Changing the default TeXlipse compiler to PDFLatex

If I understood your question correctly, you probably have a Java project with a .tex file somewhere. Something like the following image:

If we save our document, TeXlipse is configured to run the TeX builder for us. Saving the document with CTRL + S will give us the following files in my doc/ subfolder:

The default setup is to rely on latex and .dvi. In order to change this behaviour, we need to go to Project > Properties:

Just a note: if we check the builders, we will see that the project is set to run both Java and TeX builders for us.

Look for the LaTeX Project Properties tab:

The following screen will appear:

Go to the output format and change the extension from .dvi to .pdf:

The engine will automatically change to pdflatex. Click OK.

Every time we edit our .tex document and save it, pdflatex will be executed instead of latex, and we will have the following files in my doc/ subfolder:

We can also see the .pdf with the embedded viewer:

Hope it helps. :)