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johnmayegonw
johnmay
authored and
egonw
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First pass at moving from JNA to JNI inchi - some tests need adjusting.
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-458
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10 files changed

+527
-458
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‎storage/inchi/pom.xml

Lines changed: 8 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -3,30 +3,25 @@
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<artifactId>cdk-storage</artifactId>
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<groupId>org.openscience.cdk</groupId>
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<version>2.7-SNAPSHOT</version>
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</parent>
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<artifactId>cdk-inchi</artifactId>
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<name>cdk-inchi</name>
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<dependencies>
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<dependency>
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<groupId>javax.vecmath</groupId>
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<artifactId>vecmath</artifactId>
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</dependency>
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<dependency>
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<groupId>net.sf.jni-inchi</groupId>
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<artifactId>jni-inchi</artifactId>
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<exclusions>
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<exclusion>
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<groupId>log4j</groupId>
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<artifactId>log4j</artifactId>
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</exclusion>
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</exclusions>
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<groupId>io.github.dan2097</groupId>
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<artifactId>jna-inchi-core</artifactId>
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<version>1.0.1</version>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
@@ -95,7 +90,7 @@
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<artifactId>cdk-data</artifactId>
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<version>${project.parent.version}</version>
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<type>test-jar</type>
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<scope>test</scope>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>${project.groupId}</groupId>
@@ -108,7 +103,7 @@
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<artifactId>cdk-test</artifactId>
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<version>${project.parent.version}</version>
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<type>test-jar</type>
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<scope>test</scope>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>${project.groupId}</groupId>
@@ -127,7 +122,7 @@
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<artifactId>cdk-testdata</artifactId>
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<version>${project.parent.version}</version>
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<type>test-jar</type>
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<scope>test</scope>
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<scope>test</scope>
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</dependency>
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</dependencies>
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‎storage/inchi/src/main/java/net/sf/jniinchi/INCHI_OPTION.java

Lines changed: 102 additions & 0 deletions
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@@ -0,0 +1,102 @@
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/*
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* Copyright (C) 2021 John Mayfield
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*
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* Contact: cdk-devel@lists.sourceforge.net
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*
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public License
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* as published by the Free Software Foundation; either version 2.1
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* of the License, or (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
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*/
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package net.sf.jniinchi;
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import io.github.dan2097.jnainchi.InchiFlag;
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/**
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* This class provides backwards compatibility of JNA-INCHI with JNI-INCHI, this enum was exposed in the CDK API.
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* @author John Mayfield
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*/
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public enum INCHI_OPTION {
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SUCF,
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ChiralFlagON,
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ChiralFlagOFF,
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SNon,
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SAbs,
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SRel,
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SRac,
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SUU,
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NEWPS,
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RecMet,
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FixedH,
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AuxNone,
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NoADP,
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Compress,
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DoNotAddH,
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Wnumber,
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OutputSDF,
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WarnOnEmptyStructure,
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FixSp3Bug,
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FB,
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SPXYZ,
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SAsXYZ;
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public static INCHI_OPTION wrap(InchiFlag flag) {
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switch (flag) {
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case SUCF: return SUCF;
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case ChiralFlagON: return ChiralFlagON;
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case ChiralFlagOFF: return ChiralFlagOFF;
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case SNon: return SNon;
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case SRel: return SRel;
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case SRac: return SRac;
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case SUU: return SUU;
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case RecMet: return RecMet;
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case FixedH: return FixedH;
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case AuxNone: return AuxNone;
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case DoNotAddH: return DoNotAddH;
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case WarnOnEmptyStructure: return WarnOnEmptyStructure;
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default: throw new IllegalArgumentException(flag + " not supported?");
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}
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}
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public static InchiFlag wrap(INCHI_OPTION flag) {
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switch (flag) {
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case SUCF: return InchiFlag.SUCF;
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case ChiralFlagON: return InchiFlag.ChiralFlagON;
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case ChiralFlagOFF: return InchiFlag.ChiralFlagOFF;
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case SNon: return InchiFlag.SNon;
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case SRel: return InchiFlag.SRel;
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case SRac: return InchiFlag.SRac;
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case SUU: return InchiFlag.SUU;
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case RecMet: return InchiFlag.RecMet;
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case FixedH: return InchiFlag.FixedH;
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case AuxNone: return InchiFlag.AuxNone;
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case DoNotAddH: return InchiFlag.DoNotAddH;
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case WarnOnEmptyStructure: return InchiFlag.WarnOnEmptyStructure;
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default:
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System.err.println("Unsupported flag: " + flag);
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return null;
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}
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// case SAbs: return SAbs;
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// case NEWPS: return NEWPS;
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// case NoADP: return NoADP;
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// case Compress: return Compress;
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// case Wnumber: return Wnumber;
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// case OutputSDF: return OutputSDF;
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// case FixSp3Bug: return FixSp3Bug;
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// case FB: return FB;
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// case SPXYZ: return SPXYZ;
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// case SAsXYZ: return SAsXYZ;
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}
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}

‎storage/inchi/src/main/java/net/sf/jniinchi/INCHI_RET.java

Lines changed: 48 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,48 @@
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/*
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* Copyright (C) 2021 John Mayfield
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*
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* Contact: cdk-devel@lists.sourceforge.net
5+
*
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* This program is free software; you can redistribute it and/or
7+
* modify it under the terms of the GNU Lesser General Public License
8+
* as published by the Free Software Foundation; either version 2.1
9+
* of the License, or (at your option) any later version.
10+
*
11+
* This program is distributed in the hope that it will be useful,
12+
* but WITHOUT ANY WARRANTY; without even the implied warranty of
13+
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14+
* GNU Lesser General Public License for more details.
15+
*
16+
* You should have received a copy of the GNU Lesser General Public License
17+
* along with this program; if not, write to the Free Software
18+
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
19+
*/
20+
21+
package net.sf.jniinchi;
22+
23+
import io.github.dan2097.jnainchi.InchiStatus;
24+
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/**
26+
* This class provides backwards compatibility of JNA-INCHI with JNI-INCHI, this enum was exposed in the CDK API.
27+
* @author John Mayfield
28+
*/
29+
public enum INCHI_RET {
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SKIP,
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EOF,
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OKAY,
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WARNING,
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ERROR,
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FATAL,
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UNKNOWN,
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BUSY;
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39+
public static INCHI_RET wrap(InchiStatus status) {
40+
switch (status) {
41+
case SUCCESS: return INCHI_RET.OKAY;
42+
case WARNING: return INCHI_RET.WARNING;
43+
case ERROR: return INCHI_RET.ERROR;
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default:
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throw new IllegalArgumentException("Unexpected status!");
46+
}
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}
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}

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