Modify the POY source code so that it can directly read the consensus tree)

Source: Internet
Author: User

When a consistent Tree is generated, Poy writes a string (for example, Strict Consensus Tree) at the beginning of the file. If you want to use the read command to transfer the consistent Tree to the memory, it will fail, you must manually remove the start string to read the consistent tree with read. As a result, the calculation of the same tree is inconvenient and cannot be completed in a Session. For example, to calculate the supported bremer values of the consistent tree, you must first search for the consistent tree, then manually modify the consistent tree, and finally calculate the supported bremer values of the consistent tree; this process requires manual intervention to modify the consistency tree, so that the computing process cannot be fully automated once. The solution is to modify the POY source code so that it does not write the first line of string when reporting the consistency tree using the report command (to clarify the meaning of the consistency tree, you can use a string as the name of the consistent tree file. In this way, you can directly read the consistent tree through the read command and perform subsequent bremer support value calculation.

You only need to modify the treeSearch. ml source file. The changes are as follows:

$ SVN diff treesearch. ml
Index: treesearch. ml
========================================================== ======================================
--- Treesearch. ml (version 193)
+++ Treesearch. ml (working copy)
@-804,9 + 804,9 @@
In
Let fo = status. Output (filename, false, []) in
If not graphic then begin
-Status. user_message FO "@ [<v> ";
+ (* Status. user_message FO "@ [<v> ";
Status. user_message fo
-("@ [" ^ Majority_text ^ "@ Majority @ Consensus Tree @] @, @ [");
+ ("@ [" ^ Majority_text ^ "@ Majority @ Consensus Tree @] @, @ ["); *)
Status. user_message fo (AsciiTree. for_formatter false true false
Res );
Status. user_message fo "@] \ n %! ";

 

 

I hope you can understand the above diff results. It doesn't matter if you don't understand it. The actual content is to modify treeSearch. ml. Add (*, after 807 rows) before 809, meaning to comment out the three rows. During actual modification, pay attention to the version of your source code. My version is the build 193 that is extracted from the svn library. If the version is different, the number of rows to be modified may be offset.

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