johnstarmer / open-delta

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Character descriptions not matching in nexus files (+ two other issues) #237

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago
What steps will reproduce the problem?
1. run action tonex on a database
2. open the tonex.prt file and nexdata.nex files in an editor
3. compare the character descriptions in the two files

What is the expected output? What do you see instead?
The character descriptions in CHARLABELS should match those in seen in the 
tonex.prt file. Also the tonex.prt file should have an indication of the actual 
DELTA char number as well as the nexus file character number as in CHARLABELS
e.g., [1(18)] '<Body shape in female>'
that is char 1 in nexus file nexdata.nex is equivalent to char 18 in DELTA file

Explanation: DELTA automatically omits all non-categorical characters from the 
nexdata.nex output unless a keystate directive is given in the tonex file. As a 
result, character numbers in the nexdata.nex file do not match those in the 
DELTA database. The accounting needs to be maintained and annotated to both the 
nexdata.nex file and the tonex.prt file. The tonex.prt file is required as a 
list of characters used in an analysis (I have used these directly in 
publications with little modification).  

What version of the product are you using? On what operating system?
DELTA Editor 1.0 (2022)
date: 2013-05-06 13:04:33 Eastern Standard Time (New South Wales)
free memory: 214 MB 
total memory: 517 MB 
max memory: 1790 MB
java.version: 1.7.0_21
java.vendor: Oracle Corporation
os.name: Linux
os.arch: amd64
os.version: 3.2.0-41-generic
user.language: en
user.region: null
user.dir: /home/buz

Please provide any additional information below.

If you could remove the unnecessary restriction of the length of alphanumeric 
variables from the original DELTA code, it would be appreciated. One still has 
to edit the nexus file to get the character descriptions to appear correctly in 
(e.g.) Mesquite. 

Additionally, character states entirely enclosed in angle brackets do not 
output (you get only a '' ), whereas they should in the nexdata.nex file. 

Original issue reported on code.google.com by BuzWil...@gmail.com on 6 May 2013 at 3:21