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First pass at moving from JNA to JNI inchi - some tests need adjusting.
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102 changes: 102 additions & 0 deletions
102
storage/inchi/src/main/java/net/sf/jniinchi/INCHI_OPTION.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,102 @@ | ||
| /* | ||
| * Copyright (C) 2021 John Mayfield | ||
| * | ||
| * Contact: cdk-devel@lists.sourceforge.net | ||
| * | ||
| * This program is free software; you can redistribute it and/or | ||
| * modify it under the terms of the GNU Lesser General Public License | ||
| * as published by the Free Software Foundation; either version 2.1 | ||
| * of the License, or (at your option) any later version. | ||
| * | ||
| * 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 Lesser General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Lesser General Public License | ||
| * along with this program; if not, write to the Free Software | ||
| * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. | ||
| */ | ||
|
|
||
| package net.sf.jniinchi; | ||
|
|
||
| import io.github.dan2097.jnainchi.InchiFlag; | ||
|
|
||
| /** | ||
| * This class provides backwards compatibility of JNA-INCHI with JNI-INCHI, this enum was exposed in the CDK API. | ||
| * @author John Mayfield | ||
| */ | ||
| public enum INCHI_OPTION { | ||
| SUCF, | ||
| ChiralFlagON, | ||
| ChiralFlagOFF, | ||
| SNon, | ||
| SAbs, | ||
| SRel, | ||
| SRac, | ||
| SUU, | ||
| NEWPS, | ||
| RecMet, | ||
| FixedH, | ||
| AuxNone, | ||
| NoADP, | ||
| Compress, | ||
| DoNotAddH, | ||
| Wnumber, | ||
| OutputSDF, | ||
| WarnOnEmptyStructure, | ||
| FixSp3Bug, | ||
| FB, | ||
| SPXYZ, | ||
| SAsXYZ; | ||
|
|
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| public static INCHI_OPTION wrap(InchiFlag flag) { | ||
| switch (flag) { | ||
| case SUCF: return SUCF; | ||
| case ChiralFlagON: return ChiralFlagON; | ||
| case ChiralFlagOFF: return ChiralFlagOFF; | ||
| case SNon: return SNon; | ||
| case SRel: return SRel; | ||
| case SRac: return SRac; | ||
| case SUU: return SUU; | ||
| case RecMet: return RecMet; | ||
| case FixedH: return FixedH; | ||
| case AuxNone: return AuxNone; | ||
| case DoNotAddH: return DoNotAddH; | ||
| case WarnOnEmptyStructure: return WarnOnEmptyStructure; | ||
|
|
||
| default: throw new IllegalArgumentException(flag + " not supported?"); | ||
| } | ||
| } | ||
|
|
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| public static InchiFlag wrap(INCHI_OPTION flag) { | ||
| switch (flag) { | ||
| case SUCF: return InchiFlag.SUCF; | ||
| case ChiralFlagON: return InchiFlag.ChiralFlagON; | ||
| case ChiralFlagOFF: return InchiFlag.ChiralFlagOFF; | ||
| case SNon: return InchiFlag.SNon; | ||
| case SRel: return InchiFlag.SRel; | ||
| case SRac: return InchiFlag.SRac; | ||
| case SUU: return InchiFlag.SUU; | ||
| case RecMet: return InchiFlag.RecMet; | ||
| case FixedH: return InchiFlag.FixedH; | ||
| case AuxNone: return InchiFlag.AuxNone; | ||
| case DoNotAddH: return InchiFlag.DoNotAddH; | ||
| case WarnOnEmptyStructure: return InchiFlag.WarnOnEmptyStructure; | ||
| default: | ||
| System.err.println("Unsupported flag: " + flag); | ||
| return null; | ||
| } | ||
|
|
||
| // case SAbs: return SAbs; | ||
| // case NEWPS: return NEWPS; | ||
| // case NoADP: return NoADP; | ||
| // case Compress: return Compress; | ||
| // case Wnumber: return Wnumber; | ||
| // case OutputSDF: return OutputSDF; | ||
| // case FixSp3Bug: return FixSp3Bug; | ||
| // case FB: return FB; | ||
| // case SPXYZ: return SPXYZ; | ||
| // case SAsXYZ: return SAsXYZ; | ||
| } | ||
| } |
48 changes: 48 additions & 0 deletions
48
storage/inchi/src/main/java/net/sf/jniinchi/INCHI_RET.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| /* | ||
| * Copyright (C) 2021 John Mayfield | ||
| * | ||
| * Contact: cdk-devel@lists.sourceforge.net | ||
| * | ||
| * This program is free software; you can redistribute it and/or | ||
| * modify it under the terms of the GNU Lesser General Public License | ||
| * as published by the Free Software Foundation; either version 2.1 | ||
| * of the License, or (at your option) any later version. | ||
| * | ||
| * 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 Lesser General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Lesser General Public License | ||
| * along with this program; if not, write to the Free Software | ||
| * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. | ||
| */ | ||
|
|
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| package net.sf.jniinchi; | ||
|
|
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| import io.github.dan2097.jnainchi.InchiStatus; | ||
|
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| /** | ||
| * This class provides backwards compatibility of JNA-INCHI with JNI-INCHI, this enum was exposed in the CDK API. | ||
| * @author John Mayfield | ||
| */ | ||
| public enum INCHI_RET { | ||
| SKIP, | ||
| EOF, | ||
| OKAY, | ||
| WARNING, | ||
| ERROR, | ||
| FATAL, | ||
| UNKNOWN, | ||
| BUSY; | ||
|
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| public static INCHI_RET wrap(InchiStatus status) { | ||
| switch (status) { | ||
| case SUCCESS: return INCHI_RET.OKAY; | ||
| case WARNING: return INCHI_RET.WARNING; | ||
| case ERROR: return INCHI_RET.ERROR; | ||
| default: | ||
| throw new IllegalArgumentException("Unexpected status!"); | ||
| } | ||
| } | ||
| } |
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