }
                                 }
                             }
                         }
+                        if ( features_per_genome.size() > 0 ) {
+                            features_per_genome_list.add( features_per_genome );
+                        }
                     }
-                    if ( features_per_genome.size() > 0 ) {
-                        features_per_genome_list.add( features_per_genome );
-                    }
-                }
-            } // for( final PhylogenyNode external_desc : external_descs )
+                } // for( final PhylogenyNode external_desc : external_descs )
+            } // else
             if ( features_per_genome_list.size() > 0 ) {
                 SortedSet<String> intersection = calcIntersection( features_per_genome_list );
                 out.write( "\t" + intersection.size() + "\t" );
-- 
1.7.10.2