the cluster version
git-svn-id: https://hyracks.googlecode.com/svn/branches/fullstack_genomix@2957 123451ca-8445-de46-9d55-352943316053
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/AdjacentWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/AdjacentWritable.java
new file mode 100755
index 0000000..c1e9abc
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/AdjacentWritable.java
@@ -0,0 +1,95 @@
+/*
+ * Copyright 2009-2012 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package edu.uci.ics.graphbuilding;
+
+import java.io.DataInput;
+import java.io.DataOutput;
+import java.io.IOException;
+import org.apache.hadoop.io.WritableComparable;
+
+/**
+ * This class override the writablecomparable class which contain int varable
+ */
+public class AdjacentWritable implements WritableComparable<AdjacentWritable> {
+ private byte first;
+ private byte second;
+
+ public AdjacentWritable() {
+ }
+
+ public AdjacentWritable(byte first, byte second) {
+ set(first, second);
+ }
+
+ public void set(byte first, byte second) {
+ this.first = first;
+ this.second = second;
+ }
+
+ public byte getFirst() {
+ return first;
+ }
+
+ public byte getSecond() {
+ return second;
+ }
+
+ @Override
+ public void write(DataOutput out) throws IOException {
+ out.writeByte(first);
+ out.writeByte(second);
+ }
+
+ @Override
+ public void readFields(DataInput in) throws IOException {
+ first = in.readByte();
+ second = in.readByte();
+ }
+
+ @Override
+ public int hashCode() {
+ return (int) first + (int) second;
+ }
+
+ @Override
+ public boolean equals(Object o) {
+ if (o instanceof AdjacentWritable) {
+ AdjacentWritable tp = (AdjacentWritable) o;
+ return first == tp.first && second == tp.second;
+ }
+ return false;
+ }
+
+ @Override
+ public String toString() {
+ return Integer.toString(first) + "\t" + Integer.toString(second);
+ }
+
+ @Override
+ public int compareTo(AdjacentWritable tp) {
+ int cmp;
+ if (first == tp.first)
+ cmp = 0;
+ else
+ cmp = 1;
+ if (cmp != 0)
+ return cmp;
+ if (second == tp.second)
+ return 0;
+ else
+ return 1;
+ }
+
+}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/KmerBytesWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/KmerBytesWritable.java
new file mode 100644
index 0000000..f9b3653
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/KmerBytesWritable.java
@@ -0,0 +1,148 @@
+/*
+ * Copyright 2009-2012 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package edu.uci.ics.graphbuilding;
+
+import java.io.IOException;
+import java.io.DataInput;
+import java.io.DataOutput;
+import org.apache.hadoop.io.BinaryComparable;
+import org.apache.hadoop.io.WritableComparable;
+import org.apache.hadoop.io.WritableComparator;
+
+public class KmerBytesWritable extends BinaryComparable implements WritableComparable<BinaryComparable> {
+ private static final int LENGTH_BYTES = 4;
+ private static final byte[] EMPTY_BYTES = {};
+ private byte size;
+ private byte[] bytes;
+
+ public KmerBytesWritable() {
+ this(EMPTY_BYTES);
+ }
+
+ public KmerBytesWritable(byte[] bytes) {
+ this.bytes = bytes;
+ this.size = (byte) bytes.length;
+ }
+
+ @Override
+ public byte[] getBytes() {
+ return bytes;
+ }
+
+ @Deprecated
+ public byte[] get() {
+ return getBytes();
+ }
+
+ @Override
+ public int getLength() {
+ return (int) size;
+ }
+
+ @Deprecated
+ public int getSize() {
+ return getLength();
+ }
+
+ public void setSize(byte size) {
+ if ((int) size > getCapacity()) {
+ setCapacity((byte) (size * 3 / 2));
+ }
+ this.size = size;
+ }
+
+ public int getCapacity() {
+ return bytes.length;
+ }
+
+ public void setCapacity(byte new_cap) {
+ if (new_cap != getCapacity()) {
+ byte[] new_data = new byte[new_cap];
+ if (new_cap < size) {
+ size = new_cap;
+ }
+ if (size != 0) {
+ System.arraycopy(bytes, 0, new_data, 0, size);
+ }
+ bytes = new_data;
+ }
+ }
+
+ public void set(KmerBytesWritable newData) {
+ set(newData.bytes, (byte) 0, newData.size);
+ }
+
+ public void set(byte[] newData, byte offset, byte length) {
+ setSize((byte) 0);
+ setSize(length);
+ System.arraycopy(newData, offset, bytes, 0, size);
+ }
+
+ public void readFields(DataInput in) throws IOException {
+ setSize((byte) 0); // clear the old data
+ setSize(in.readByte());
+ in.readFully(bytes, 0, size);
+ }
+
+ @Override
+ public void write(DataOutput out) throws IOException {
+ out.writeByte(size);
+ out.write(bytes, 0, size);
+ }
+
+ @Override
+ public int hashCode() {
+ return super.hashCode();
+ }
+
+ @Override
+ public boolean equals(Object right_obj) {
+ if (right_obj instanceof KmerBytesWritable)
+ return super.equals(right_obj);
+ return false;
+ }
+
+ @Override
+ public String toString() {
+ StringBuffer sb = new StringBuffer(3 * size);
+ for (int idx = 0; idx < (int) size; idx++) {
+ // if not the first, put a blank separator in
+ if (idx != 0) {
+ sb.append(' ');
+ }
+ String num = Integer.toHexString(0xff & bytes[idx]);
+ // if it is only one digit, add a leading 0.
+ if (num.length() < 2) {
+ sb.append('0');
+ }
+ sb.append(num);
+ }
+ return sb.toString();
+ }
+
+ public static class Comparator extends WritableComparator {
+ public Comparator() {
+ super(KmerBytesWritable.class);
+ }
+
+ public int compare(byte[] b1, int s1, int l1, byte[] b2, int s2, int l2) {
+ return compareBytes(b1, s1 + LENGTH_BYTES, l1 - LENGTH_BYTES, b2, s2 + LENGTH_BYTES, l2 - LENGTH_BYTES);
+ }
+ }
+
+ static { // register this comparator
+ WritableComparator.define(KmerBytesWritable.class, new Comparator());
+ }
+}
diff --git a/genomix/genomix-hadoop/target/appassembler/bin/maxclique b/genomix/genomix-hadoop/target/appassembler/bin/maxclique
new file mode 100644
index 0000000..5eab8d0
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/bin/maxclique
@@ -0,0 +1,113 @@
+#!/bin/sh
+# ----------------------------------------------------------------------------
+# Copyright 2001-2006 The Apache Software Foundation.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ----------------------------------------------------------------------------
+#
+# Copyright (c) 2001-2006 The Apache Software Foundation. All rights
+# reserved.
+
+
+# resolve links - $0 may be a softlink
+PRG="$0"
+
+while [ -h "$PRG" ]; do
+ ls=`ls -ld "$PRG"`
+ link=`expr "$ls" : '.*-> \(.*\)$'`
+ if expr "$link" : '/.*' > /dev/null; then
+ PRG="$link"
+ else
+ PRG=`dirname "$PRG"`/"$link"
+ fi
+done
+
+PRGDIR=`dirname "$PRG"`
+BASEDIR=`cd "$PRGDIR/.." >/dev/null; pwd`
+
+
+
+# OS specific support. $var _must_ be set to either true or false.
+cygwin=false;
+darwin=false;
+case "`uname`" in
+ CYGWIN*) cygwin=true ;;
+ Darwin*) darwin=true
+ if [ -z "$JAVA_VERSION" ] ; then
+ JAVA_VERSION="CurrentJDK"
+ else
+ echo "Using Java version: $JAVA_VERSION"
+ fi
+ if [ -z "$JAVA_HOME" ] ; then
+ JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/${JAVA_VERSION}/Home
+ fi
+ ;;
+esac
+
+if [ -z "$JAVA_HOME" ] ; then
+ if [ -r /etc/gentoo-release ] ; then
+ JAVA_HOME=`java-config --jre-home`
+ fi
+fi
+
+# For Cygwin, ensure paths are in UNIX format before anything is touched
+if $cygwin ; then
+ [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
+ [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --unix "$CLASSPATH"`
+fi
+
+# If a specific java binary isn't specified search for the standard 'java' binary
+if [ -z "$JAVACMD" ] ; then
+ if [ -n "$JAVA_HOME" ] ; then
+ if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+ # IBM's JDK on AIX uses strange locations for the executables
+ JAVACMD="$JAVA_HOME/jre/sh/java"
+ else
+ JAVACMD="$JAVA_HOME/bin/java"
+ fi
+ else
+ JAVACMD=`which java`
+ fi
+fi
+
+if [ ! -x "$JAVACMD" ] ; then
+ echo "Error: JAVA_HOME is not defined correctly." 1>&2
+ echo " We cannot execute $JAVACMD" 1>&2
+ exit 1
+fi
+
+if [ -z "$REPO" ]
+then
+ REPO="$BASEDIR"/lib
+fi
+
+CLASSPATH=$CLASSPATH_PREFIX:"$BASEDIR"/etc:"$REPO"/hadoop-core-0.20.2.jar:"$REPO"/commons-cli-1.2.jar:"$REPO"/xmlenc-0.52.jar:"$REPO"/commons-httpclient-3.0.1.jar:"$REPO"/commons-codec-1.3.jar:"$REPO"/commons-net-1.4.1.jar:"$REPO"/jetty-6.1.14.jar:"$REPO"/jetty-util-6.1.14.jar:"$REPO"/jasper-runtime-5.5.12.jar:"$REPO"/jasper-compiler-5.5.12.jar:"$REPO"/jsp-api-2.1-6.1.14.jar:"$REPO"/jsp-2.1-6.1.14.jar:"$REPO"/ant-1.6.5.jar:"$REPO"/commons-el-1.0.jar:"$REPO"/jets3t-0.7.1.jar:"$REPO"/servlet-api-2.5-6.1.14.jar:"$REPO"/kfs-0.3.jar:"$REPO"/hsqldb-1.8.0.10.jar:"$REPO"/oro-2.0.8.jar:"$REPO"/core-3.1.1.jar:"$REPO"/slf4j-jcl-1.6.3.jar:"$REPO"/commons-logging-1.1.1.jar:"$REPO"/slf4j-api-1.6.3.jar:"$REPO"/args4j-2.0.16.jar:"$REPO"/genomix-hadoop-0.2.3-SNAPSHOT.jar
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin; then
+ [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --windows "$CLASSPATH"`
+ [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --path --windows "$JAVA_HOME"`
+ [ -n "$HOME" ] && HOME=`cygpath --path --windows "$HOME"`
+ [ -n "$BASEDIR" ] && BASEDIR=`cygpath --path --windows "$BASEDIR"`
+ [ -n "$REPO" ] && REPO=`cygpath --path --windows "$REPO"`
+fi
+
+exec "$JAVACMD" $JAVA_OPTS \
+ -classpath "$CLASSPATH" \
+ -Dapp.name="maxclique" \
+ -Dapp.pid="$$" \
+ -Dapp.repo="$REPO" \
+ -Dapp.home="$BASEDIR" \
+ -Dbasedir="$BASEDIR" \
+ edu.uci.ics.maxclique.Driver \
+ "$@"
diff --git a/genomix/genomix-hadoop/target/appassembler/bin/maxclique.bat b/genomix/genomix-hadoop/target/appassembler/bin/maxclique.bat
new file mode 100644
index 0000000..6a043d0
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/bin/maxclique.bat
@@ -0,0 +1,108 @@
+@REM ----------------------------------------------------------------------------
+@REM Copyright 2001-2006 The Apache Software Foundation.
+@REM
+@REM Licensed under the Apache License, Version 2.0 (the "License");
+@REM you may not use this file except in compliance with the License.
+@REM You may obtain a copy of the License at
+@REM
+@REM http://www.apache.org/licenses/LICENSE-2.0
+@REM
+@REM Unless required by applicable law or agreed to in writing, software
+@REM distributed under the License is distributed on an "AS IS" BASIS,
+@REM WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@REM See the License for the specific language governing permissions and
+@REM limitations under the License.
+@REM ----------------------------------------------------------------------------
+@REM
+@REM Copyright (c) 2001-2006 The Apache Software Foundation. All rights
+@REM reserved.
+
+@echo off
+
+set ERROR_CODE=0
+
+:init
+@REM Decide how to startup depending on the version of windows
+
+@REM -- Win98ME
+if NOT "%OS%"=="Windows_NT" goto Win9xArg
+
+@REM set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" @setlocal
+
+@REM -- 4NT shell
+if "%eval[2+2]" == "4" goto 4NTArgs
+
+@REM -- Regular WinNT shell
+set CMD_LINE_ARGS=%*
+goto WinNTGetScriptDir
+
+@REM The 4NT Shell from jp software
+:4NTArgs
+set CMD_LINE_ARGS=%$
+goto WinNTGetScriptDir
+
+:Win9xArg
+@REM Slurp the command line arguments. This loop allows for an unlimited number
+@REM of arguments (up to the command line limit, anyway).
+set CMD_LINE_ARGS=
+:Win9xApp
+if %1a==a goto Win9xGetScriptDir
+set CMD_LINE_ARGS=%CMD_LINE_ARGS% %1
+shift
+goto Win9xApp
+
+:Win9xGetScriptDir
+set SAVEDIR=%CD%
+%0\
+cd %0\..\..
+set BASEDIR=%CD%
+cd %SAVEDIR%
+set SAVE_DIR=
+goto repoSetup
+
+:WinNTGetScriptDir
+set BASEDIR=%~dp0\..
+
+:repoSetup
+
+
+if "%JAVACMD%"=="" set JAVACMD=java
+
+if "%REPO%"=="" set REPO=%BASEDIR%\lib
+
+set CLASSPATH="%BASEDIR%"\etc;"%REPO%"\hadoop-core-0.20.2.jar;"%REPO%"\commons-cli-1.2.jar;"%REPO%"\xmlenc-0.52.jar;"%REPO%"\commons-httpclient-3.0.1.jar;"%REPO%"\commons-codec-1.3.jar;"%REPO%"\commons-net-1.4.1.jar;"%REPO%"\jetty-6.1.14.jar;"%REPO%"\jetty-util-6.1.14.jar;"%REPO%"\jasper-runtime-5.5.12.jar;"%REPO%"\jasper-compiler-5.5.12.jar;"%REPO%"\jsp-api-2.1-6.1.14.jar;"%REPO%"\jsp-2.1-6.1.14.jar;"%REPO%"\ant-1.6.5.jar;"%REPO%"\commons-el-1.0.jar;"%REPO%"\jets3t-0.7.1.jar;"%REPO%"\servlet-api-2.5-6.1.14.jar;"%REPO%"\kfs-0.3.jar;"%REPO%"\hsqldb-1.8.0.10.jar;"%REPO%"\oro-2.0.8.jar;"%REPO%"\core-3.1.1.jar;"%REPO%"\slf4j-jcl-1.6.3.jar;"%REPO%"\commons-logging-1.1.1.jar;"%REPO%"\slf4j-api-1.6.3.jar;"%REPO%"\args4j-2.0.16.jar;"%REPO%"\genomix-hadoop-0.2.3-SNAPSHOT.jar
+goto endInit
+
+@REM Reaching here means variables are defined and arguments have been captured
+:endInit
+
+%JAVACMD% %JAVA_OPTS% -classpath %CLASSPATH_PREFIX%;%CLASSPATH% -Dapp.name="maxclique" -Dapp.repo="%REPO%" -Dapp.home="%BASEDIR%" -Dbasedir="%BASEDIR%" edu.uci.ics.maxclique.Driver %CMD_LINE_ARGS%
+if ERRORLEVEL 1 goto error
+goto end
+
+:error
+if "%OS%"=="Windows_NT" @endlocal
+set ERROR_CODE=%ERRORLEVEL%
+
+:end
+@REM set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" goto endNT
+
+@REM For old DOS remove the set variables from ENV - we assume they were not set
+@REM before we started - at least we don't leave any baggage around
+set CMD_LINE_ARGS=
+goto postExec
+
+:endNT
+@REM If error code is set to 1 then the endlocal was done already in :error.
+if %ERROR_CODE% EQU 0 @endlocal
+
+
+:postExec
+
+if "%FORCE_EXIT_ON_ERROR%" == "on" (
+ if %ERROR_CODE% NEQ 0 exit %ERROR_CODE%
+)
+
+exit /B %ERROR_CODE%
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/ant-1.6.5.jar b/genomix/genomix-hadoop/target/appassembler/lib/ant-1.6.5.jar
new file mode 100644
index 0000000..3beb3b8
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/ant-1.6.5.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/args4j-2.0.16.jar b/genomix/genomix-hadoop/target/appassembler/lib/args4j-2.0.16.jar
new file mode 100644
index 0000000..cfb6a29
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/args4j-2.0.16.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-cli-1.2.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-cli-1.2.jar
new file mode 100644
index 0000000..ce4b9ff
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-cli-1.2.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-codec-1.3.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-codec-1.3.jar
new file mode 100644
index 0000000..957b675
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-codec-1.3.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-el-1.0.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-el-1.0.jar
new file mode 100644
index 0000000..608ed79
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-el-1.0.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-httpclient-3.0.1.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-httpclient-3.0.1.jar
new file mode 100644
index 0000000..cfc777c
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-httpclient-3.0.1.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-logging-1.1.1.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-logging-1.1.1.jar
new file mode 100644
index 0000000..1deef14
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-logging-1.1.1.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-net-1.4.1.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-net-1.4.1.jar
new file mode 100644
index 0000000..9666a92
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-net-1.4.1.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/core-3.1.1.jar b/genomix/genomix-hadoop/target/appassembler/lib/core-3.1.1.jar
new file mode 100644
index 0000000..ae0b635
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/core-3.1.1.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/genomix-hadoop-0.2.3-SNAPSHOT.jar b/genomix/genomix-hadoop/target/appassembler/lib/genomix-hadoop-0.2.3-SNAPSHOT.jar
new file mode 100644
index 0000000..9188416
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/genomix-hadoop-0.2.3-SNAPSHOT.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/hadoop-core-0.20.2.jar b/genomix/genomix-hadoop/target/appassembler/lib/hadoop-core-0.20.2.jar
new file mode 100644
index 0000000..0568eaf
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/hadoop-core-0.20.2.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/hsqldb-1.8.0.10.jar b/genomix/genomix-hadoop/target/appassembler/lib/hsqldb-1.8.0.10.jar
new file mode 100644
index 0000000..e010269
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/hsqldb-1.8.0.10.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jasper-compiler-5.5.12.jar b/genomix/genomix-hadoop/target/appassembler/lib/jasper-compiler-5.5.12.jar
new file mode 100644
index 0000000..2a410b4
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jasper-compiler-5.5.12.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jasper-runtime-5.5.12.jar b/genomix/genomix-hadoop/target/appassembler/lib/jasper-runtime-5.5.12.jar
new file mode 100644
index 0000000..743d906
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jasper-runtime-5.5.12.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jets3t-0.7.1.jar b/genomix/genomix-hadoop/target/appassembler/lib/jets3t-0.7.1.jar
new file mode 100644
index 0000000..d87e4d1
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jets3t-0.7.1.jar
Binary files differ
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diff --git a/genomix/genomix-hadoop/target/genomix-hadoop-0.2.3-SNAPSHOT-jar-with-dependencies.jar b/genomix/genomix-hadoop/target/genomix-hadoop-0.2.3-SNAPSHOT-jar-with-dependencies.jar
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diff --git a/genomix/genomix-hadoop/target/genomix-hadoop-0.2.3-SNAPSHOT.jar b/genomix/genomix-hadoop/target/genomix-hadoop-0.2.3-SNAPSHOT.jar
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diff --git a/genomix/genomix-hadoop/target/maven-archiver/pom.properties b/genomix/genomix-hadoop/target/maven-archiver/pom.properties
new file mode 100644
index 0000000..7dbdb75
--- /dev/null
+++ b/genomix/genomix-hadoop/target/maven-archiver/pom.properties
@@ -0,0 +1,5 @@
+#Generated by Maven
+#Wed Feb 20 16:45:32 PST 2013
+version=0.2.3-SNAPSHOT
+groupId=edu.uci.ics.hyracks
+artifactId=genomix-hadoop
diff --git a/genomix/genomix-hadoop/target/surefire-reports/TEST-edu.uci.ics.graphbuilding.GraphBuildingTest.xml b/genomix/genomix-hadoop/target/surefire-reports/TEST-edu.uci.ics.graphbuilding.GraphBuildingTest.xml
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--- /dev/null
+++ b/genomix/genomix-hadoop/target/surefire-reports/TEST-edu.uci.ics.graphbuilding.GraphBuildingTest.xml
@@ -0,0 +1,70 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<testsuite failures="0" time="7.738" errors="0" skipped="0" tests="1" name="edu.uci.ics.graphbuilding.GraphBuildingTest">
+ <properties>
+ <property name="java.runtime.name" value="Java(TM) SE Runtime Environment"/>
+ <property name="sun.boot.library.path" value="/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries"/>
+ <property name="java.vm.version" value="20.10-b01-428"/>
+ <property name="awt.nativeDoubleBuffering" value="true"/>
+ <property name="gopherProxySet" value="false"/>
+ <property name="mrj.build" value="11M3811"/>
+ <property name="java.vm.vendor" value="Apple Inc."/>
+ <property name="java.vendor.url" value="http://www.apple.com/"/>
+ <property name="path.separator" value=":"/>
+ <property name="java.vm.name" value="Java HotSpot(TM) 64-Bit Server VM"/>
+ <property name="file.encoding.pkg" value="sun.io"/>
+ <property name="java.util.logging.config.file" value="src/test/resources/logging.properties"/>
+ <property name="user.country" value="CN"/>
+ <property name="sun.java.launcher" value="SUN_STANDARD"/>
+ <property name="sun.os.patch.level" value="unknown"/>
+ <property name="java.vm.specification.name" value="Java Virtual Machine Specification"/>
+ <property name="user.dir" value="/Users/hadoop/Desktop/fullstack_genomix/genomix/genomix-hadoop"/>
+ <property name="java.runtime.version" value="1.6.0_35-b10-428-11M3811"/>
+ <property name="java.awt.graphicsenv" value="apple.awt.CGraphicsEnvironment"/>
+ <property name="basedir" value="/Users/hadoop/Desktop/fullstack_genomix/genomix/genomix-hadoop"/>
+ <property name="java.endorsed.dirs" value="/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/endorsed"/>
+ <property name="os.arch" value="x86_64"/>
+ <property name="java.io.tmpdir" value="/var/folders/qw/7w4vv3bx43lchk4nz_4cdpxw0000gp/T/"/>
+ <property name="line.separator" value="
+"/>
+ <property name="java.vm.specification.vendor" value="Sun Microsystems Inc."/>
+ <property name="os.name" value="Mac OS X"/>
+ <property name="sun.jnu.encoding" value="EUC_CN"/>
+ <property name="java.library.path" value=".:/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java"/>
+ <property name="surefire.test.class.path" value="/Users/hadoop/Desktop/fullstack_genomix/genomix/genomix-hadoop/target/test-classes:/Users/hadoop/Desktop/fullstack_genomix/genomix/genomix-hadoop/target/classes:/Users/hadoop/.m2/repository/junit/junit/4.8.1/junit-4.8.1.jar:/Users/hadoop/.m2/repository/org/apache/hadoop/hadoop-core/0.20.2/hadoop-core-0.20.2.jar:/Users/hadoop/.m2/repository/commons-cli/commons-cli/1.2/commons-cli-1.2.jar:/Users/hadoop/.m2/repository/xmlenc/xmlenc/0.52/xmlenc-0.52.jar:/Users/hadoop/.m2/repository/commons-httpclient/commons-httpclient/3.0.1/commons-httpclient-3.0.1.jar:/Users/hadoop/.m2/repository/commons-codec/commons-codec/1.3/commons-codec-1.3.jar:/Users/hadoop/.m2/repository/commons-net/commons-net/1.4.1/commons-net-1.4.1.jar:/Users/hadoop/.m2/repository/org/mortbay/jetty/jetty/6.1.14/jetty-6.1.14.jar:/Users/hadoop/.m2/repository/org/mortbay/jetty/jetty-util/6.1.14/jetty-util-6.1.14.jar:/Users/hadoop/.m2/repository/tomcat/jasper-runtime/5.5.12/jasper-runtime-5.5.12.jar:/Users/hadoop/.m2/repository/tomcat/jasper-compiler/5.5.12/jasper-compiler-5.5.12.jar:/Users/hadoop/.m2/repository/org/mortbay/jetty/jsp-api-2.1/6.1.14/jsp-api-2.1-6.1.14.jar:/Users/hadoop/.m2/repository/org/mortbay/jetty/jsp-2.1/6.1.14/jsp-2.1-6.1.14.jar:/Users/hadoop/.m2/repository/ant/ant/1.6.5/ant-1.6.5.jar:/Users/hadoop/.m2/repository/commons-el/commons-el/1.0/commons-el-1.0.jar:/Users/hadoop/.m2/repository/net/java/dev/jets3t/jets3t/0.7.1/jets3t-0.7.1.jar:/Users/hadoop/.m2/repository/org/mortbay/jetty/servlet-api-2.5/6.1.14/servlet-api-2.5-6.1.14.jar:/Users/hadoop/.m2/repository/net/sf/kosmosfs/kfs/0.3/kfs-0.3.jar:/Users/hadoop/.m2/repository/hsqldb/hsqldb/1.8.0.10/hsqldb-1.8.0.10.jar:/Users/hadoop/.m2/repository/oro/oro/2.0.8/oro-2.0.8.jar:/Users/hadoop/.m2/repository/org/eclipse/jdt/core/3.1.1/core-3.1.1.jar:/Users/hadoop/.m2/repository/org/apache/hadoop/hadoop-test/0.20.2/hadoop-test-0.20.2.jar:/Users/hadoop/.m2/repository/org/apache/ftpserver/ftplet-api/1.0.0/ftplet-api-1.0.0.jar:/Users/hadoop/.m2/repository/org/apache/mina/mina-core/2.0.0-M5/mina-core-2.0.0-M5.jar:/Users/hadoop/.m2/repository/org/apache/ftpserver/ftpserver-core/1.0.0/ftpserver-core-1.0.0.jar:/Users/hadoop/.m2/repository/org/apache/ftpserver/ftpserver-deprecated/1.0.0-M2/ftpserver-deprecated-1.0.0-M2.jar:/Users/hadoop/.m2/repository/commons-io/commons-io/1.3.1/commons-io-1.3.1.jar:/Users/hadoop/.m2/repository/org/slf4j/slf4j-jcl/1.6.3/slf4j-jcl-1.6.3.jar:/Users/hadoop/.m2/repository/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar:/Users/hadoop/.m2/repository/org/slf4j/slf4j-api/1.6.3/slf4j-api-1.6.3.jar:/Users/hadoop/.m2/repository/args4j/args4j/2.0.16/args4j-2.0.16.jar:"/>
+ <property name="java.specification.name" value="Java Platform API Specification"/>
+ <property name="java.class.version" value="50.0"/>
+ <property name="sun.management.compiler" value="HotSpot 64-Bit Tiered Compilers"/>
+ <property name="os.version" value="10.8.1"/>
+ <property name="http.nonProxyHosts" value="local|*.local|169.254/16|*.169.254/16"/>
+ <property name="user.home" value="/Users/hadoop"/>
+ <property name="user.timezone" value="America/Los_Angeles"/>
+ <property name="java.awt.printerjob" value="apple.awt.CPrinterJob"/>
+ <property name="java.specification.version" value="1.6"/>
+ <property name="file.encoding" value="UTF-8"/>
+ <property name="user.name" value="hadoop"/>
+ <property name="java.class.path" value="/Users/hadoop/Desktop/fullstack_genomix/genomix/genomix-hadoop/target/surefire/surefirebooter2183187004114487162.jar"/>
+ <property name="java.vm.specification.version" value="1.0"/>
+ <property name="sun.arch.data.model" value="64"/>
+ <property name="java.home" value="/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home"/>
+ <property name="sun.java.command" value="/Users/hadoop/Desktop/fullstack_genomix/genomix/genomix-hadoop/target/surefire/surefirebooter2183187004114487162.jar /Users/hadoop/Desktop/fullstack_genomix/genomix/genomix-hadoop/target/surefire/surefire4524658770404556182tmp /Users/hadoop/Desktop/fullstack_genomix/genomix/genomix-hadoop/target/surefire/surefire7668612702385218861tmp"/>
+ <property name="java.specification.vendor" value="Sun Microsystems Inc."/>
+ <property name="user.language" value="zh"/>
+ <property name="awt.toolkit" value="apple.awt.CToolkit"/>
+ <property name="java.vm.info" value="mixed mode"/>
+ <property name="hadoop.log.dir" value="logs"/>
+ <property name="java.version" value="1.6.0_35"/>
+ <property name="java.ext.dirs" value="/Library/Java/Extensions:/System/Library/Java/Extensions:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/ext"/>
+ <property name="sun.boot.class.path" value="/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jsfd.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/classes.jar:/System/Library/Frameworks/JavaVM.framework/Frameworks/JavaRuntimeSupport.framework/Resources/Java/JavaRuntimeSupport.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/ui.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/laf.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/sunrsasign.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jsse.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jce.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/charsets.jar"/>
+ <property name="java.vendor" value="Apple Inc."/>
+ <property name="localRepository" value="/Users/hadoop/.m2/repository"/>
+ <property name="file.separator" value="/"/>
+ <property name="java.vendor.url.bug" value="http://bugreport.apple.com/"/>
+ <property name="sun.cpu.endian" value="little"/>
+ <property name="sun.io.unicode.encoding" value="UnicodeLittle"/>
+ <property name="mrj.version" value="1070.1.6.0_35-428"/>
+ <property name="socksNonProxyHosts" value="local|*.local|169.254/16|*.169.254/16"/>
+ <property name="ftp.nonProxyHosts" value="local|*.local|169.254/16|*.169.254/16"/>
+ <property name="sun.cpu.isalist" value=""/>
+ </properties>
+ <testcase time="7.683" classname="edu.uci.ics.graphbuilding.GraphBuildingTest" name="test"/>
+</testsuite>
\ No newline at end of file
diff --git a/genomix/genomix-hadoop/target/surefire-reports/edu.uci.ics.graphbuilding.GraphBuildingTest.txt b/genomix/genomix-hadoop/target/surefire-reports/edu.uci.ics.graphbuilding.GraphBuildingTest.txt
new file mode 100644
index 0000000..ee383c5
--- /dev/null
+++ b/genomix/genomix-hadoop/target/surefire-reports/edu.uci.ics.graphbuilding.GraphBuildingTest.txt
@@ -0,0 +1,4 @@
+-------------------------------------------------------------------------------
+Test set: edu.uci.ics.graphbuilding.GraphBuildingTest
+-------------------------------------------------------------------------------
+Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.737 sec
diff --git a/genomix/genomix-hadoop/target/test-classes/edu/uci/ics/graphbuilding/GraphBuildingTest.class b/genomix/genomix-hadoop/target/test-classes/edu/uci/ics/graphbuilding/GraphBuildingTest.class
new file mode 100644
index 0000000..1609650
--- /dev/null
+++ b/genomix/genomix-hadoop/target/test-classes/edu/uci/ics/graphbuilding/GraphBuildingTest.class
Binary files differ
diff --git a/genomix/genomix-hadoop/target/test-classes/edu/uci/ics/utils/TestUtils.class b/genomix/genomix-hadoop/target/test-classes/edu/uci/ics/utils/TestUtils.class
new file mode 100644
index 0000000..1eba8b0
--- /dev/null
+++ b/genomix/genomix-hadoop/target/test-classes/edu/uci/ics/utils/TestUtils.class
Binary files differ
diff --git a/genomix/genomix-hadoop/testactual/source.txt b/genomix/genomix-hadoop/testactual/source.txt
new file mode 100644
index 0000000..3665e18
--- /dev/null
+++ b/genomix/genomix-hadoop/testactual/source.txt
@@ -0,0 +1,3 @@
+39 41 0c 1 1
+e4 04 31 24 1
+93 13 c4 16 1