Added a @deprecated tag on the nonotify data classes, pointing to the…

… silent implementation Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
cdk · Dec 29, 2011 · d283686 · d283686
1 parent 5ef20b1
commit d283686
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Showing 39 changed files with 42 additions and 2 deletions.
diff --git a/src/main/org/openscience/cdk/nonotify/NNAdductFormula.java b/src/main/org/openscience/cdk/nonotify/NNAdductFormula.java
@@ -25,12 +25,13 @@
 package org.openscience.cdk.nonotify;
 
 import org.openscience.cdk.formula.AdductFormula;
-import org.openscience.cdk.interfaces.IMolecularFormula;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.interfaces.IMolecularFormula;
 
 /**
  * @cdk.module  nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.AdductFormula} instead.
  */
 public class NNAdductFormula extends AdductFormula {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNAminoAcid.java b/src/main/org/openscience/cdk/nonotify/NNAminoAcid.java
@@ -34,6 +34,7 @@
 /**
  *  @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.AminoAcid} instead.
  */
 public class NNAminoAcid extends AminoAcid {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNAtom.java b/src/main/org/openscience/cdk/nonotify/NNAtom.java
@@ -36,6 +36,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.Atom} instead.
  */
 public class NNAtom extends Atom {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNAtomContainer.java b/src/main/org/openscience/cdk/nonotify/NNAtomContainer.java
@@ -31,6 +31,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.AtomContainer} instead.
  */
 public class NNAtomContainer extends AtomContainer {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNAtomContainerSet.java b/src/main/org/openscience/cdk/nonotify/NNAtomContainerSet.java
@@ -31,6 +31,7 @@
 /**
  * @cdk.module    nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.AtomContainerSet} instead.
  */
 public class NNAtomContainerSet extends AtomContainerSet {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNAtomParity.java b/src/main/org/openscience/cdk/nonotify/NNAtomParity.java
@@ -34,6 +34,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.AtomParity} instead.
  */
 public class NNAtomParity extends AtomParity  {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNAtomType.java b/src/main/org/openscience/cdk/nonotify/NNAtomType.java
@@ -36,6 +36,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.AtomType} instead.
  */
 public class NNAtomType extends AtomType {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNBioPolymer.java b/src/main/org/openscience/cdk/nonotify/NNBioPolymer.java
@@ -34,6 +34,7 @@
 /**
  * @cdk.module  nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.BioPolymer} instead.
  */
 public class NNBioPolymer extends BioPolymer {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNBond.java b/src/main/org/openscience/cdk/nonotify/NNBond.java
@@ -33,6 +33,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.Bond} instead.
  */
 public class NNBond extends Bond {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNChemFile.java b/src/main/org/openscience/cdk/nonotify/NNChemFile.java
@@ -31,6 +31,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.ChemFile} instead.
  */
 public class NNChemFile extends ChemFile {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNChemModel.java b/src/main/org/openscience/cdk/nonotify/NNChemModel.java
@@ -31,6 +31,7 @@
 /** 
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.ChemModel} instead.
  */
 public class NNChemModel extends ChemModel {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNChemObject.java b/src/main/org/openscience/cdk/nonotify/NNChemObject.java
@@ -37,6 +37,7 @@
 /**
  * @cdk.module    nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.ChemObject} instead.
  */
 public class NNChemObject extends ChemObject {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNChemSequence.java b/src/main/org/openscience/cdk/nonotify/NNChemSequence.java
@@ -31,6 +31,7 @@
 /** 
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.ChemSequence} instead.
  */
 public class NNChemSequence extends ChemSequence {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNCrystal.java b/src/main/org/openscience/cdk/nonotify/NNCrystal.java
@@ -31,6 +31,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.Crystal} instead.
  */
 public class NNCrystal extends Crystal {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNElectronContainer.java b/src/main/org/openscience/cdk/nonotify/NNElectronContainer.java
@@ -32,6 +32,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.ElectronContainer} instead.
  */
 public class NNElectronContainer extends ElectronContainer {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNElement.java b/src/main/org/openscience/cdk/nonotify/NNElement.java
@@ -32,6 +32,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.Element} instead.
  */
 public class NNElement extends Element {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNFragmentAtom.java b/src/main/org/openscience/cdk/nonotify/NNFragmentAtom.java
@@ -34,6 +34,7 @@
  * 
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.FragmentAtom} instead.
  * 
  * @author egonw
  */

diff --git a/src/main/org/openscience/cdk/nonotify/NNIsotope.java b/src/main/org/openscience/cdk/nonotify/NNIsotope.java
@@ -36,6 +36,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.Isotope} instead.
  */
 public class NNIsotope extends Isotope {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNLonePair.java b/src/main/org/openscience/cdk/nonotify/NNLonePair.java
@@ -32,6 +32,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.LonePair} instead.
  */
 public class NNLonePair extends LonePair {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNMapping.java b/src/main/org/openscience/cdk/nonotify/NNMapping.java
@@ -32,6 +32,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.Mapping} instead.
  */
 public class NNMapping extends Mapping {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNMolecularFormula.java b/src/main/org/openscience/cdk/nonotify/NNMolecularFormula.java
@@ -30,6 +30,7 @@
 /**
  * @cdk.module  nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.MolecularFormula} instead.
  */
 public class NNMolecularFormula extends MolecularFormula {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNMolecularFormulaSet.java b/src/main/org/openscience/cdk/nonotify/NNMolecularFormulaSet.java
@@ -31,6 +31,7 @@
 /**
  * @cdk.module  nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.MolecularFormulaSet} instead.
  */
 public class NNMolecularFormulaSet extends MolecularFormulaSet {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNMolecule.java b/src/main/org/openscience/cdk/nonotify/NNMolecule.java
@@ -31,6 +31,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.Molecule} instead.
  */
 public class NNMolecule extends Molecule {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNMoleculeSet.java b/src/main/org/openscience/cdk/nonotify/NNMoleculeSet.java
@@ -30,6 +30,7 @@
 /** 
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.MoleculeSet} instead.
  */
 public class NNMoleculeSet extends MoleculeSet {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNMonomer.java b/src/main/org/openscience/cdk/nonotify/NNMonomer.java
@@ -34,6 +34,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.Monomer} instead.
  */
 public class NNMonomer extends Monomer {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNPDBAtom.java b/src/main/org/openscience/cdk/nonotify/NNPDBAtom.java
@@ -36,6 +36,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.PDBAtom} instead.
  */
 public class NNPDBAtom extends PDBAtom {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNPDBMonomer.java b/src/main/org/openscience/cdk/nonotify/NNPDBMonomer.java
@@ -34,6 +34,7 @@
 /**
  * @cdk.module  nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.PDBMonomer} instead.
  */
 public class NNPDBMonomer extends PDBMonomer {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNPDBPolymer.java b/src/main/org/openscience/cdk/nonotify/NNPDBPolymer.java
@@ -34,6 +34,7 @@
 /**
  * @cdk.module  nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.PDBPolymer} instead.
  */
 public class NNPDBPolymer extends PDBPolymer {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNPDBStructure.java b/src/main/org/openscience/cdk/nonotify/NNPDBStructure.java
@@ -34,6 +34,7 @@
 /**
  * @cdk.module  nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.PDBStructure} instead.
  */
 public class NNPDBStructure extends PDBStructure {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNPolymer.java b/src/main/org/openscience/cdk/nonotify/NNPolymer.java
@@ -34,6 +34,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.Polymer} instead.
  */
 public class NNPolymer extends Polymer { 
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNPseudoAtom.java b/src/main/org/openscience/cdk/nonotify/NNPseudoAtom.java
@@ -37,6 +37,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.PseudoAtom} instead.
  */
 public class NNPseudoAtom extends PseudoAtom {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNReaction.java b/src/main/org/openscience/cdk/nonotify/NNReaction.java
@@ -35,7 +35,8 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
- */
+  * @deprecated    Use the {@link org.openscience.cdk.silent.Reaction} instead.
+*/
 public class NNReaction extends Reaction {
 
 	private static final long serialVersionUID = 2951866794445339044L;

diff --git a/src/main/org/openscience/cdk/nonotify/NNReactionScheme.java b/src/main/org/openscience/cdk/nonotify/NNReactionScheme.java
@@ -30,6 +30,7 @@
 
 /** 
  * @cdk.module nonotify
+ * @deprecated    Use the {@link org.openscience.cdk.silent.ReactionScheme} instead.
  */
 public class NNReactionScheme extends ReactionScheme {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNReactionSet.java b/src/main/org/openscience/cdk/nonotify/NNReactionSet.java
@@ -30,6 +30,7 @@
 /** 
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.ReactionSet} instead.
  */
 public class NNReactionSet extends ReactionSet {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNRing.java b/src/main/org/openscience/cdk/nonotify/NNRing.java
@@ -31,6 +31,7 @@
 /** 
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.Ring} instead.
  */
 public class NNRing extends Ring {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNRingSet.java b/src/main/org/openscience/cdk/nonotify/NNRingSet.java
@@ -31,6 +31,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.RingSet} instead.
  */
 public class NNRingSet extends RingSet {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNSingleElectron.java b/src/main/org/openscience/cdk/nonotify/NNSingleElectron.java
@@ -32,6 +32,7 @@
 /**
  * @cdk.module nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.SingleElectron} instead.
  */
 public class NNSingleElectron extends SingleElectron {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NNStrand.java b/src/main/org/openscience/cdk/nonotify/NNStrand.java
@@ -34,6 +34,7 @@
 /**
  * @cdk.module  nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link org.openscience.cdk.silent.Strand} instead.
  */
 public class NNStrand extends Strand {
 

diff --git a/src/main/org/openscience/cdk/nonotify/NoNotificationChemObjectBuilder.java b/src/main/org/openscience/cdk/nonotify/NoNotificationChemObjectBuilder.java
@@ -64,6 +64,7 @@
 import org.openscience.cdk.interfaces.IRingSet;
 import org.openscience.cdk.interfaces.ISingleElectron;
 import org.openscience.cdk.interfaces.IStrand;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
 
 /**
  * A helper class to instantiate a {@link IChemObject} for the original CDK
@@ -72,6 +73,7 @@
  * @author        egonw
  * @cdk.module    nonotify
  * @cdk.githash
+ * @deprecated    Use the {@link SilentChemObjectBuilder} instead.
  */
 public class NoNotificationChemObjectBuilder implements IChemObjectBuilder {