I have made pretty good changes in the validation of an SBML task. If you refer my  blog post which I have written earlier, clicking on the validation button displays the errors in an unembellished way if there are any errors in the selected file. There was no user friendly message if the selected file has no errors in it. So my main task was to make the UI look good as well as to display user friendly error messages.

So, I have implemented the SBMLError class to validate the selected sbml file. That was a very easy task. But I had some problems while displaying them in the output pane of the validation dialog box. Earlier, I implemented textArea which has a setText and append functions on it. So, it was very  simple to display the errors using the textArea. But the problem arose when I got to know that textArea doesn’t have support for styling the font with colors and I found that textPane has an awesome support which enables us to style the text in it.

When I was ready to implement the textPane, I found that there was no append function on textPane. Hence I wrote a separate append function to display the data in the textPane. Refer append function in ValidatePanel.java

The following screen shots depicts the working of validation of sbml file.

1st screen- On clicking validate button

Figure 1: Clicking on Validate button on the main panel displays this dialog.

2nd screen -Choosing a sbml file-without errors

Figure 2: Choosing a valid SBML file from the directory. Here, the BIOMD0000000001.xml doesn’t have any errors.

3rd screen-output

Figure 3: Displays the output in the output pane.

4th screen- choosing a file with errors

Figure 4: Choosing a file with errors. Here, I have removed some three lines in the algebraicrules.xml which makes the file an invalid sbml file.

5th screen- errors shown on the pane

Figure 5: Displays all the errors with the severity level, line number and the error message.

6th screen-extension of 5th

Figure 6: Extension of the figure 5.


Note: The sbml files are taken from http://www.ebi.ac.uk/biomodels-main/BIOMD0000000001

and      http://svn.bigcat.unimaas.nl/pvplugins/SBML/trunk/testdata/level-2/algebraicrules.xml

I have completed this task in the last week. I am very sorry for posting it so late.


Sri Harsha.P


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