Rename setter to match getter.

johnmay · johnmay · commit 8bc33293c9f1 · 2021-02-06T11:59:29.000Z
diff --git a/base/core/src/main/java/org/openscience/cdk/stereo/AbstractStereo.java b/base/core/src/main/java/org/openscience/cdk/stereo/AbstractStereo.java
@@ -122,7 +122,7 @@ public int getGroupInfo() {
     /**
      * {@inheritDoc}
      */
-    public void setGrpConfig(int grp) {
+    public void setGroupInfo(int grp) {
         value &= ~IStereoElement.GRP_MASK;
         value |= (grp & IStereoElement.GRP_MASK);
     }
diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IStereoElement.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IStereoElement.java
@@ -297,7 +297,7 @@ public interface IStereoElement<F extends IChemObject, C extends IChemObject>
      * Set the stereo group information - see class doc.
      * @param grp the group info
      */
-    void setGrpConfig(int grp);
+    void setGroupInfo(int grp);
 
     /**
      * Does the stereo element contain the provided atom.
diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java
@@ -549,7 +549,7 @@ private IAtomContainer readAtomContainer(IAtomContainer molecule) throws CDKExce
             if (chiral == 0) {
                 for (IStereoElement<?,?> se : outputContainer.stereoElements()) {
                     if (se.getConfigClass() == IStereoElement.TH) {
-                        se.setGrpConfig(IStereoElement.GRP_AND1);
+                        se.setGroupInfo(IStereoElement.GRP_AND1);
                     }
                 }
             }
diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java
@@ -251,16 +251,16 @@ public IAtomContainer readConnectionTable(IChemObjectBuilder builder) throws CDK
                         continue;
                     Integer grpinfo = stereoflags.get(idx);
                     if (grpinfo != null)
-                        se.setGrpConfig(grpinfo);
+                        se.setGroupInfo(grpinfo);
                     else if (!chiral)
-                        se.setGrpConfig(defaultRacGrp);
+                        se.setGroupInfo(defaultRacGrp);
                 }
             } else if (!chiral) {
                 // chiral flag not set which means this molecule is this stereoisomer "and" the enantiomer, mark all
                 // Tetrahedral stereo as AND1 (&1)
                 for (IStereoElement<?, ?> se : readData.stereoElements()) {
                     if (se.getConfigClass() == IStereoElement.TH) {
-                        se.setGrpConfig(IStereoElement.GRP_AND1);
+                        se.setGroupInfo(IStereoElement.GRP_AND1);
                     }
                 }
             }
diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesParser.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesParser.java
@@ -415,7 +415,7 @@ private void handleFragmentGrouping(IReaction rxn, CxSmilesState cxstate) {
                 for (IStereoElement<?, ?> e : mol.stereoElements()) {
                     // maybe also Al and AT?
                     if (e.getConfigClass() == IStereoElement.TH) {
-                        e.setGrpConfig(IStereoElement.GRP_AND1);
+                        e.setGroupInfo(IStereoElement.GRP_AND1);
                     }
                 }
             }
@@ -770,15 +770,15 @@ else if (chemObj instanceof IAtomContainer)
                 for (IStereoElement<?, ?> e : ((IAtomContainer) chemObj).stereoElements()) {
                     // maybe also Al and AT?
                     if (e.getConfigClass() == IStereoElement.TH) {
-                        e.setGrpConfig(IStereoElement.GRP_AND1);
+                        e.setGroupInfo(IStereoElement.GRP_AND1);
                     }
                 }
             } else if (chemObj instanceof IReaction) {
                 for (IAtomContainer mol : ReactionManipulator.getAllAtomContainers((IReaction) chemObj)) {
                     for (IStereoElement<?, ?> e : mol.stereoElements()) {
                         // maybe also Al and AT?
                         if (e.getConfigClass() == IStereoElement.TH) {
-                            e.setGrpConfig(IStereoElement.GRP_AND1);
+                            e.setGroupInfo(IStereoElement.GRP_AND1);
                         }
                     }
                 }
@@ -794,7 +794,7 @@ else if (chemObj instanceof IAtomContainer)
                     // maybe also Al and AT?
                     if (stereo.getConfigClass() == IStereoElement.TH &&
                             stereo.getFocus().equals(atm)) {
-                        stereo.setGrpConfig(e.getValue());
+                        stereo.setGroupInfo(e.getValue());
                     }
                 }
             }

Original file line number	Diff line number	Diff line change
`@@ -122,7 +122,7 @@ public int getGroupInfo() {`
`122`	`122`	`/**`
`123`	`123`	`* {@inheritDoc}`
`124`	`124`	`*/`
`125`		`- public void setGrpConfig(int grp) {`
	`125`	`+ public void setGroupInfo(int grp) {`
`126`	`126`	`value &= ~IStereoElement.GRP_MASK;`
`127`	`127`	`value \|= (grp & IStereoElement.GRP_MASK);`
`128`	`128`	`}`
Original file line number	Diff line number	Diff line change
`@@ -549,7 +549,7 @@ private IAtomContainer readAtomContainer(IAtomContainer molecule) throws CDKExce`
`549`	`549`	`if (chiral == 0) {`
`550`	`550`	`for (IStereoElement<?,?> se : outputContainer.stereoElements()) {`
`551`	`551`	`if (se.getConfigClass() == IStereoElement.TH) {`
`552`		`- se.setGrpConfig(IStereoElement.GRP_AND1);`
	`552`	`+ se.setGroupInfo(IStereoElement.GRP_AND1);`
`553`	`553`	`}`
`554`	`554`	`}`
`555`	`555`	`}`
Original file line number	Diff line number	Diff line change
`@@ -251,16 +251,16 @@ public IAtomContainer readConnectionTable(IChemObjectBuilder builder) throws CDK`
`251`	`251`	`continue;`
`252`	`252`	`Integer grpinfo = stereoflags.get(idx);`
`253`	`253`	`if (grpinfo != null)`
`254`		`- se.setGrpConfig(grpinfo);`
	`254`	`+ se.setGroupInfo(grpinfo);`
`255`	`255`	`else if (!chiral)`
`256`		`- se.setGrpConfig(defaultRacGrp);`
	`256`	`+ se.setGroupInfo(defaultRacGrp);`
`257`	`257`	`}`
`258`	`258`	`} else if (!chiral) {`
`259`	`259`	`// chiral flag not set which means this molecule is this stereoisomer "and" the enantiomer, mark all`
`260`	`260`	`// Tetrahedral stereo as AND1 (&1)`
`261`	`261`	`for (IStereoElement<?, ?> se : readData.stereoElements()) {`
`262`	`262`	`if (se.getConfigClass() == IStereoElement.TH) {`
`263`		`- se.setGrpConfig(IStereoElement.GRP_AND1);`
	`263`	`+ se.setGroupInfo(IStereoElement.GRP_AND1);`
`264`	`264`	`}`
`265`	`265`	`}`
`266`	`266`	`}`
Original file line number	Diff line number	Diff line change
`@@ -415,7 +415,7 @@ private void handleFragmentGrouping(IReaction rxn, CxSmilesState cxstate) {`
`415`	`415`	`for (IStereoElement<?, ?> e : mol.stereoElements()) {`
`416`	`416`	`// maybe also Al and AT?`
`417`	`417`	`if (e.getConfigClass() == IStereoElement.TH) {`
`418`		`- e.setGrpConfig(IStereoElement.GRP_AND1);`
	`418`	`+ e.setGroupInfo(IStereoElement.GRP_AND1);`
`419`	`419`	`}`
`420`	`420`	`}`
`421`	`421`	`}`
`@@ -770,15 +770,15 @@ else if (chemObj instanceof IAtomContainer)`
`770`	`770`	`for (IStereoElement<?, ?> e : ((IAtomContainer) chemObj).stereoElements()) {`
`771`	`771`	`// maybe also Al and AT?`
`772`	`772`	`if (e.getConfigClass() == IStereoElement.TH) {`
`773`		`- e.setGrpConfig(IStereoElement.GRP_AND1);`
	`773`	`+ e.setGroupInfo(IStereoElement.GRP_AND1);`
`774`	`774`	`}`
`775`	`775`	`}`
`776`	`776`	`} else if (chemObj instanceof IReaction) {`
`777`	`777`	`for (IAtomContainer mol : ReactionManipulator.getAllAtomContainers((IReaction) chemObj)) {`
`778`	`778`	`for (IStereoElement<?, ?> e : mol.stereoElements()) {`
`779`	`779`	`// maybe also Al and AT?`
`780`	`780`	`if (e.getConfigClass() == IStereoElement.TH) {`
`781`		`- e.setGrpConfig(IStereoElement.GRP_AND1);`
	`781`	`+ e.setGroupInfo(IStereoElement.GRP_AND1);`
`782`	`782`	`}`
`783`	`783`	`}`
`784`	`784`	`}`
`@@ -794,7 +794,7 @@ else if (chemObj instanceof IAtomContainer)`
`794`	`794`	`// maybe also Al and AT?`
`795`	`795`	`if (stereo.getConfigClass() == IStereoElement.TH &&`
`796`	`796`	`stereo.getFocus().equals(atm)) {`
`797`		`- stereo.setGrpConfig(e.getValue());`
	`797`	`+ stereo.setGroupInfo(e.getValue());`
`798`	`798`	`}`
`799`	`799`	`}`
`800`	`800`	`}`