From bbdafb43d4df0f63511d1160dff41812e52542ae Mon Sep 17 00:00:00 2001 From: John Mayfield Date: Fri, 12 May 2023 09:25:11 +0100 Subject: [PATCH] Code Smell: Variable renaming. --- .../openscience/cdk/io/MDLV2000Writer.java | 26 +++++++++---------- .../openscience/cdk/io/MDLV3000Writer.java | 13 +++++----- 2 files changed, 20 insertions(+), 19 deletions(-) diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java index 8bff2ca1a1..12fd1b7b5b 100644 --- a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java +++ b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java @@ -219,11 +219,11 @@ public static SPIN_MULTIPLICITY ofValue(int value) throws CDKException { @Deprecated private BooleanIOSetting writeQueryFormatValencies; - private BooleanIOSetting writeDefaultProps; + private BooleanIOSetting writeTrailingZeros; - private BooleanIOSetting optWriteData; + private BooleanIOSetting writeDataOpt; - private BooleanIOSetting optTruncateData; + private BooleanIOSetting truncateDataOpt; private StringIOSetting programNameOpt; @@ -559,7 +559,7 @@ public void writeMolecule(IAtomContainer container) throws Exception { line.append(formatMDLInt(atomprops[0], 2)); // dd (mass-number) line.append(formatMDLInt(atomprops[1], 3)); // ccc (charge) int last = atomprops.length-1; - if (!writeDefaultProps.isSet()) + if (!writeTrailingZeros.isSet()) { while (last >= 0) { if (atomprops[last] != 0) @@ -686,7 +686,7 @@ else if (e.equals(new Expr(Expr.Type.ALIPHATIC_ORDER, 2).or(new Expr(Expr.Type.I default: line.append("0"); } - if (writeDefaultProps.isSet()) + if (writeTrailingZeros.isSet()) line.append(" 0 0 0"); line.append('\n'); writer.write(line.toString()); @@ -832,12 +832,12 @@ else if (e.equals(new Expr(Expr.Type.ALIPHATIC_ORDER, 2).or(new Expr(Expr.Type.I writer.write('\n'); // write non-structural data (mol properties in our case) - if (optWriteData.isSet()) { + if (writeDataOpt.isSet()) { MDLV2000Writer.writeNonStructuralData(writer, container, SD_TAGS_TO_IGNORE, acceptedSdTags, - optTruncateData.isSet()); + truncateDataOpt.isSet()); } writer.flush(); @@ -1517,18 +1517,18 @@ private void initIOSettings() { "Should aromatic bonds be written as bond type 4?", "false")); writeQueryFormatValencies = addSetting(new BooleanIOSetting(OptWriteQueryFormatValencies, IOSetting.Importance.LOW, "Should valencies be written in the MDL Query format? (deprecated)", "false")); - writeDefaultProps = addSetting(new BooleanIOSetting(OptWriteDefaultProperties, - IOSetting.Importance.LOW, - "Write trailing zero's on atom/bond property blocks even if they're not used.", - "true")); + writeTrailingZeros = addSetting(new BooleanIOSetting(OptWriteDefaultProperties, + IOSetting.Importance.LOW, + "Write trailing zero's on atom/bond property blocks even if they're not used.", + "true")); programNameOpt = addSetting(new StringIOSetting(OptProgramName, IOSetting.Importance.LOW, "Program name to write at the top of the molfile header, should be exactly 8 characters long", "CDK")); - optWriteData = addSetting(new BooleanIOSetting(OptWriteData, + writeDataOpt = addSetting(new BooleanIOSetting(OptWriteData, IOSetting.Importance.LOW, "Should molecule properties be written as non-structural data", "false")); - optTruncateData = addSetting(new BooleanIOSetting(OptTruncateLongData, + truncateDataOpt = addSetting(new BooleanIOSetting(OptTruncateLongData, IOSetting.Importance.LOW, "Truncate long data files >200 characters", "false")); } diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Writer.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Writer.java index 784797d2b8..9ebf25dfb7 100644 --- a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Writer.java +++ b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Writer.java @@ -95,9 +95,10 @@ public final class MDLV3000Writer extends DefaultChemObjectWriter { private V30LineWriter writer; private StringIOSetting programNameOpt; - private BooleanIOSetting optWriteData; + private BooleanIOSetting writeDataOpt; + + private BooleanIOSetting truncateDataOpt; - private BooleanIOSetting optTruncateData; private Set acceptedSdTags; /** @@ -725,12 +726,12 @@ private void writeMol(IAtomContainer mol) throws IOException, CDKException { writer.write("END CTAB\n"); writer.writeDirect("M END\n"); // write non-structural data (mol properties in our case) - if (optWriteData.isSet()) { + if (writeDataOpt.isSet()) { MDLV2000Writer.writeNonStructuralData(writer.writer, mol, MDLV2000Writer.SD_TAGS_TO_IGNORE, acceptedSdTags, - optTruncateData.isSet()); + truncateDataOpt.isSet()); } writer.writer.flush(); } @@ -1016,10 +1017,10 @@ private void initIOSettings() { IOSetting.Importance.LOW, "Program name to write at the top of the molfile header, should be exactly 8 characters long", "CDK")); - optWriteData = addSetting(new BooleanIOSetting(OptWriteData, + writeDataOpt = addSetting(new BooleanIOSetting(OptWriteData, IOSetting.Importance.LOW, "Should molecule properties be written as non-structural data", "false")); - optTruncateData = addSetting(new BooleanIOSetting(OptTruncateLongData, + truncateDataOpt = addSetting(new BooleanIOSetting(OptTruncateLongData, IOSetting.Importance.LOW, "Truncate long data files >200 characters", "false")); }