#******************************************************************************
#  Author :Shahmil Merchant
#  Created :09/02/02
#  Revision History: $Id: Makefile,v 1.18 2003/06/10 18:07:17 pavlidis Exp $
#  Description:MakeFile
#*******************************************************************************

OPTIONS = -g -O

RUN_OPTIONS= -Xmx1024M

SOURCEPATH = .

CLASSPATH = .
OUTPUTDIR = ./

DOCDIR = ../doc

JAVAC = /usr/java/j2sdk1.4.1_03/bin/javac

JAVA = /usr/java/j2sdk1.4.1_03/bin/java

JAR = /usr/java/j2sdk1.4.1_03/bin/jar

APP_PACKAGE = classScore

PACKAGES =${APP_PACKAGE}

APP_PACKAGE_PATH=.

WINDOWTITLE = 'Java 2 Platform v1.4 API Specification for Class Scores'
DOCTITLE = 'Class Scores<sup><font size="-2">TM</font></sup> v1.4 API Specification'
HEADER = '<b>CLASS_SCORES</b><br><font size="-1">Columbia</font>'
BOTTOM = '<font size="-1"><a href="mailto:pp175@columbia.edu">Submit a bug or feature request</a><br><br>Class Score is Copyright 2002 (C) Columbia Genome Center,<br>NY, U.S.A.All Rights Reserved.</font>'

CLASS_FILES= \
	${OUTPUTDIR}${APP_PACKAGE_PATH}/classScore/classresult.class  \
	${OUTPUTDIR}${APP_PACKAGE_PATH}/classScore/ClassMap.class  \
	${OUTPUTDIR}${APP_PACKAGE_PATH}/classScore/class_correls.class  \
	${OUTPUTDIR}${APP_PACKAGE_PATH}/classScore/exp_class_scores.class  \
	${OUTPUTDIR}${APP_PACKAGE_PATH}/classScore/class_pvals.class  \
	${OUTPUTDIR}${APP_PACKAGE_PATH}/classScore/corr_class_scores.class  \
	${OUTPUTDIR}${APP_PACKAGE_PATH}/classScore/histogram.class  \
	${OUTPUTDIR}${APP_PACKAGE_PATH}/classScore/Pval_parse.class  \
	${OUTPUTDIR}${APP_PACKAGE_PATH}/classScore/Group_Parse.class \
	${OUTPUTDIR}${APP_PACKAGE_PATH}/classScore/GoName_parse.class \
        ${OUTPUTDIR}${APP_PACKAGE_PATH}/classScore/Class_Frame.class \
	${OUTPUTDIR}${APP_PACKAGE_PATH}/util/Matrix.class  \
	${OUTPUTDIR}${APP_PACKAGE_PATH}/util/Stats.class  \
	${OUTPUTDIR}${APP_PACKAGE_PATH}/util/SpecFunc.class  \
	${OUTPUTDIR}${APP_PACKAGE_PATH}/util/geneNpval.class  \
	${OUTPUTDIR}${APP_PACKAGE_PATH}/util/ConstantStuff.class  \
        ${OUTPUTDIR}erminecmd.class

all: class_score commandline dist

run: runner

tags: *.java
	etags *.java classScore/*.java util/*.java


class_score: ${CLASS_FILES}


${OUTPUTDIR}%.class	: ${SOURCEPATH}/%.java
	${JAVAC} ${OPTIONS} \
	-sourcepath ${SOURCEPATH} \
	-classpath ${CLASSPATH} \
	-d ${OUTPUTDIR} $<

runner: ${CLASS_FILES}
	${JAVA} ${RUN_OPTIONS} -classpath ${CLASSPATH} classScore.Class_Frame

doc:
	javadoc -version -author -use -d ${DOCDIR} -windowtitle ${WINDOWTITLE} -doctitle ${DOCTITLE} -header ${HEADER} -bottom ${BOTTOM} -classpath ${CLASSPATH} -sourcepath ${SOURCEPATH} ${PACKAGES}

# force this to relink.
commandline: 
	${JAVAC} ${OPTIONS} \
	-sourcepath ${SOURCEPATH} \
	-classpath ${CLASSPATH} \
	erminecmd.java

clean:
#	find ./ -name "*~" -exec rm {} \;
	find ./ -name "*.class" -exec rm -f {} \;
#	rm -rf ${OUTPUTDIR}*.class;
#	rm -r -f ${OUTPUTDIR}*;
#	rm -r -f ${DOCDIR}/*;
#	mkdir ${OUTPUTDIR};
#	mkdir ${DOCDIR};

dist : class_score 
	${JAR} cfm \
	classScore.jar  gui.manifest.add \
	util/*.class \
	classScore/*.class


cmdline : class_score classScore.jar
	${JAR} cmf cmdline.manifest.add \
	classScorecmd.jar \
	util/*.class \
	classScore/*.class \
	erminecmd.class	


#	jar cf \
