[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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