#
# fairSIM make file
#
# To work, either 'java6' has to point to a java
# compiler (vers. 1.6), or change the line below to
# 'java' instead of 'java6'

JC = javac
JAR = jar

# Options for the java compiler
EXTDIR="./external"

JFLAGS = -g -Xlint:unchecked -Xlint:deprecation -extdirs ${EXTDIR} -d ./
#JFLAGS = -g -Xlint:unchecked -extdirs ${EXTDIR} -d ./
JFLAGS+= -target 1.6 -source 1.6
JFLAGS+= -cp ~/test/fairSIM/ij.jar


# remove command to clean up
RM = rm -vf

.PHONY: all org/fairsim/git-version.txt

all:    jtrans
    $(JC) $(JFLAGS) org/fairsim/*/*.java

linalg:
    $(JC) $(JFLAGS) org/fairsim/linalg/*.java
utils:
    $(JC) $(JFLAGS) org/fairsim/utils/*.java
fiji:
    $(JC) $(JFLAGS) org/fairsim/fiji/*.java
#tests:
#   $(JC) $(JFLAGS) org/fairsim/tests/*.java
sim_algorithm:
    $(JC) $(JFLAGS) org/fairsim/sim_algorithm/*.java
sim_gui:
    $(JC) $(JFLAGS) org/fairsim/sim_gui/*.java

jtrans: org/fairsim/extern/jtransforms/FloatFFT_2D.class
org/fairsim/extern/jtransforms/FloatFFT_2D.class: $(wildcard org/fairsim/extern/jtransforms/*.java)
    $(JC) $(JFLAGS) org/fairsim/extern/jtransforms/*.java





# misc rules


git-version :
    git rev-parse HEAD > org/fairsim/git-version.txt  ; \
    git tag --contains >> org/fairsim/git-version.txt ; \
    echo "n/a" >> org/fairsim/git-version.txt


jarsrc  : git-verison
    $(JAR) -cvfm fairSIM-source_$(shell head -c 10 org/fairsim/git-version.txt).jar \
    Manifest.txt plugins.config \
    org/fairsim/git-version.txt \
    org/fairsim/*/*.class  org/fairsim/extern/*/*.class  \
    org/fairsim/resources/* \
    Makefile org/fairsim/*/*.java  org/fairsim/extern/*/*.java

tarsrc  : git-version
    tar -cvjf fairSIM-source_$(shell head -c 10 org/fairsim/git-version.txt).tar.bz2 \
    Manifest.txt plugins.config \
    org/fairsim/git-version.txt \
    org/fairsim/resources/* \
    Makefile org/fairsim/*/*.java  org/fairsim/extern/*/*.java


jar:    git-version
    $(JAR) -cvfm fairSIM_plugin_$(shell head -c 10 org/fairsim/git-version.txt).jar \
    Manifest.txt plugins.config \
    org/fairsim/git-version.txt \
    org/fairsim/resources/* \
    org/fairsim/*/*.class  org/fairsim/extern/*/*.class


doc:    doc/index.html

doc/index.html : $(wildcard org/fairsim/*/*.java)
    javadoc -d doc/ -classpath ./ -extdirs ${EXTDIR} \
    -subpackages org.fairsim -exclude org.fairsim.extern.jtransforms
#   org/fairsim/*/*.java

clean :
    $(RM) fairSIM_*.jar fairSIM_*.tar.bz2
    $(RM) org/fairsim/*/*.class org/fairsim/git-version.txt
    $(RM) -r doc/*

clean-all: clean
    $(RM) org/fairsim/extern/*/*.class