From 9a9355bd1937c2fa4af48637ca8d6b1b85765f61 Mon Sep 17 00:00:00 2001 From: John May Date: Tue, 7 Feb 2017 11:45:50 +0000 Subject: [PATCH] Move deprecated classes out of cdk-smiles. --- .../AbstractFixedLengthFingerprinterTest.java | 7 ++--- .../cdk/smiles/DeduceBondSystemTool.java | 0 .../cdk/smiles/FixBondOrdersTool.java | 0 .../cdk/smiles/DeduceBondSystemToolTest.java | 28 +++++++++++-------- .../cdk/smiles/FixBondOrdersToolTest.java | 0 5 files changed, 19 insertions(+), 16 deletions(-) rename {storage/smiles => legacy}/src/main/java/org/openscience/cdk/smiles/DeduceBondSystemTool.java (100%) rename {storage/smiles => legacy}/src/main/java/org/openscience/cdk/smiles/FixBondOrdersTool.java (100%) rename {storage/smiles => legacy}/src/test/java/org/openscience/cdk/smiles/DeduceBondSystemToolTest.java (96%) rename {storage/smiles => legacy}/src/test/java/org/openscience/cdk/smiles/FixBondOrdersToolTest.java (100%) diff --git a/base/test-standard/src/test/java/org/openscience/cdk/fingerprint/AbstractFixedLengthFingerprinterTest.java b/base/test-standard/src/test/java/org/openscience/cdk/fingerprint/AbstractFixedLengthFingerprinterTest.java index 8339efd001c..f0e1f2eac2b 100644 --- a/base/test-standard/src/test/java/org/openscience/cdk/fingerprint/AbstractFixedLengthFingerprinterTest.java +++ b/base/test-standard/src/test/java/org/openscience/cdk/fingerprint/AbstractFixedLengthFingerprinterTest.java @@ -22,9 +22,6 @@ */ package org.openscience.cdk.fingerprint; -import java.io.InputStream; -import java.util.BitSet; - import org.junit.Assert; import org.junit.Test; import org.openscience.cdk.AtomContainer; @@ -39,10 +36,12 @@ import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.io.IChemObjectReader.Mode; import org.openscience.cdk.io.MDLV2000Reader; -import org.openscience.cdk.smiles.FixBondOrdersTool; import org.openscience.cdk.tools.CDKHydrogenAdder; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; +import java.io.InputStream; +import java.util.BitSet; + import static org.hamcrest.CoreMatchers.is; /** diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/DeduceBondSystemTool.java b/legacy/src/main/java/org/openscience/cdk/smiles/DeduceBondSystemTool.java similarity index 100% rename from storage/smiles/src/main/java/org/openscience/cdk/smiles/DeduceBondSystemTool.java rename to legacy/src/main/java/org/openscience/cdk/smiles/DeduceBondSystemTool.java diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/FixBondOrdersTool.java b/legacy/src/main/java/org/openscience/cdk/smiles/FixBondOrdersTool.java similarity index 100% rename from storage/smiles/src/main/java/org/openscience/cdk/smiles/FixBondOrdersTool.java rename to legacy/src/main/java/org/openscience/cdk/smiles/FixBondOrdersTool.java diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/DeduceBondSystemToolTest.java b/legacy/src/test/java/org/openscience/cdk/smiles/DeduceBondSystemToolTest.java similarity index 96% rename from storage/smiles/src/test/java/org/openscience/cdk/smiles/DeduceBondSystemToolTest.java rename to legacy/src/test/java/org/openscience/cdk/smiles/DeduceBondSystemToolTest.java index 0fb9a632db3..897c337a1c1 100644 --- a/storage/smiles/src/test/java/org/openscience/cdk/smiles/DeduceBondSystemToolTest.java +++ b/legacy/src/test/java/org/openscience/cdk/smiles/DeduceBondSystemToolTest.java @@ -1,20 +1,24 @@ -/* Copyright (C) 2006-2007 Rajarshi Guha +/* + * Copyright (c) 2017 John May * * 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 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. All we ask is that proper credit is given + * for our work, which includes - but is not limited to - adding the above + * copyright notice to the beginning of your source code files, and to any + * copyright notice that you may distribute with programs based on this work. * - * 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. + * 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. + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U */ package org.openscience.cdk.smiles; @@ -29,13 +33,13 @@ import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IAtomType.Hybridization; -import org.openscience.cdk.interfaces.IBond.Order; import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IBond.Order; import org.openscience.cdk.ringsearch.AllRingsFinder; -import org.openscience.cdk.silent.SilentChemObjectBuilder; import org.openscience.cdk.silent.Atom; import org.openscience.cdk.silent.AtomContainer; import org.openscience.cdk.silent.Bond; +import org.openscience.cdk.silent.SilentChemObjectBuilder; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/FixBondOrdersToolTest.java b/legacy/src/test/java/org/openscience/cdk/smiles/FixBondOrdersToolTest.java similarity index 100% rename from storage/smiles/src/test/java/org/openscience/cdk/smiles/FixBondOrdersToolTest.java rename to legacy/src/test/java/org/openscience/cdk/smiles/FixBondOrdersToolTest.java