Fix compile error after a recent ImgLib (1!!!) update

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Bye-bye imglib2-ui

Recent ImgLib does not make that .jar file any longer.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
MiniMaven: refactor access to the local Maven repository

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Fiji Build (MiniMaven): make sure to exclude clojure from building

Clojure requires antrun to build, which we do not support in MiniMaven.

While at it, make sure that the current pom is not re-parsed.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Plug a resource leak in MiniMaven

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Fiji Build: reuse MiniMaven instances

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
MiniMaven: fix thinko

We do not need to re-parse after we updated the snapshot version

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
TrackMate_: improve verboseness when loading a XML file

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
TrackMate_: minor missing or incorrect messages

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Outcommented the stuff that causes problems in between imglib.jar and the imglib submodule
Update the submodule "modules/TrakEM2"

Signed-off-by: Albert Cardona <sapristi@gmail.com>
Merge branch 'master' of ssh+git://pacific.mpi-cbg.de/srv/git/fiji
TrackMate_: considerably speed up loading of large XML files

Thanks to a cache of spot IDs. But now, the XML reader has a state.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Merge branch 'master' of ssh://pacific.mpi-cbg.de/srv/git/fiji
Soft-commit TrakEM2: small performance fix and correctness fix for CachingThread.
Revert javac's Infer.java to initial OpenJDK7's

In my endless hours of debugging, I found that OpenJDK7's Infer class is
much simpler than what IcedTea6 has. So I started my attempts at fixing
the stupid compilation errors we have with ImgLib and SPIM Registration
from there.

Recap: as detailed in commit 82bd295(Revert javac update partially to make
SPIM_Registration compile), the javac from IcedTea6 was able to compile
ImgLib with advanced (read: challeging javac) generic constructs but not
SPIM Registration. The partial revert made SPIM Registration work, but
required work-arounds (read: removal of the constructs challenging javac)
in ImgLib.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
javac: fix compile problems with ImgLib

ImgLib really challenges the generic-parsing-fu of any java compiler.
Unfortunately, we did not have access to the source code of any javac that
compiled ImgLib successfully, so we had to provide a couple of nasty, ugly
workarounds.

The solution I found is based on a mixture of the current OpenJDK6 javac
source code, a single method borrowed from the initial OpenJDK7 javac
source code, and the insight that all of our problems were caused by an
incomplete generic type resolution.

I realized that whenever we have compile errors with our javac that we do
not have with Sun's javac of JDK6 Update 24 nor with Eclipse's compiler,
the instantiateMethod() method of com.sun.tools.javac.comp.Infer handles a
list of unresolved generic types (restvars) that is not empty.

A lesson I learnt from Knud Poulsen: if something fails, just try again.
So I copied the code that resolves the generic types and tried again, and
got less compile errors. Wrapping the resolution code into a loop that
repeats as often as new types could be resolved finally fixed my
compilation problems.

As the bulk of the change is an indentation change, it might be nicer to
look at this commit using 'git show -w'.

Now, this might not be the most elegant solution, and it might be too
greedy, resolving too-specific types, but it compiles all of Fiji, and if
people do not like it and do not come up with a better solution
themselves, they can come, find & kiss me.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Precompile javac

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Compile all of ImgLib with MiniMaven

This includes ImgLib1 still.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
MiniMaven: respect the main-class

This is needed to produce a javac that can be called with

	java -jar javac.jar <argument>...

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>