I\'m looking for a diff tool that will allow me to compare just a sub-section of a file with a section of another file, or even of itself. Preferably eclipse based but will
Two two tools I have used to root out duplicate code are Simian and CopyPasteKiller. Both are useful, although IMO CopyPasteKiller is a little easier to get started with. It appears there is an Eclipse plugin for Simian, although I have not used it myself.
CheckStyle is nicely integrated with Eclipse and will do the job. It will notify to you and error/warning if your code is duplicated, how much times... etc...
http://eclipse-cs.sourceforge.net/
Kdiff3 would be the other choice. Not Eclipse integrated, but a very nice free, cross-platform tool for merging, comparing files etc.
See SD CloneDR, a tool that detects exact and near-miss clones according to language syntax, for a large number of languages (Java, C#, PHP, C++, C, COBOL, Ada, ...). An Eclipse API is being readied at this moment, and is likely available January 1, 2010.
Try using Diffuse. Just paste the two sub-sections you wish to compare into separate panes and press CTRL-L to re-align them. You could also load the files and manually adjust the alignment to match up the sub-sections of interest.
I've been playing with Atomiq, which finds duplicates within a single file. So far it looks to be a decent tool.