matUtils extract --reroot: retain rerooted leaf, rename leaf from former internal node #380
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…mer internal node This addresses two corner cases that we hadn't thought through yet for --reroot: * First, when rerooting to a leaf node, that node was converted into an internal node (the new root), losing its leaf status, so when the result was written out, the tree no longer had that leaf. To fix this, when rerooting to a leaf, we add a new leaf with the same name on the new root node. * Second, when the old root had no leaf children and only one internal node child, after rerooting it became a new leaf node, keeping its original ID of 'node_1'. However, the saved protobuf could not be read back in by matUtils because when parsing the Newick string, 'node_1' is assigned to the first node encountered, and it is an error for any subsequent node to have the name 'node_1' (even a leaf) because node_1 is already in the tree. To prevent that error, when the old root becomes a leaf node, we change the old root's name to former_root -- unless there is already a former_root in the tree, in which case we make a new former_root_<serialNumber> that does not already exist in the tree.
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This addresses two corner cases that we hadn't thought through yet for --reroot:
First, when rerooting to a leaf node, that node was converted into an internal node (the new root), losing its leaf status, so when the result was written out, the tree no longer had that leaf. To fix this, when rerooting to a leaf, we add a new leaf with the same name on the new root node.
Second, when the old root had no leaf children and only one internal node child, after rerooting it became a new leaf node, keeping its original ID of
node_1. However, the saved protobuf could not be read back in by matUtils because when parsing the Newick string,node_1is assigned to the first node encountered, and it is an error for any subsequent node to have the namenode_1(even a leaf) becausenode_1is already in the tree. To prevent that error, when the old root becomes a leaf node, we change the old-root-new-leaf's name toformer_root-- unless there is already aformer_rootin the tree, in which case we make a newformer_root_serialNumber that does not already exist in the tree.