[Git][java-team/cdk][master] 4 commits: Manpages are not used any more

Andreas Tille gitlab at salsa.debian.org
Tue Nov 19 17:28:49 GMT 2019



Andreas Tille pushed to branch master at Debian Java Maintainers / cdk


Commits:
2d755e68 by Andreas Tille at 2019-11-19T16:56:21Z
Manpages are not used any more

- - - - -
9de14645 by Andreas Tille at 2019-11-19T16:57:13Z
Ant is not used any more

- - - - -
ef9dad96 by Andreas Tille at 2019-11-19T17:00:07Z
Drop old file that was used by ant

- - - - -
8c07b71f by Andreas Tille at 2019-11-19T17:28:24Z
Add templates for reference and edam ontology for Egon to be continued

- - - - -


14 changed files:

- − debian/ant.properties
- − debian/cdk-manpages/cdk-dbadmin.xml
- − debian/cdk-manpages/cdk-download.xml
- − debian/cdk-manpages/cdk-fileconvert.xml
- − debian/cdk-manpages/cdk-fingerprinter.xml
- − debian/cdk-manpages/cdk-guessformat.xml
- − debian/cdk-manpages/cdk-iupacname.xml
- − debian/cdk-manpages/cdk-substructure.xml
- − debian/cdk-manpages/cdk-test.xml
- − debian/cdk-manpages/cdk-validate.xml
- − debian/cdk-manpages/cdk-view.xml
- − debian/compile.excludes
- + debian/upstream/edam_
- + debian/upstream/metadata_


Changes:

=====================================
debian/ant.properties deleted
=====================================
@@ -1,10 +0,0 @@
-jar=/usr/share/java
-lib=/usr/share/java
-devellib=/usr/share/java
-nowarn=on
-
-# CDK 1.0.x does not compile against Weka 2.5.7, see SF bug report #1895295
-weka.jar=skip
-
-# CDK 1.0.x is not tested againt Batik 1.7, see SF feature request #1895300
-compile.batik=false


=====================================
debian/cdk-manpages/cdk-dbadmin.xml deleted
=====================================
@@ -1,123 +0,0 @@
-<refentry id="cdk-dbadmin">
-
-  <refmeta>
-    <refentrytitle>cdk-dbadmin</refentrytitle>
-    <manvolnum>1</manvolnum>
-  </refmeta>
-
-  <refnamediv>
-    <refname>cdk-dbadmin</refname>
-    <refpurpose>administrate chemical database</refpurpose>
-  </refnamediv>
-
-  <refsynopsisdiv>
-    <cmdsynopsis>
-      <command>cdk-dbadmin</command>
-      <arg>--useHost [hostname]</arg>
-      <arg>--useDatabase [database name]</arg>
-      <arg>--useDriver [mysql|postgresql]</arg>
-      <arg>--username [username]</arg>
-      <arg>--passwd [pwd]</arg>
-      <arg>--createDefaultTables</arg>
-      <arg>--listTables</arg>
-      <arg>--deleteTables</arg>
-    </cmdsynopsis>
-  </refsynopsisdiv>
-
-  <refsect1>
-    <title>OPTIONS</title>
-    <variablelist>
-      <varlistentry>
-        <term>--useHost [hostname]</term>
-        <listitem>
-          <para>sets the hostname of the machine on which the database is run</para>
-        </listitem>
-      </varlistentry>
-      <varlistentry>
-        <term>--useDatabase [database name]</term>
-        <listitem>
-          <para>sets the name of the database in which the tables are stored</para>
-        </listitem>
-      </varlistentry>
-      <varlistentry>
-        <term>--useDriver [mysql|postgresql]</term>
-        <listitem>
-          <para>sets the JDBC driver used to access the database (Only MySQL is currently working.)</para>
-        </listitem>
-      </varlistentry>
-      <varlistentry>
-        <term>--username [username]</term>
-        <listitem>
-          <para>sets the username of the account with which the database can be accessed</para>
-        </listitem>
-      </varlistentry>
-      <varlistentry>
-        <term>--passwd [pwd]</term>
-        <listitem>
-          <para>sets the password for the account with which the database can be accessed</para>
-        </listitem>
-      </varlistentry>
-      <varlistentry>
-        <term>--createDefaultTables</term>
-        <listitem>
-          <para>create the default tables in the chemical database</para>
-        </listitem>
-      </varlistentry>
-      <varlistentry>
-        <term>--listTables</term>
-        <listitem>
-          <para>lists all information on the tables in the chemical database</para>
-        </listitem>
-      </varlistentry>
-      <varlistentry>
-        <term>--deleteTables</term>
-        <listitem>
-          <para>deletes all tables from the chemical database</para>
-        </listitem>
-      </varlistentry>
-    </variablelist>
-  </refsect1>
-
-  <refsect1>
-    <title>DESCRIPTION</title>
-    <para>
-      <command>cdk-dbadmin</command> is used to prepare and delete tables from
-	  a chemical database.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>VERSION</title>
-    <para>
-      $Id: cdk-dbadmin.xml,v 1.1 2002/08/31 14:43:07 egonw Exp $
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>COPYRIGHT</title>
-    <para>
-      Copyright (C) 2001-2002 The CDK Project
-    </para>
-    <para>
-This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or
-(at your option) any later version.
-    </para>
-    <para>
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>AUTHOR</title>
-    <para>
-      Egon Willighagen <email>egonw at sci.kun.nl</email>
-    </para>
-  </refsect1>
-
-</refentry>
-


=====================================
debian/cdk-manpages/cdk-download.xml deleted
=====================================
@@ -1,73 +0,0 @@
-<refentry id="cdk-download">
-
-  <refmeta>
-    <refentrytitle>cdk-download</refentrytitle>
-    <manvolnum>1</manvolnum>
-  </refmeta>
-
-  <refnamediv>
-    <refname>cdk-download</refname>
-    <refpurpose>download chemical information from the internet</refpurpose>
-  </refnamediv>
-
-  <refsynopsisdiv>
-    <cmdsynopsis>
-      <command>cdk-download</command>
-      <arg>CAS NUMBER</arg>
-    </cmdsynopsis>
-  </refsynopsisdiv>
-
-  <refsect1>
-    <title>OPTIONS</title>
-    <variablelist>
-      <varlistentry>
-        <term>CAS NUMBER</term>
-        <listitem>
-          <para>CAS number of the structure you want to download</para>
-        </listitem>
-      </varlistentry>
-    </variablelist>
-  </refsect1>
-
-  <refsect1>
-    <title>DESCRIPTION</title>
-    <para>
-      <command>cdk-download</command> retrieves the 2D coordiante file
-      of the requested compound.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>VERSION</title>
-    <para>
-      $Id: cdk-download.xml,v 1.1 2002/08/31 14:43:07 egonw Exp $
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>COPYRIGHT</title>
-    <para>
-      Copyright (C) 2002 The CDK Project
-    </para>
-    <para>
-This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or
-(at your option) any later version.
-    </para>
-    <para>
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>AUTHOR</title>
-    <para>
-      Egon Willighagen <email>egonw at sci.kun.nl</email>
-    </para>
-  </refsect1>
-
-</refentry>


=====================================
debian/cdk-manpages/cdk-fileconvert.xml deleted
=====================================
@@ -1,111 +0,0 @@
-<refentry id="cdk-fileconvert">
-
-  <refmeta>
-    <refentrytitle>cdk-fileconvert</refentrytitle>
-    <manvolnum>1</manvolnum>
-  </refmeta>
-
-  <refnamediv>
-    <refname>cdk-fileconvert</refname>
-    <refpurpose>converts one or more files to another format</refpurpose>
-  </refnamediv>
-
-  <refsynopsisdiv>
-    <cmdsynopsis>
-      <command>cdk-fileconvert</command>
-      <arg>OPTIONS</arg>
-      <arg>input files</arg>
-    </cmdsynopsis>
-  </refsynopsisdiv>
-
-  <refsect1>
-    <title>OPTIONS</title>
-    <variablelist>
-      <varlistentry>
-        <term>-h/--help</term>
-        <listitem>
-          <para>Print the help</para>
-        </listitem>
-      </varlistentry>
-      <varlistentry>
-        <term>-o[format]/--outputformat:[format]</term>
-        <listitem>
-          <para>Defines the output format to use. (See below for a list of
-            possible formats)</para>
-        </listitem>
-      </varlistentry>
-      <varlistentry>
-        <term>--quesion:[none|fewest|some|all]</term>
-        <listitem>
-          <para>Defines the level of customization of the file IO.</para>
-        </listitem>
-      </varlistentry>
-      <varlistentry>
-        <term>--listoptions:[format]</term>
-        <listitem>
-          <para>Lists the options of customization of the given file format.</para>
-        </listitem>
-      </varlistentry>
-      <varlistentry>
-        <term>--properties:[format]</term>
-        <listitem>
-          <para>Use a Java properties file to define the file IO option
-            values.</para>
-        </listitem>
-      </varlistentry>
-    </variablelist>
-  </refsect1>
-
-  <refsect1>
-    <title>DESCRIPTION</title>
-    <para>
-      <command>cdk-fileconvert</command> reads a input file and converts
-      it to a new file with an other format.
-      Supported input formats are
-      <acronym>CML</acronym>,
-      <acronym>MDL Molfile</acronym>,
-      <acronym>PDB</acronym>,
-      <acronym>PMP</acronym>,
-      <acronym>SHELX</acronym> and
-      <acronym>XYZ</acronym>. The input format is automatically detected.
-    </para>
-    <para>
-      Supported output formats are: cml, gin, mol, pdb, shelx, smi, svg and
-      xyz.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>VERSION</title>
-    <para>
-      $Id: cdk-fileconvert.xml,v 1.3 2003/07/03 08:48:56 egonw Exp $
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>COPYRIGHT</title>
-    <para>
-      Copyright (C) 2001-2003 The CDK Project
-    </para>
-    <para>
-This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or
-(at your option) any later version.
-    </para>
-    <para>
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>AUTHOR</title>
-    <para>
-      Egon Willighagen <email>egonw at sci.kun.nl</email>
-    </para>
-  </refsect1>
-
-</refentry>


=====================================
debian/cdk-manpages/cdk-fingerprinter.xml deleted
=====================================
@@ -1,61 +0,0 @@
-<refentry id="cdk-fingerprinter">
-
-  <refmeta>
-    <refentrytitle>cdk-fingerprinter</refentrytitle>
-    <manvolnum>1</manvolnum>
-  </refmeta>
-
-  <refnamediv>
-    <refname>cdk-fingerprinter</refname>
-    <refpurpose>generates CDK fingerprints for the given molecules</refpurpose>
-  </refnamediv>
-
-  <refsynopsisdiv>
-    <cmdsynopsis>
-      <command>cdk-fingerprinter</command>
-      <arg>file</arg>
-    </cmdsynopsis>
-  </refsynopsisdiv>
-
-  <refsect1>
-    <title>DESCRIPTION</title>
-    <para>
-      <command>cdk-fingerprinter</command> reads one or more input files
-      and generates CDK fingerprints for all the molecules it finds.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>VERSION</title>
-    <para>
-      $Id: cdk-fingerprinter.xml,v 1.1 2004/01/12 11:50:58 egonw Exp $
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>COPYRIGHT</title>
-    <para>
-      Copyright (C) 2003-2004 The CDK Project
-    </para>
-    <para>
-This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or
-(at your option) any later version.
-    </para>
-    <para>
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>AUTHOR</title>
-    <para>
-      Egon Willighagen <email>egonw at sci.kun.nl</email>
-    </para>
-  </refsect1>
-
-</refentry>


=====================================
debian/cdk-manpages/cdk-guessformat.xml deleted
=====================================
@@ -1,61 +0,0 @@
-<refentry id="cdk-guessformat">
-
-  <refmeta>
-    <refentrytitle>cdk-guessformat</refentrytitle>
-    <manvolnum>1</manvolnum>
-  </refmeta>
-
-  <refnamediv>
-    <refname>cdk-guessformat</refname>
-    <refpurpose>guesses the file format of a file</refpurpose>
-  </refnamediv>
-
-  <refsynopsisdiv>
-    <cmdsynopsis>
-      <command>cdk-guessformat</command>
-      <arg>file</arg>
-    </cmdsynopsis>
-  </refsynopsisdiv>
-
-  <refsect1>
-    <title>DESCRIPTION</title>
-    <para>
-      <command>cdk-guessformat</command> reads an input file and tries
-      to determine the file format.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>VERSION</title>
-    <para>
-      $Id: cdk-guessformat.xml,v 1.1 2003/05/27 14:33:52 egonw Exp $
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>COPYRIGHT</title>
-    <para>
-      Copyright (C) 2003 The CDK Project
-    </para>
-    <para>
-This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or
-(at your option) any later version.
-    </para>
-    <para>
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>AUTHOR</title>
-    <para>
-      Egon Willighagen <email>egonw at sci.kun.nl</email>
-    </para>
-  </refsect1>
-
-</refentry>


=====================================
debian/cdk-manpages/cdk-iupacname.xml deleted
=====================================
@@ -1,67 +0,0 @@
-<refentry id="cdk-iupacname">
-
-  <refmeta>
-    <refentrytitle>cdk-iupacname</refentrytitle>
-    <manvolnum>1</manvolnum>
-  </refmeta>
-
-  <refnamediv>
-    <refname>cdk-iupacname</refname>
-    <refpurpose>generates the IUPAC name for the given molecule</refpurpose>
-  </refnamediv>
-
-  <refsynopsisdiv>
-    <cmdsynopsis>
-      <command>cdk-iupacname</command>
-      <arg>file</arg>
-    </cmdsynopsis>
-  </refsynopsisdiv>
-
-  <refsect1>
-    <title>DESCRIPTION</title>
-    <para>
-      <command>cdk-iupacname</command> reads an input file and tries
-      to generate a IUPAC name for this structure. Currently only
-      a few IUPAC rules are implemented, but simple alkane structures
-      can be named.
-    </para>
-    <para>
-      The output language can be set using <arg>--dutch</arg> or
-      <arg>--german</arg>.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>VERSION</title>
-    <para>
-      $Id: cdk-iupacname.xml,v 1.1 2003/08/15 08:13:40 egonw Exp $
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>COPYRIGHT</title>
-    <para>
-      Copyright (C) 2003 The CDK Project
-    </para>
-    <para>
-This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or
-(at your option) any later version.
-    </para>
-    <para>
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>AUTHOR</title>
-    <para>
-      Egon Willighagen <email>egonw at sci.kun.nl</email>
-    </para>
-  </refsect1>
-
-</refentry>


=====================================
debian/cdk-manpages/cdk-substructure.xml deleted
=====================================
@@ -1,64 +0,0 @@
-<refentry id="cdk-substructure">
-
-  <refmeta>
-    <refentrytitle>cdk-substructure</refentrytitle>
-    <manvolnum>1</manvolnum>
-  </refmeta>
-
-  <refnamediv>
-    <refname>cdk-substructure</refname>
-    <refpurpose>searches through a set of files to find a given
-      substructure</refpurpose>
-  </refnamediv>
-
-  <refsynopsisdiv>
-    <cmdsynopsis>
-      <command>cdk-substructure</command>
-      <arg>SMILES</arg>
-      <arg>files</arg>
-    </cmdsynopsis>
-  </refsynopsisdiv>
-
-  <refsect1>
-    <title>DESCRIPTION</title>
-    <para>
-      <command>cdk-substructure</command> reads one or more an input files
-      and determines wether the structure given by the SMILES (after removal
-      of hydrogens) is a substructure of the input file.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>VERSION</title>
-    <para>
-      $Id: cdk-substructure.xml,v 1.1 2003/08/15 08:13:40 egonw Exp $
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>COPYRIGHT</title>
-    <para>
-      Copyright (C) 2003 The CDK Project
-    </para>
-    <para>
-This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or
-(at your option) any later version.
-    </para>
-    <para>
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>AUTHOR</title>
-    <para>
-      Egon Willighagen <email>egonw at sci.kun.nl</email>
-    </para>
-  </refsect1>
-
-</refentry>


=====================================
debian/cdk-manpages/cdk-test.xml deleted
=====================================
@@ -1,61 +0,0 @@
-<refentry id="cdk-test">
-
-  <refmeta>
-    <refentrytitle>cdk-test</refentrytitle>
-    <manvolnum>1</manvolnum>
-  </refmeta>
-
-  <refnamediv>
-    <refname>cdk-test</refname>
-    <refpurpose>perform JUnit tests on CDK classes</refpurpose>
-  </refnamediv>
-
-  <refsynopsisdiv>
-    <cmdsynopsis>
-      <command>cdk-test</command> <arg>JUnit test</arg>
-    </cmdsynopsis>
-  </refsynopsisdiv>
-
-  <refsect1>
-    <title>DESCRIPTION</title>
-    <para>
-      <command>cdk-test</command> opens up a JUnit window for testing
-      CDK classes. The optional argument is used to set the JUnit test
-      that is loaded, e.g. org.openscience.cdk.test.CDKTests.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>VERSION</title>
-    <para>
-      $Id: cdk-test.xml,v 1.1 2003/01/01 16:42:09 egonw Exp $
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>COPYRIGHT</title>
-    <para>
-      Copyright (C) 2001-2003 The CDK Project
-    </para>
-    <para>
-This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or
-(at your option) any later version.
-    </para>
-    <para>
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>AUTHOR</title>
-    <para>
-      Egon Willighagen <email>egonw at sci.kun.nl</email>
-    </para>
-  </refsect1>
-
-</refentry>


=====================================
debian/cdk-manpages/cdk-validate.xml deleted
=====================================
@@ -1,62 +0,0 @@
-<refentry id="cdk-validate">
-
-  <refmeta>
-    <refentrytitle>cdk-validate</refentrytitle>
-    <manvolnum>1</manvolnum>
-  </refmeta>
-
-  <refnamediv>
-    <refname>cdk-validate</refname>
-    <refpurpose>checks the chemical content of a file</refpurpose>
-  </refnamediv>
-
-  <refsynopsisdiv>
-    <cmdsynopsis>
-      <command>cdk-validate</command>
-      <arg>file</arg>
-    </cmdsynopsis>
-  </refsynopsisdiv>
-
-  <refsect1>
-    <title>DESCRIPTION</title>
-    <para>
-      <command>cdk-validate</command> reads an input file and checks wether
-      the chemistry that is described in that file is correct, or might contain
-      problems.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>VERSION</title>
-    <para>
-      $Id: cdk-validate.xml,v 1.1 2003/07/14 20:57:59 egonw Exp $
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>COPYRIGHT</title>
-    <para>
-      Copyright (C) 2003 The CDK Project
-    </para>
-    <para>
-This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or
-(at your option) any later version.
-    </para>
-    <para>
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>AUTHOR</title>
-    <para>
-      Egon Willighagen <email>egonw at sci.kun.nl</email>
-    </para>
-  </refsect1>
-
-</refentry>


=====================================
debian/cdk-manpages/cdk-view.xml deleted
=====================================
@@ -1,92 +0,0 @@
-<refentry id="cdk-view">
-
-  <refmeta>
-    <refentrytitle>cdk-view</refentrytitle>
-    <manvolnum>1</manvolnum>
-  </refmeta>
-
-  <refnamediv>
-    <refname>cdk-view</refname>
-    <refpurpose>view content of chemical file</refpurpose>
-  </refnamediv>
-
-  <refsynopsisdiv>
-    <cmdsynopsis>
-      <command>cdk-view</command> <arg>--nojava3d</arg> <arg>--no3d</arg> <arg>--useJmol</arg> <arg>file.xml</arg>
-      <command>cdk-view</command> <arg>--smiles</arg> <arg>SMILES</arg>
-    </cmdsynopsis>
-  </refsynopsisdiv>
-
-  <refsect1>
-    <title>OPTIONS</title>
-    <variablelist>
-      <varlistentry>
-        <term>--nojava3d</term>
-        <listitem>
-          <para>do not try to use Java3D for viewing 3D coordinates</para>
-        </listitem>
-      </varlistentry>
-      <varlistentry>
-        <term>--no3d</term>
-        <listitem>
-          <para>do not view 3D coordinates</para>
-        </listitem>
-      </varlistentry>
-      <varlistentry>
-        <term>--smiles</term>
-        <listitem>
-          <para>show a 2D representation of the SMILES</para>
-        </listitem>
-      </varlistentry>
-      <varlistentry>
-        <term>--useTree</term>
-        <listitem>
-          <para>shows a ChemObjectTree of the loaded file</para>
-        </listitem>
-      </varlistentry>
-    </variablelist>
-  </refsect1>
-
-  <refsect1>
-    <title>DESCRIPTION</title>
-    <para>
-      <command>cdk-view</command> displays to content of the file
-      <filename>file.xml</filename> with the format CML, IChI, MDLMol,
-      PDB and XYZ.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>VERSION</title>
-    <para>
-      $Id: cdk-view.xml,v 1.3 2003/01/01 16:42:09 egonw Exp $
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>COPYRIGHT</title>
-    <para>
-      Copyright (C) 2001-2002 The CDK Project
-    </para>
-    <para>
-This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or
-(at your option) any later version.
-    </para>
-    <para>
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-    </para>
-  </refsect1>
-
-  <refsect1>
-    <title>AUTHOR</title>
-    <para>
-      Egon Willighagen <email>egonw at sci.kun.nl</email>
-    </para>
-  </refsect1>
-
-</refentry>


=====================================
debian/compile.excludes deleted
=====================================
@@ -1,11 +0,0 @@
-**/Convertor.java
-**/CMLWriter.java
-**/RssWriter.java
-**/PDBAtomCustomizer.java
-**/MDMoleculeCustomizer.java
-**/R/RModel.java
-**/CNNClassificationModel.java
-**/R/CNNRegressionModel.java
-**/R/LinearRegressionModel.java
-**/PLSRegressionModel.java
-**/QSARCustomizer.java


=====================================
debian/upstream/edam_
=====================================
@@ -0,0 +1,29 @@
+---
+ontology: EDAM (1.16)
+topic:
+  - Sequence analysis
+scopes:
+  - name: summary
+    function:
+      - Multiple sequence alignment
+    input:
+      - data: Sequence
+        formats:
+          - EMBL format
+          - FASTA
+          - GCG
+          - GenBank format
+          - nbrf/pir
+          - PHYLIP format
+          - UniProtKB format
+      - data: Gene tree
+    output:
+      - data: Alignment
+        formats:
+          - FASTA-aln
+          - PHYLIP format
+          - selex
+          - Stockholm format
+          - Vienna local RNA secondary structure format
+      - data: Phylogenetic tree
+        formats: [Phylip tree format]


=====================================
debian/upstream/metadata_
=====================================
@@ -0,0 +1,12 @@
+Reference:
+  Author: 
+  Title: 
+  Journal: 
+  Year: 
+  Volume: 
+  Number: 
+  Pages: 
+  DOI: 
+  PMID:
+  URL: 
+  eprint: 



View it on GitLab: https://salsa.debian.org/java-team/cdk/compare/1c4ac36f122b08b13711f2de7c671e961e21a853...8c07b71f62ab375e8d37bd501f05d48279e16a69

-- 
View it on GitLab: https://salsa.debian.org/java-team/cdk/compare/1c4ac36f122b08b13711f2de7c671e961e21a853...8c07b71f62ab375e8d37bd501f05d48279e16a69
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