Changeset 875


Ignore:
Timestamp:
Dec 5, 2008, 10:53:19 AM (13 years ago)
Author:
Jari Häkkinen
Message:

Addresses #157 and #56. Creating se.lu.onk.Center.

Location:
plugins/base1
Files:
5 added
5 edited
4 copied
1 moved

Legend:

Unmodified
Added
Removed
  • plugins/base1/se.lu.onk.Center/trunk/README

    r874 r875  
    11$Id$
    22
    3 = About `se.lu.onk.MergeBioAssay` =
    4 
    5 The `se.lu.onk.MergeBioAssay` plug-in merge bioassays by grouping them
     3= About `se.lu.onk.Center` =
     4
     5The `se.lu.onk.Center` plug-in merge bioassays by grouping them
    66according to annotation types or syntactical differences in the
    77name. See ``Documentation`` below fo further information about the
    88plug-in.
    99
    10 `se.lu.onk.MergeBioAssay` is free software. See the file license.txt for
     10`se.lu.onk.Center` is free software. See the file license.txt for
    1111copying conditions.
    1212
     
    1717== Downloading ==
    1818
    19 `se.lu.onk.MergeBioAssay` can be obtained from
     19`se.lu.onk.Center` can be obtained from
    2020
    2121  http://baseplugins.thep.lu.se/wiki/PluginDownload
     
    4343{{{
    4444  # cd /path/to/base/plugins
    45   # download MergeBioAssay-version.tgz
    46   # untar MergeBioAssay-version.tgz
    47   # ln -s MergeBioAssay-version MergeBioAssay
     45  # download Center-version.tgz
     46  # untar Center-version.tgz
     47  # ln -s Center-version Center
    4848}}}
    4949The symbolic link in the last line above allows for easier change to
     
    6262    of this parameter and `Plugin executables path` should add up to
    6363    the absolute path to the binary `run`, i.e.,
    64     /path/to/base/plugins/MergeBioAssay/run. How this string looks
     64    /path/to/base/plugins/Center/run. How this string looks
    6565    like depends on your plug-in directory structure.
    6666  # Test the plug-ins and when you are satisfied, share it to your
     
    7171== Compiling ==
    7272
    73 You must checkout the `se.lu.onk.MergeBioAssay` from the repository,
     73You must checkout the `se.lu.onk.Center` from the repository,
    7474follow the instructions below. Then download and untar the
    7575`se.lu.onk.BaseFile` package available from
     
    7878{{{
    7979  check out project, see instructions below
    80   # cd /path/to/se.lu.onk.MergeBioAssay
     80  # cd /path/to/se.lu.onk.Center
    8181  # wget http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.BaseFile/BaseFile-1.0.tgz?format=raw -O BaseFile-1.0.tgz
    8282  # wget http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.BaseFile/BaseFile-1.0.tgz.MD5?format=raw -O BaseFile-1.0.tgz.MD5
     
    8989It is important that the `BaseFile` package is located in directory
    9090`BaseFile`. Now simple issue `ant`. This will create a jar file
    91 `dist/MergeBioAssay.jar`.
     91`dist/Center.jar`.
    9292
    9393
     
    101101== Bug Reporting ==
    102102
    103 You can report `se.lu.onk.MergeBioAssay` bugs on
     103You can report `se.lu.onk.Center` bugs on
    104104
    105105  http://baseplugins.thep.lu.se/newticket
     
    110110== Subversion Access ==
    111111
    112 The `se.lu.onk.MergeBioAssay` source repository is available via anonymous
     112The `se.lu.onk.Center` source repository is available via anonymous
    113113subversion access, issue:
    114114
    115   `svn co http://baseplugins.thep.lu.se/svn/plugins/base1/se.lu.onk.MergeBioAssay/trunk se.lu.onk.MergeBioAssay`
     115  `svn co http://baseplugins.thep.lu.se/svn/plugins/base1/se.lu.onk.Center/trunk se.lu.onk.Center`
    116116
    117117There is no guarantees about the contents or quality of the latest
     
    236236Copyright (C) 2008 Jari Häkkinen
    237237
    238 This file is part of the se.lu.onk.MergeBioAssay plug-in for
    239 BASE. Available at http://baseplugins.thep.lu.se/ and BASE web site is
     238This file is part of the se.lu.onk.Center plug-in for BASE. Available
     239at http://baseplugins.thep.lu.se/ and BASE web site is
    240240http://base.thep.lu.se
    241241
  • plugins/base1/se.lu.onk.Center/trunk/build.xml

    r874 r875  
    66    Copyright (C) 2008 Jari Häkkinen
    77
    8     This file is part of the se.lu.onk.MergeBioAssay plug-in for
     8    This file is part of the se.lu.onk.Center plug-in for
    99    BASE. Available at http://baseplugins.thep.lu.se/ and BASE web
    1010    site is http://base.thep.lu.se
     
    2323    along with BASE. If not, see <http://www.gnu.org/licenses/>.
    2424-->
    25 <project name="se.lu.onk.MergeBioAssay plug-in for BASE"
     25<project name="se.lu.onk.Center plug-in for BASE"
    2626         default="dist" basedir=".">
    2727  <description>
    28     This build file is used for se.lu.onk.MergeBioAssay plug-in for
     28    This build file is used for se.lu.onk.Center plug-in for
    2929    BASE created at the Department of Oncology, Lund University,
    3030    Sweden.
     
    4040       1.0, 1.1, 1.2pre
    4141    -->
    42   <property name="version" value="2.2pre" />
     42  <property name="version" value="2.1pre" />
    4343
    4444  <property name="basefilejar" value="BaseFile" />
     
    4747  <property name="doc" location="doc" />
    4848  <property name="package" value="mergebioassay"/>
    49   <property name="packagestring" value="MergeBioAssay-${version}" />
     49  <property name="packagestring" value="Center-${version}" />
    5050  <property name="src" location="src" />
    5151 
     
    8787  <target name="dist" depends="compile">
    8888    <mkdir dir="${dist}" />
    89     <jar destfile="${dist}/MergeBioAssay.jar">
     89    <jar destfile="${dist}/Center.jar">
    9090      <fileset dir="${build}" />
    9191      <manifest>
    9292        <attribute name="Built-By" value="${user.name}"/>
    93         <attribute name="Main-Class" value="mergebioassay.MergeBioAssay"/>
     93        <attribute name="Main-Class" value="Main"/>
    9494      </manifest>
    9595    </jar>
     
    104104    <mkdir dir="${package}/${basefilejar}"/>
    105105    <copy todir="${package}">
    106       <fileset file="${dist}/MergeBioAssay.jar" />
     106      <fileset file="${dist}/Center.jar" />
    107107      <fileset dir="${doc}" />
    108108      <fileset file="license.txt" />
  • plugins/base1/se.lu.onk.Center/trunk/misc/run

    r874 r875  
    66# Copyright (C) 2008 Jari Häkkinen
    77#
    8 # This file is part of the se.lu.onk.MergeBioAssay plug-in for
     8# This file is part of the se.lu.onk.Center plug-in for
    99# BASE. Available at http://baseplugins.thep.lu.se/ and BASE web site
    1010# is http://base.thep.lu.se
     
    2525
    2626progdir="`dirname \"$0\"`"
    27 java -cp "$CLASSPATH:$progdir/BaseFile/BaseFile.jar:$progdir/MergeBioAssay.jar" mergebioassay/MergeBioAssay stdin.txt
     27java -cp "$CLASSPATH:$progdir/BaseFile/BaseFile.jar:$progdir/Center.jar" Main stdin.txt
  • plugins/base1/se.lu.onk.Center/trunk/src/center/AssayRow.java

    r149 r875  
     1/*
     2 * $Id$
     3 *
     4 * Copyright (C) 2005 Johan Enell
     5 * Copyright (C) 2008 Jari Häkkinen
     6
     7 * This file is part of the se.lu.onk.Center plug-in for
     8 * BASE. Available at http://baseplugins.thep.lu.se/ and BASE web site
     9 * is http://base.thep.lu.se
     10
     11 * This is free software; you can redistribute it and/or modify it
     12 * under the terms of the GNU General Public License as published by
     13 * the Free Software Foundation; either version 3 of the License, or
     14 * (at your option) any later version.
     15
     16 * The software is distributed in the hope that it will be useful, but
     17 * WITHOUT ANY WARRANTY; without even the implied warranty of
     18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
     19 * General Public License for more details.
     20
     21 * You should have received a copy of the GNU General Public License
     22 * along with this software. If not, see <http://www.gnu.org/licenses/>.
     23 */
     24
    125package center;
    2 
    3 /*
    4  * Center
    5  * Copyright (C) 2005 Johan Enell
    6  *
    7  * This program is free software; you can redistribute it and/or
    8  * modify it under the terms of the GNU General Public License
    9  * as published by the Free Software Foundation; either version 2
    10  * of the License, or (at your option) any later version.
    11  *
    12  * This program is distributed in the hope that it will be useful,
    13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
    14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    15  * GNU General Public License for more details.
    16  *
    17  * You should have received a copy of the GNU General Public License
    18  * along with this program; if not, write to the Free Software
    19  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
    20  */
    2126
    2227class AssayRow
  • plugins/base1/se.lu.onk.Center/trunk/src/center/Center.java

    r149 r875  
     1/*
     2 * $Id$
     3 *
     4 * Copyright (C) 2005 Johan Enell
     5 * Copyright (C) 2008 Jari Häkkinen
     6
     7 * This file is part of the se.lu.onk.Center plug-in for
     8 * BASE. Available at http://baseplugins.thep.lu.se/ and BASE web site
     9 * is http://base.thep.lu.se
     10
     11 * This is free software; you can redistribute it and/or modify it
     12 * under the terms of the GNU General Public License as published by
     13 * the Free Software Foundation; either version 3 of the License, or
     14 * (at your option) any later version.
     15
     16 * The software is distributed in the hope that it will be useful, but
     17 * WITHOUT ANY WARRANTY; without even the implied warranty of
     18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
     19 * General Public License for more details.
     20
     21 * You should have received a copy of the GNU General Public License
     22 * along with this software. If not, see <http://www.gnu.org/licenses/>.
     23 */
     24
    125package center;
    226
     
    1337import java.util.List;
    1438import java.util.Map;
    15 /*
    16  * Center
    17  * Copyright (C) 2005 Johan Enell
    18  *
    19  * This program is free software; you can redistribute it and/or
    20  * modify it under the terms of the GNU General Public License
    21  * as published by the Free Software Foundation; either version 2
    22  * of the License, or (at your option) any later version.
    23  *
    24  * This program is distributed in the hope that it will be useful,
    25  * but WITHOUT ANY WARRANTY; without even the implied warranty of
    26  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    27  * GNU General Public License for more details.
    28  *
    29  * You should have received a copy of the GNU General Public License
    30  * along with this program; if not, write to the Free Software
    31  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
    32  */
    3339
    3440class Center
  • plugins/base1/se.lu.onk.Center/trunk/src/center/Main.java

    r149 r875  
     1/*
     2 * $Id$
     3 *
     4 * Copyright (C) 2005 Johan Enell
     5 * Copyright (C) 2008 Jari Häkkinen
     6
     7 * This file is part of the se.lu.onk.Center plug-in for
     8 * BASE. Available at http://baseplugins.thep.lu.se/ and BASE web site
     9 * is http://base.thep.lu.se
     10
     11 * This is free software; you can redistribute it and/or modify it
     12 * under the terms of the GNU General Public License as published by
     13 * the Free Software Foundation; either version 3 of the License, or
     14 * (at your option) any later version.
     15
     16 * The software is distributed in the hope that it will be useful, but
     17 * WITHOUT ANY WARRANTY; without even the implied warranty of
     18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
     19 * General Public License for more details.
     20
     21 * You should have received a copy of the GNU General Public License
     22 * along with this software. If not, see <http://www.gnu.org/licenses/>.
     23 */
     24
    125package center;
    226
     
    731import java.io.FileOutputStream;
    832import java.io.PrintStream;
    9 /*
    10  * Center
    11  * Copyright (C) 2005 Johan Enell
    12  *
    13  * This program is free software; you can redistribute it and/or
    14  * modify it under the terms of the GNU General Public License
    15  * as published by the Free Software Foundation; either version 2
    16  * of the License, or (at your option) any later version.
    17  *
    18  * This program is distributed in the hope that it will be useful,
    19  * but WITHOUT ANY WARRANTY; without even the implied warranty of
    20  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    21  * GNU General Public License for more details.
    22  *
    23  * You should have received a copy of the GNU General Public License
    24  * along with this program; if not, write to the Free Software
    25  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
    26  */
    2733
    2834public class Main
  • plugins/base1/se.lu.onk.Center/trunk/src/center/Spot.java

    r149 r875  
    11/*
    2  * plugins
     2 * $Id$
     3 *
    34 * Copyright (C) 2006 Johan Enell
    4  *
    5  * This program is free software; you can redistribute it and/or
    6  * modify it under the terms of the GNU General Public License
    7  * as published by the Free Software Foundation; either version 2
    8  * of the License, or (at your option) any later version.
    9  *
    10  * This program is distributed in the hope that it will be useful,
    11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
    12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    13  * GNU General Public License for more details.
    14  *
     5 * Copyright (C) 2008 Jari Häkkinen
     6
     7 * This file is part of the se.lu.onk.Center plug-in for
     8 * BASE. Available at http://baseplugins.thep.lu.se/ and BASE web site
     9 * is http://base.thep.lu.se
     10
     11 * This is free software; you can redistribute it and/or modify it
     12 * under the terms of the GNU General Public License as published by
     13 * the Free Software Foundation; either version 3 of the License, or
     14 * (at your option) any later version.
     15
     16 * The software is distributed in the hope that it will be useful, but
     17 * WITHOUT ANY WARRANTY; without even the implied warranty of
     18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
     19 * General Public License for more details.
     20
    1521 * You should have received a copy of the GNU General Public License
    16  * along with this program; if not, write to the Free Software
    17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
     22 * along with this software. If not, see <http://www.gnu.org/licenses/>.
    1823 */
     24
    1925package center;
    2026
  • plugins/base1/se.lu.onk/trunk/build.xml

    r776 r875  
    2424  <property name="virtualarray.src" location="VirtualArray/src" />
    2525  <property name="qpackage.src" location="QPackage/src" />
    26   <property name="center.src" location="Center/src" />
    2726  <property name="normalization.src" location="Normalization/src" />
    2827  <property name="null.src" location="NullPlugin/src" />
     
    3736  <property name="virtualarray.bin" location="${bin}/VirtualArray" />
    3837  <property name="qpackage.bin" location="${bin}/QPackage" />
    39   <property name="center.bin" location="${bin}/Center" />
    4038  <property name="normalization.bin" location="${bin}/Normalization" />
    4139  <property name="null.bin" location="${bin}/NullPlugin" />
     
    6563    <ant target="virtualarray.compile" />
    6664    <ant target="qpackage.compile" />
    67     <ant target="center.compile" />
    6865    <ant target="normalization.compile" />
    6966    <ant target="smooth.compile" />
     
    115112 
    116113  <!-- - - - - - - - - - - - - - - - - -
    117       target: center.compile
    118      - - - - - - - - - - - - - - - - - -->
    119     <target name="center.compile" depends="basefile.compile">
    120       <mkdir dir="${center.bin}"/>
    121       <javac
    122         srcdir="${center.src}"
    123         destdir="${center.bin}"
    124         classpath="${basefile.bin}"
    125         debug="true"
    126         deprecation="true"
    127         encoding="ISO-8859-1"
    128       />
    129     </target>
    130  
    131   <!-- - - - - - - - - - - - - - - - - -
    132114      target: normalization.compile
    133115     - - - - - - - - - - - - - - - - - -->
     
    235217  <target name="dist"
    236218    depends="virtualarray.dist,
    237       qpackage.dist, center.dist, lowess.dist, smooth.dist"
     219      qpackage.dist, lowess.dist, smooth.dist"
    238220    description="--> Creates a ditributable gzipfile for each package">
    239221  </target>
     
    268250        <manifest>
    269251          <attribute name="Built-By" value="${user.name}"/>
    270         </manifest>
    271     </jar>
    272   </target>
    273  
    274   <!-- - - - - - - - - - - - - - - - - -
    275       target: center.dist                     
    276      - - - - - - - - - - - - - - - - - -->
    277   <target name="center.dist" depends="center.compile">
    278     <mkdir dir="${dist}" />
    279     <jar destfile="${dist}/center.jar">
    280       <fileset dir="${basefile.src}" />
    281       <fileset dir="${basefile.bin}" />
    282       <fileset dir="${center.bin}" />
    283       <fileset dir="${center.src}" />
    284         <manifest>
    285           <attribute name="Built-By" value="${user.name}"/>
    286           <attribute name="Main-Class" value="center.Center"/>
    287252        </manifest>
    288253    </jar>
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