From 50c5d24552e1aaa7566d60c7fcefc6d03d09e15d Mon Sep 17 00:00:00 2001
From: Florent Angly <florent.angly@gmail.com>
Date: Thu, 27 Jun 2013 10:03:15 +1000
Subject: [PATCH] Boolean return status for merge_lineage()

Fix conflicts:

	t/RemoteDB/Taxonomy.t
---
 Bio/Tree/TreeFunctionsI.pm | 34 ++++++++++++++++++----------------
 t/RemoteDB/Taxonomy.t      |  4 ++--
 2 files changed, 20 insertions(+), 18 deletions(-)

diff --git a/Bio/Tree/TreeFunctionsI.pm b/Bio/Tree/TreeFunctionsI.pm
index 01f452a47..2daac2261 100644
--- a/Bio/Tree/TreeFunctionsI.pm
+++ b/Bio/Tree/TreeFunctionsI.pm
@@ -465,7 +465,7 @@ sub get_lca {
  Title   : merge_lineage
  Usage   : merge_lineage($node)
  Function: Merge a lineage of nodes with this tree.
- Returns : n/a
+ Returns : true for success, false (and a warning) otherwise
  Args    : Bio::Tree::TreeI with only one leaf, OR
            Bio::Tree::NodeI which has an ancestor
 
@@ -495,37 +495,39 @@ sub merge_lineage {
     my ($self, $thing) = @_;
     $self->throw("Must supply an object reference") unless ref($thing);
 
-    my ($lineage_tree, $lineage_leaf);
+    my $lineage_leaf;
     if ($thing->isa('Bio::Tree::TreeI')) {
         my @leaves = $thing->get_leaf_nodes;
         $self->throw("The supplied Tree can only have one leaf") unless @leaves == 1;
-        $lineage_tree = $thing;
         $lineage_leaf = shift(@leaves);
     }
     elsif ($thing->isa('Bio::Tree::NodeI')) {
         $self->throw("The supplied Node must have an ancestor") unless $thing->ancestor;
-        $lineage_tree = $self->new(-node => $thing);
         $lineage_leaf = $thing;
     }
 
     # see if any node in the supplied lineage is in our tree - that will be
     # our lca and we can merge at the node below
     my @lineage = ($lineage_leaf, reverse($self->get_lineage_nodes($lineage_leaf)));
-    my $merged = 0;
-    for my $i (0..$#lineage) {
-        my $lca = $self->find_node(-internal_id => $lineage[$i]->internal_id) || next;
 
-        if ($i == 0) {
-            # the supplied thing to merge is already in the tree, nothing to do
-            return;
+    my $merged;
+    for my $i (0..$#lineage) {
+        my $node = $self->find_node(-internal_id => $lineage[$i]->internal_id);
+        if (defined $node) {
+            # if $i == 0, the supplied thing to merge is already in the tree, nothing to do
+            if ($i > 0) {
+                # $i is the node, so the previous node is new to the tree and should
+                # be merged on
+                $node->add_Descendent($lineage[$i-1]);
+            }
+            $merged = 1;
+            last;
         }
-        # $i is the lca, so the previous node is new to the tree and should
-        # be merged on
-        $lca->add_Descendent($lineage[$i-1]);
-        $merged = 1;
-        last;
     }
-    $merged || ($self->warn("Couldn't merge the lineage of ".$lineage_leaf->id." with the rest of the tree!\n") && return);
+    if (not $merged) {
+        $self->warn("Could not merge the lineage of ".$lineage_leaf->id." with the rest of the tree");
+    }
+    return $merged;
 }
 
 
diff --git a/t/RemoteDB/Taxonomy.t b/t/RemoteDB/Taxonomy.t
index dce25973e..b95d2cbf4 100644
--- a/t/RemoteDB/Taxonomy.t
+++ b/t/RemoteDB/Taxonomy.t
@@ -7,7 +7,7 @@ BEGIN {
     use lib '.';
     use Bio::Root::Test;
 
-    test_begin(-tests => 150,
+    test_begin(-tests => 152,
         -requires_module => 'XML::Twig');
 
     use_ok('Bio::DB::Taxonomy');
@@ -263,7 +263,7 @@ for my $name ('Human', 'Hominidae') {
     my $node = $db_flatfile->get_taxon(-taxonid => $ncbi_id);
 
     if ($tree) {
-        $tree->merge_lineage($node);
+        ok $tree->merge_lineage($node);
     }
     else {
         ok $tree = Bio::Tree::Tree->new(-node => $node);
-- 
2.11.4.GIT