Sunday, May 15, 2011

First Run & Cleanup

First Run:

I have been successful in getting the project to run. The program accepts command line arguments so you can either enter the filenames as a command line parameter or temporarily hard code the name of the files in the
On a windows platform you need to specify the paths as follows.

String intreeFile = "src\\testTree.nwk";
String coordFile = "src\\testCoords.csv";
String metadata = "n";

If you wish to use the metadata file, you will to specify "y" in metadata and use the file testCoordsMeta.csv
When you run the program after this, a kml file testfile.kml is generated.

Cleanup of the folder:

So finally I cleaned up the project folder. The following are the exact changes that I did. I will call this version 1.0 aka the starting point for my project.

  1. cd phyloGeoRef
  2. git rm -r .metadata (This will remove the metadata folder from version control)
  3. Now you can safely delete this folder.
  4. Modify the README, with the new instructions.
  5. git add . (This will stage all changes)
  6. Initially I was trying to add the extra packages as separater jars. But now I think that it is a good idea to include the relevant packages in the library itself so that the end user has minimum overhead of downloading extra jars. The jars required have been mentioned along with the sources in the README.
  7. cd phyloGeoRef (This is actually the netbeans project folder)
  8. git rm -r .settings/ (Deletes the .settings folder)
  9. git rm -r bin/        (Deleted the bin folder)
  10. cd src/
  11. git rm -r jak/        (This folder is not needed because we'll be including the JavaAPIforKml.jar)
  12. git rm -r javapaiforkml
  13. git rm -r NeXML/         (Will add the relevant packages instead of the whole folder)
  14. git rm -r opencsv-2.2/   ( "" )
  15. Now copy the following folders in src
  16. Copy the nexml folder to src/org (This package will provide support for nexml parsing)
  17. And copy folder au to src/ (This package will provide support for opencsv parsing)
  18. git add . (Stage the changes)
  19. git commit -m "first commit of the cleaned up folder"  (Do the first commit.)
  20. git tag -a v1.0 -m 'This is the version 1.0"
  21. Then push the changes to the github repo.

Now the folder looks a bit more clean. And it's still forked from the last year's project. So a bit of relief for me now !!!

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