v0

.gitignore

@@ -21,3 +21,7 @@
 
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*
+
+# build directory
+build/
+.DS_Store

README.md

@@ -1,2 +1,40 @@
-# stem-sim
+# STEM-SIM
 Multi-scale simulation of neoplasm formation.
+
+
+## Requirements
+
+### Ant
+Ant is an open source software building tool available at ant.apache.org.
+
+### Java 1.5
+StemSim is pure Java and requires Java 1.5 or later.  Java is available at
+java.sun.com.
+
+
+
+## Building StemSim
+To build StemSim, cd into the StemSim directory and type: ant.
+
+
+
+## Running a StemSim Simulation
+1. Modify the run.properties file as needed
+    - the default run.properties is set up to run a default simulation
+    - review each parameter and change as needed
+
+2. To run the simulation: 
+    - cd StemSim
+    - ./bin/sim run.properties
+
+StemSim will create a directory named after the time the simulation was kicked
+off.  All files created by the simulation will be found in this directory.
+
+
+
+## Computing Statistics
+StemSim cancer statistics are computed after the runs have completed from the XML simulation files.  To generate the statistics:
+
+`./bin/stat <sim xml directory>`
+
+The stat command will create files with names based on the XML directory.

bin/run

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+# echo $0 > $2
+scriptdir=`dirname $0`
+libdir=$scriptdir/../lib/
+builddir=$scriptdir/../build/
+cp=""
+for f in `find $builddir -name "*.jar"`;
+do
+  cp=${cp}$f:
+done
+
+for f in `find $libdir -name "*.jar"`;
+do
+  cp=${cp}$f:
+done
+
+# echo cp=$cp
+
+java -Xms256m -Xmx1536m -classpath $cp $*
+

bin/sim

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+# echo $0 > $2
+scriptdir=`dirname $0`
+$scriptdir/run stemsim.simulation.SimulationRunner $*
+

bin/stat

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# echo $0 > $2
+scriptdir=`dirname $0`
+
+#scriptdir/run stemsim.statxml.CancerStat $*
+#$scriptdir/run stemsim.statxml.MutationStat $*
+#$scriptdir/run stemsim.statxml.FitnessStat $*
+#$scriptdir/run stemsim.statxml.DistanceStat $*
+
+#$scriptdir/run stemsim.stat.CryptStat $*
+#$scriptdir/run stemsim.stat.DivStat $*
+$scriptdir/run stemsim.stat.TissuePopStat $*

build.properties

@@ -0,0 +1,23 @@
+# INSTALLATOIN PROPERTIES
+jarfile=stemsim
+
+# for to scp files to remote host
+# remote.webapp.dir
+# remote.host
+# remote.user
+
+# BUILD MECHANICS PROPERTIES
+# DO NOT EDIT
+source=src
+source.java=${source}/java
+source.java-test=${source}/java-test
+build=build
+build.classes=${build}/classes
+build.testresults=${build}/testresults
+build.tmp=${build}/tmp
+lib=lib
+prop=prop
+test=test
+test.data=${test}/data
+test.java=${test}/java
+

build.xml

@@ -0,0 +1,92 @@
+<project name="stemsim" default="unittest" basedir=".">
+
+    <!-- mechanical and installation properties -->
+    <property file="build.properties"/>
+
+
+    <!-- Compile and install locally -->
+    <target name="install" depends="compile" description="install app">
+       <fail unless="install.dir">
+         please define the install.dir property in build.properties 
+       </fail>
+
+       <copy file="${build}/${jarfile}.jar"
+             todir="${install.dir}"/>
+    </target>
+
+
+    <!-- Default target.  Just compiles the code.  No installation -->
+    <target name="compile" description="compile the source code">
+        <mkdir dir="${build.classes}"/>
+
+	    <javac srcdir="${source}"
+               destdir="${build.classes}"
+               sourcepath="${source.java}"
+               deprecation="on"
+               debug="on">
+            <classpath>
+                <fileset dir="${lib}">
+                    <include name="**/*.jar"/>
+                    <include name="**/*.zip"/>
+                </fileset>
+	    </classpath>
+        </javac>
+
+        <javac srcdir="${test.java}"
+               destdir="${build.classes}"
+               deprecation="on"
+               debug="on">
+            <classpath>
+                <fileset dir="${lib}">
+                    <include name="**/*.jar"/>
+                    <include name="**/*.zip"/>
+                </fileset>
+            </classpath>
+        </javac>
+
+        <jar destfile="${build}/${jarfile}.jar"
+             basedir="${build.classes}"/>
+    </target>
+
+    <!-- Run the unit tests  -->
+    <target name="unittest" description="run JUnit unit tests"
+        depends="compile">
+        <mkdir dir="${build.testresults}"/>
+        <mkdir dir="${build.tmp}"/>
+        <junit printsummary="yes" haltonfailure="yes">
+            <sysproperty key="testdata.dir" value="${test.data}"/>
+            <sysproperty key="tmp.dir" value="${build.tmp}"/>
+            <sysproperty key="testresults.dir" value="${build.testresults}"/>
+            <classpath>
+                <pathelement path="${java.class.path}" />
+                <fileset dir="${build}">
+                    <include name="**/*.jar"/>
+                    <include name="**/*.zip"/>
+                </fileset>
+                <fileset dir="${lib}">
+                    <include name="**/*.jar"/>
+                    <include name="**/*.zip"/>
+                </fileset>
+            </classpath>
+            <formatter type="plain"/>
+            <test if="test.class" name="${test.class}" fork="no" 
+                  todir="${reports.tests}">
+            </test>
+            <batchtest unless="test.class"
+                       fork="no"
+                       todir="${build.testresults}">
+                <fileset dir="${test.java}">
+                    <include name="**/*Test*.java"/>
+                    <exclude name="**/*Tests.java"/>
+                    <exclude name="**/*TestCase.java"/>
+                </fileset>
+            </batchtest>
+        </junit>
+    </target>
+
+    <!-- clean up a previous build for a fresh start -->
+    <target name="clean">
+        <delete dir="${build}"/>
+    </target>
+
+</project>