Detecting Bio-Deltas Readme File


This file lists the required information for running the program and 
illustrates the file structure and the workflow of the application.

1. The JDK version used is:  j2sdk1.4.0_01
   Platform worked on:  Windows 2000 Professional

2. To execute the program:

   a. Copy the folder 'biodelta' to any directory.

   b. To start up the program:

      Double-click the 'biodelta.jar' file under the '/biodelta'
      directory.

   c. Now the swing window should appear and the program runs.

   d. To transform a flat-file into XML format:

      Click the 'Open' tool button or 'File/Open...' menu item.
      
      A file dialog shows up for choosing the file path for the flat 
      file. A file at any directory can be selected. Note that the 
      file types of GenBank/EMBL/Swiss-Port entries should be in .txt
      format, while the file type of PDB entries should be .pdb.

      Some testing cases are included in '/biodelta/testing/' directory.

      After selecting the file path, a dialog of choosing the database
      format pops up. In this dialog, the suitable database format must 
      be correctly specified for XML transformation. The name of the
      XML file should also be entered in the form of '***.xml', such as
      'file1.xml'. 

      After clicking the 'OK' button, the XML file is generated and
      stored in '/biodelta/temp/' folder. The tree-view of the XML file
      is shown in the main window.

      The file paths of both the origin flat files and the XML files are
      shown in a tree-view format on the upper left panel. By expanding
      and clicking on the tree item, the user can view the files.

      Multiple files can be transformed by using the 'Open' function. 
      All the paths will be appended into the tree-view directories.

   e. To detect the differences between two data entries:

      First, ensure that both the entries are already converted into
      XML format.

      Click the 'Compare' tool button or 'Tool/Compare...' menu item.

      A dialog shows up for choosing the files to be compared. First, 
      specify the database type. Then, the user can check the 'with
      heuristics' item for a heuristic comparison. Then, both the
      absolute paths of the two XML files must be entered by either
      filling the text boxes manually or clicking the file-chooser 
      button. If the XML files are obtained by the 'Open' function, the
      resulting XML files will be located in the '/biodelta/temp/' 
      folder. 

      After clicking the 'OK' button, the two XML files are compared 
      and the results are shown in the bottom panel. 

   f. The DTD files can be viewed by clicking the 'Tool/Show dtd files'
      menu item.

3. The files included are:

   a. biodelta.jar: the executable jar file containing all the class
      files.

   b. file folder: all the rule bases, DTD files, and images.

   c. temp folder: a folder containing all the temporary files generated
      during execution including the XML files transformed.

   d. testing folder: all the testing flat-files.

   e. sources folder: all the source code.

   f. readme.txt: the readme file.


