| 1 | <?xml version="1.0" encoding="UTF-8"?> |
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| 2 | <!-- ====================================================================== |
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| 3 | Oct 10, 2005 3:32:31 PM |
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| 4 | |
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| 5 | Base plugins |
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| 6 | This buildfile is used for base-plugins created at the oncology department in Lund, Sweden |
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| 7 | |
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| 8 | johan |
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| 9 | ====================================================================== --> |
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| 10 | <project name="Base plugins" default="dist" basedir="."> |
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| 11 | <description>This buildfile is used for base-plugins created at the oncology department in Lund, Sweden</description> |
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| 12 | |
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| 13 | <!-- doc --> |
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| 14 | <property name="doc" value="doc"/> |
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| 15 | |
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| 16 | <property name="replicateerror.lib" location="ReplicateError/lib" /> |
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| 17 | <property name="virtualarray.lib" location="VirtualArray/lib" /> |
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| 18 | <property name="mergebioassay.doc" location="MergeBioAssay/doc" /> |
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| 19 | <property name="qpackage.lib" location="QPackage/lib" /> |
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| 20 | <property name="smooth.doc" location="smooth/doc" /> |
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| 21 | |
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| 22 | <!-- src --> |
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| 23 | <property name="basefile.src" location="BaseFile/src" /> |
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| 24 | <property name="virtualarray.src" location="VirtualArray/src" /> |
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| 25 | <property name="replicateerror.src" location="ReplicateError/src" /> |
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| 26 | <property name="mergebioassay.src" location="MergeBioAssay/src" /> |
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| 27 | <property name="qpackage.src" location="QPackage/src" /> |
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| 28 | <property name="center.src" location="Center/src" /> |
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| 29 | <property name="normalization.src" location="Normalization/src" /> |
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| 30 | <property name="null.src" location="NullPlugin/src" /> |
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| 31 | <property name="smooth.src" location="Smooth/src" /> |
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| 32 | <property name="gominer.src" location="GoMiner/src" /> |
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| 33 | <property name="ztest.src" location="ZTest/src" /> |
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| 34 | |
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| 35 | <!-- bin --> |
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| 36 | <property name="bin" location="build" /> |
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| 37 | <property name="basefile.bin" location="${bin}/BaseFile" /> |
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| 38 | <property name="virtualarray.bin" location="${bin}/VirtualArray" /> |
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| 39 | <property name="replicateerror.bin" location="${bin}/ReplicateError" /> |
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| 40 | <property name="mergebioassay.bin" location="${bin}/MergeBioAssay" /> |
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| 41 | <property name="qpackage.bin" location="${bin}/QPackage" /> |
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| 42 | <property name="center.bin" location="${bin}/Center" /> |
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| 43 | <property name="normalization.bin" location="${bin}/Normalization" /> |
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| 44 | <property name="null.bin" location="${bin}/NullPlugin" /> |
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| 45 | <property name="smooth.bin" location="${bin}/Smooth" /> |
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| 46 | <property name="gominer.bin" location="${bin}/GoMiner" /> |
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| 47 | <property name="ztest.bin" location="${bin}/ZTest" /> |
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| 48 | |
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| 49 | <!-- dist --> |
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| 50 | <property name="dist" location="dist" /> |
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| 51 | |
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| 52 | <!-- package --> |
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| 53 | <property name="mergebioassay.pac" value="${dist}/mergebioassay"/> |
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| 54 | <property name="smooth.pac" value="${dist}/smooth"/> |
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| 55 | |
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| 56 | |
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| 57 | <!-- ================================= |
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| 58 | target: compile |
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| 59 | ================================== --> |
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| 60 | <target name="compile" description="--> Compiles all the packages"> |
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| 61 | <ant target="virtualarray.compile" /> |
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| 62 | <ant target="replicateerror.compile" /> |
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| 63 | <ant target="mergebioassay.compile" /> |
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| 64 | <ant target="qpackage.compile" /> |
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| 65 | <ant target="center.compile" /> |
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| 66 | <ant target="normalization.compile" /> |
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| 67 | <ant target="smooth.compile" /> |
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| 68 | </target> |
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| 69 | |
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| 70 | <!-- - - - - - - - - - - - - - - - - - |
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| 71 | target: basefile.compile |
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| 72 | - - - - - - - - - - - - - - - - - --> |
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| 73 | <target name="basefile.compile"> |
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| 74 | <mkdir dir="${basefile.bin}"/> |
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| 75 | <javac |
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| 76 | srcdir="${basefile.src}" |
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| 77 | destdir="${basefile.bin}" |
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| 78 | debug="true" |
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| 79 | deprecation="true" |
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| 80 | encoding="ISO-8859-1" |
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| 81 | /> |
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| 82 | </target> |
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| 83 | |
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| 84 | <!-- - - - - - - - - - - - - - - - - - |
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| 85 | target: virtualarray.compile |
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| 86 | - - - - - - - - - - - - - - - - - --> |
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| 87 | <target name="virtualarray.compile" depends="basefile.compile"> |
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| 88 | <mkdir dir="${virtualarray.bin}"/> |
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| 89 | <javac |
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| 90 | srcdir="${virtualarray.src}" |
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| 91 | destdir="${virtualarray.bin}" |
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| 92 | classpath="${basefile.bin}" |
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| 93 | debug="true" |
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| 94 | deprecation="true" |
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| 95 | encoding="ISO-8859-1" |
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| 96 | /> |
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| 97 | </target> |
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| 98 | |
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| 99 | <!-- - - - - - - - - - - - - - - - - - |
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| 100 | target: replicateerror.compile |
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| 101 | - - - - - - - - - - - - - - - - - --> |
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| 102 | <target name="replicateerror.compile" depends="basefile.compile"> |
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| 103 | <mkdir dir="${replicateerror.bin}"/> |
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| 104 | <javac |
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| 105 | srcdir="${replicateerror.src}" |
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| 106 | destdir="${replicateerror.bin}" |
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| 107 | classpath="${basefile.bin}" |
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| 108 | debug="true" |
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| 109 | deprecation="true" |
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| 110 | encoding="ISO-8859-1" |
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| 111 | /> |
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| 112 | </target> |
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| 113 | |
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| 114 | <!-- - - - - - - - - - - - - - - - - - |
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| 115 | target: mergebioassay.compile |
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| 116 | - - - - - - - - - - - - - - - - - --> |
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| 117 | <target name="mergebioassay.compile" depends="basefile.compile"> |
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| 118 | <mkdir dir="${mergebioassay.bin}"/> |
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| 119 | <javac |
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| 120 | srcdir="${mergebioassay.src}" |
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| 121 | destdir="${mergebioassay.bin}" |
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| 122 | classpath="${basefile.bin}" |
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| 123 | debug="true" |
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| 124 | deprecation="true" |
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| 125 | encoding="ISO-8859-1" |
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| 126 | /> |
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| 127 | </target> |
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| 128 | |
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| 129 | <!-- - - - - - - - - - - - - - - - - - |
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| 130 | target: qpackage.compile |
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| 131 | - - - - - - - - - - - - - - - - - --> |
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| 132 | <target name="qpackage.compile" depends="basefile.compile"> |
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| 133 | <mkdir dir="${qpackage.bin}"/> |
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| 134 | <javac |
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| 135 | srcdir="${qpackage.src}" |
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| 136 | destdir="${qpackage.bin}" |
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| 137 | classpath="${basefile.bin}" |
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| 138 | debug="true" |
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| 139 | deprecation="true" |
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| 140 | encoding="ISO-8859-1" |
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| 141 | /> |
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| 142 | </target> |
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| 143 | |
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| 144 | <!-- - - - - - - - - - - - - - - - - - |
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| 145 | target: center.compile |
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| 146 | - - - - - - - - - - - - - - - - - --> |
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| 147 | <target name="center.compile" depends="basefile.compile"> |
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| 148 | <mkdir dir="${center.bin}"/> |
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| 149 | <javac |
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| 150 | srcdir="${center.src}" |
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| 151 | destdir="${center.bin}" |
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| 152 | classpath="${basefile.bin}" |
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| 153 | debug="true" |
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| 154 | deprecation="true" |
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| 155 | encoding="ISO-8859-1" |
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| 156 | /> |
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| 157 | </target> |
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| 158 | |
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| 159 | <!-- - - - - - - - - - - - - - - - - - |
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| 160 | target: normalization.compile |
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| 161 | - - - - - - - - - - - - - - - - - --> |
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| 162 | <target name="normalization.compile" depends="basefile.compile"> |
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| 163 | <mkdir dir="${normalization.bin}"/> |
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| 164 | <javac |
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| 165 | srcdir="${normalization.src}" |
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| 166 | destdir="${normalization.bin}" |
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| 167 | classpath="${basefile.bin}" |
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| 168 | debug="true" |
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| 169 | deprecation="true" |
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| 170 | encoding="ISO-8859-1" |
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| 171 | /> |
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| 172 | </target> |
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| 173 | |
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| 174 | <!-- - - - - - - - - - - - - - - - - - |
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| 175 | target: smooth.compile |
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| 176 | - - - - - - - - - - - - - - - - - --> |
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| 177 | <target name="smooth.compile" depends="basefile.compile"> |
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| 178 | <mkdir dir="${smooth.bin}"/> |
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| 179 | <javac |
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| 180 | srcdir="${smooth.src}" |
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| 181 | destdir="${smooth.bin}" |
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| 182 | classpath="${basefile.bin}" |
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| 183 | debug="true" |
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| 184 | deprecation="true" |
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| 185 | encoding="ISO-8859-1" |
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| 186 | /> |
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| 187 | </target> |
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| 188 | |
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| 189 | <!-- - - - - - - - - - - - - - - - - - |
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| 190 | target: null.compile |
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| 191 | - - - - - - - - - - - - - - - - - --> |
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| 192 | <target name="null.compile" depends="basefile.compile"> |
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| 193 | <mkdir dir="${null.bin}"/> |
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| 194 | <javac |
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| 195 | srcdir="${null.src}" |
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| 196 | destdir="${null.bin}" |
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| 197 | classpath="${basefile.bin}" |
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| 198 | debug="true" |
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| 199 | deprecation="true" |
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| 200 | encoding="ISO-8859-1" |
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| 201 | /> |
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| 202 | </target> |
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| 203 | |
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| 204 | <!-- - - - - - - - - - - - - - - - - - |
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| 205 | target: gominer.compile |
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| 206 | - - - - - - - - - - - - - - - - - --> |
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| 207 | <target name="gominer.compile" depends="basefile.compile"> |
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| 208 | <mkdir dir="${gominer.bin}"/> |
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| 209 | <javac |
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| 210 | srcdir="${gominer.src}" |
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| 211 | destdir="${gominer.bin}" |
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| 212 | classpath="${basefile.bin}" |
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| 213 | debug="true" |
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| 214 | deprecation="true" |
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| 215 | encoding="ISO-8859-1" |
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| 216 | /> |
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| 217 | </target> |
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| 218 | |
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| 219 | <!-- - - - - - - - - - - - - - - - - - |
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| 220 | target: ztest.compile |
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| 221 | - - - - - - - - - - - - - - - - - --> |
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| 222 | <target name="ztest.compile" depends="basefile.compile"> |
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| 223 | <mkdir dir="${ztest.bin}"/> |
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| 224 | <javac |
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| 225 | srcdir="${ztest.src}" |
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| 226 | destdir="${ztest.bin}" |
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| 227 | classpath="${basefile.bin}" |
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| 228 | debug="true" |
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| 229 | deprecation="true" |
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| 230 | encoding="ISO-8859-1" |
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| 231 | /> |
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| 232 | </target> |
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| 233 | |
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| 234 | |
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| 235 | |
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| 236 | <!-- ================================= |
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| 237 | target: clean |
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| 238 | ================================= --> |
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| 239 | <target name="clean" description="--> Remove all generated files"> |
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| 240 | <delete dir="${dist}" /> |
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| 241 | <delete dir="${bin}" /> |
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| 242 | </target> |
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| 243 | |
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| 244 | |
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| 245 | <!-- ================================= |
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| 246 | target: dist |
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| 247 | ================================== --> |
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| 248 | <target name="dist" |
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| 249 | depends="virtualarray.dist, replicateerror.dist, mergebioassay.dist, |
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| 250 | qpackage.dist, center.dist, lowess.dist, smooth.dist" |
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| 251 | description="--> Creates a ditributable gzipfile for each package"> |
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| 252 | </target> |
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| 253 | |
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| 254 | <!-- - - - - - - - - - - - - - - - - - |
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| 255 | target: virtualarray.dist |
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| 256 | - - - - - - - - - - - - - - - - - --> |
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| 257 | <target name="virtualarray.dist" depends="virtualarray.compile"> |
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| 258 | <mkdir dir="${dist}" /> |
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| 259 | <jar destfile="${dist}/virtualarray.jar"> |
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| 260 | <fileset dir="${basefile.src}" /> |
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| 261 | <fileset dir="${basefile.bin}" /> |
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| 262 | <fileset dir="${virtualarray.bin}" /> |
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| 263 | <fileset dir="${virtualarray.src}" /> |
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| 264 | <manifest> |
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| 265 | <attribute name="Built-By" value="${user.name}" /> |
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| 266 | <attribute name="Main-Class" value="virtualarray.VirtualArray" /> |
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| 267 | </manifest> |
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| 268 | </jar> |
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| 269 | </target> |
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| 270 | |
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| 271 | <!-- - - - - - - - - - - - - - - - - - |
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| 272 | target: replicateerror.dist |
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| 273 | - - - - - - - - - - - - - - - - - --> |
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| 274 | <target name="replicateerror.dist" depends="replicateerror.compile"> |
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| 275 | <mkdir dir="${dist}" /> |
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| 276 | <jar destfile="${dist}/replicateerror.jar"> |
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| 277 | <fileset dir="${basefile.src}" /> |
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| 278 | <fileset dir="${basefile.bin}" /> |
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| 279 | <fileset dir="${replicateerror.bin}" /> |
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| 280 | <fileset dir="${replicateerror.src}" /> |
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| 281 | <manifest> |
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| 282 | <attribute name="Built-By" value="${user.name}"/> |
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| 283 | <attribute name="Main-Class" value="replicateerror.ReplicateError"/> |
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| 284 | </manifest> |
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| 285 | </jar> |
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| 286 | </target> |
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| 287 | |
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| 288 | <!-- - - - - - - - - - - - - - - - - - |
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| 289 | target: mergebioassay.dist |
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| 290 | - - - - - - - - - - - - - - - - - --> |
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| 291 | <target name="mergebioassay.dist" depends="mergebioassay.compile"> |
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| 292 | <mkdir dir="${dist}" /> |
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| 293 | <jar destfile="${dist}/mergebioassay.jar"> |
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| 294 | <fileset dir="${basefile.src}" /> |
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| 295 | <fileset dir="${basefile.bin}" /> |
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| 296 | <fileset dir="${mergebioassay.bin}" /> |
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| 297 | <fileset dir="${mergebioassay.src}" /> |
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| 298 | <manifest> |
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| 299 | <attribute name="Built-By" value="${user.name}"/> |
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| 300 | <attribute name="Main-Class" value="mergebioassay.MergeBioAssay"/> |
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| 301 | </manifest> |
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| 302 | </jar> |
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| 303 | </target> |
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| 304 | |
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| 305 | <!-- - - - - - - - - - - - - - - - - - |
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| 306 | target: qpackage.dist |
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| 307 | - - - - - - - - - - - - - - - - - --> |
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| 308 | <target name="qpackage.dist" depends="qpackage.compile"> |
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| 309 | <mkdir dir="${dist}" /> |
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| 310 | <jar destfile="${dist}/qpackage.jar"> |
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| 311 | <fileset dir="${basefile.src}" /> |
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| 312 | <fileset dir="${basefile.bin}" /> |
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| 313 | <fileset dir="${qpackage.bin}" /> |
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| 314 | <fileset dir="${qpackage.src}" /> |
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| 315 | <manifest> |
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| 316 | <attribute name="Built-By" value="${user.name}"/> |
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| 317 | </manifest> |
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| 318 | </jar> |
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| 319 | </target> |
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| 320 | |
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| 321 | <!-- - - - - - - - - - - - - - - - - - |
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| 322 | target: center.dist |
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| 323 | - - - - - - - - - - - - - - - - - --> |
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| 324 | <target name="center.dist" depends="center.compile"> |
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| 325 | <mkdir dir="${dist}" /> |
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| 326 | <jar destfile="${dist}/center.jar"> |
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| 327 | <fileset dir="${basefile.src}" /> |
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| 328 | <fileset dir="${basefile.bin}" /> |
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| 329 | <fileset dir="${center.bin}" /> |
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| 330 | <fileset dir="${center.src}" /> |
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| 331 | <manifest> |
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| 332 | <attribute name="Built-By" value="${user.name}"/> |
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| 333 | <attribute name="Main-Class" value="center.Center"/> |
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| 334 | </manifest> |
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| 335 | </jar> |
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| 336 | </target> |
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| 337 | |
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| 338 | <!-- - - - - - - - - - - - - - - - - - |
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| 339 | target: lowess.dist |
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| 340 | - - - - - - - - - - - - - - - - - --> |
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| 341 | <target name="lowess.dist" depends="normalization.compile"> |
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| 342 | <mkdir dir="${dist}" /> |
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| 343 | <jar destfile="${dist}/lowess.jar"> |
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| 344 | <fileset dir="${basefile.src}" /> |
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| 345 | <fileset dir="${basefile.bin}" /> |
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| 346 | <fileset dir="${normalization.bin}" includes="lowess/**" /> |
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| 347 | <fileset dir="${normalization.src}" includes="lowess/**" /> |
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| 348 | <manifest> |
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| 349 | <attribute name="Built-By" value="${user.name}" /> |
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| 350 | <attribute name="Main-Class" value="lowess.Lowess" /> |
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| 351 | </manifest> |
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| 352 | </jar> |
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| 353 | </target> |
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| 354 | |
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| 355 | <!-- - - - - - - - - - - - - - - - - - |
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| 356 | target: smooth.dist |
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| 357 | - - - - - - - - - - - - - - - - - --> |
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| 358 | <target name="smooth.dist" depends="smooth.compile"> |
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| 359 | <mkdir dir="${dist}" /> |
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| 360 | <jar destfile="${dist}/smooth.jar"> |
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| 361 | <fileset dir="${basefile.src}" /> |
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| 362 | <fileset dir="${basefile.bin}" /> |
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| 363 | <fileset dir="${smooth.bin}" /> |
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| 364 | <fileset dir="${smooth.src}" /> |
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| 365 | <manifest> |
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| 366 | <attribute name="Built-By" value="${user.name}"/> |
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| 367 | <attribute name="Main-Class" value="smooth.SmoothMain"/> |
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| 368 | </manifest> |
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| 369 | </jar> |
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| 370 | </target> |
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| 371 | |
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| 372 | <!-- - - - - - - - - - - - - - - - - - |
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| 373 | target: null.dist |
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| 374 | - - - - - - - - - - - - - - - - - --> |
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| 375 | <target name="null.dist" depends="null.compile"> |
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| 376 | <mkdir dir="${dist}" /> |
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| 377 | <jar destfile="${dist}/nullbase1plugin.jar"> |
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| 378 | <fileset dir="${basefile.src}" /> |
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| 379 | <fileset dir="${basefile.bin}" /> |
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| 380 | <fileset dir="${null.bin}" /> |
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| 381 | <fileset dir="${null.src}" /> |
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| 382 | <manifest> |
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| 383 | <attribute name="Built-By" value="${user.name}"/> |
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| 384 | <attribute name="Main-Class" value="base1null.Base1NullPlugin"/> |
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| 385 | </manifest> |
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| 386 | </jar> |
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| 387 | </target> |
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| 388 | |
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| 389 | <!-- - - - - - - - - - - - - - - - - - |
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| 390 | target: gominer.dist |
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| 391 | - - - - - - - - - - - - - - - - - --> |
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| 392 | <target name="gominer.dist" depends="gominer.compile"> |
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| 393 | <mkdir dir="${dist}" /> |
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| 394 | <jar destfile="${dist}/gominer.jar"> |
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| 395 | <fileset dir="${basefile.src}" /> |
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| 396 | <fileset dir="${basefile.bin}" /> |
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| 397 | <fileset dir="${gominer.bin}" /> |
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| 398 | <fileset dir="${gominer.src}" /> |
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| 399 | <manifest> |
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| 400 | <attribute name="Built-By" value="${user.name}"/> |
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| 401 | <attribute name="Main-Class" value="net.sf.basedb.plugin.gominer.GoMinerExport"/> |
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| 402 | </manifest> |
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| 403 | </jar> |
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| 404 | </target> |
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| 405 | |
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| 406 | <!-- - - - - - - - - - - - - - - - - - |
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| 407 | target: ztest.dist |
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| 408 | - - - - - - - - - - - - - - - - - --> |
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| 409 | <target name="ztest.dist" depends="ztest.compile"> |
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| 410 | <mkdir dir="${dist}" /> |
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| 411 | <jar destfile="${dist}/ztest.jar"> |
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| 412 | <fileset dir="${basefile.src}" /> |
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| 413 | <fileset dir="${basefile.bin}" /> |
|---|
| 414 | <fileset dir="${ztest.bin}" /> |
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| 415 | <fileset dir="${ztest.src}" /> |
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| 416 | <manifest> |
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| 417 | <attribute name="Built-By" value="${user.name}"/> |
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| 418 | <attribute name="Main-Class" value="net.sf.basedb.plugin.ztest.Start"/> |
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| 419 | </manifest> |
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| 420 | </jar> |
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| 421 | </target> |
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| 422 | |
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| 423 | |
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| 424 | <!-- ================================= |
|---|
| 425 | target: mergebioassay.package |
|---|
| 426 | ================================= --> |
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| 427 | <target name="mergebioassay.package" depends="mergebioassay.dist" description="--> Create a zip file containting all files necessary for distribution."> |
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| 428 | <mkdir dir="${mergebioassay.pac}"/> |
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| 429 | <copy file="${dist}/mergebioassay.jar" todir="${mergebioassay.pac}" /> |
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| 430 | <copy file="${doc}/gpl.txt" todir="${mergebioassay.pac}" /> |
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| 431 | <copy file="${mergebioassay.doc}/run" todir="${mergebioassay.pac}" /> |
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| 432 | <copy file="${mergebioassay.doc}/mergebioassay.base" todir="${mergebioassay.pac}" /> |
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| 433 | <zip destfile="mergebioassay.zip" basedir="${mergebioassay.pac}" /> |
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| 434 | </target> |
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| 435 | |
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| 436 | <!-- ================================= |
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| 437 | target: smooth.package |
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| 438 | ================================= --> |
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| 439 | <target name="smooth.package" depends="smooth.dist" description="--> Create a zip file containting all files necessary for distribution."> |
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| 440 | <mkdir dir="${smooth.pac}"/> |
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| 441 | <copy file="${dist}/smooth.jar" todir="${smooth.pac}" /> |
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| 442 | <copy file="${doc}/gpl.txt" todir="${smooth.pac}" /> |
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| 443 | <copy file="${smooth.doc}/run" todir="${smooth.pac}" /> |
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| 444 | <copy file="${smooth.doc}/smooth.base" todir="${smooth.pac}" /> |
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| 445 | <zip destfile="smooth.zip" basedir="${smooth.pac}" /> |
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| 446 | </target> |
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| 447 | |
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| 448 | </project> |
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