From 08c202dd3ef0f34bde305c11da9eec03520174dc Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 20 Jul 2016 16:25:25 +0100 Subject: [PATCH] JAL-1926 JAL-2106 fix name for flag controlling addition of secondary structure annotation from 3D data --- src/jalview/ext/jmol/JmolParser.java | 2 +- src/jalview/io/StructureFile.java | 4 ++-- src/jalview/structure/StructureImportSettings.java | 16 ++++++++-------- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java index a791558..0ce5f9a 100644 --- a/src/jalview/ext/jmol/JmolParser.java +++ b/src/jalview/ext/jmol/JmolParser.java @@ -186,7 +186,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener prot.add(chainseq); } - if (StructureImportSettings.isPredictSecondaryStructure()) + if (StructureImportSettings.isProcessSecondaryStructure()) { createAnnotation(chainseq, chain, ms.at); } diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java index de4affa..b2e5b23 100644 --- a/src/jalview/io/StructureFile.java +++ b/src/jalview/io/StructureFile.java @@ -70,7 +70,7 @@ public abstract class StructureFile extends AlignFile this.visibleChainAnnotation = StructureImportSettings .isVisibleChainAnnotation(); this.predictSecondaryStructure = StructureImportSettings - .isPredictSecondaryStructure(); + .isProcessSecondaryStructure(); this.externalSecondaryStructure = StructureImportSettings .isExternalSecondaryStructure(); @@ -271,7 +271,7 @@ public abstract class StructureFile extends AlignFile StructureImportSettings.setShowSeqFeatures(false); StructureImportSettings.setVisibleChainAnnotation(false); StructureImportSettings - .setPredictSecondaryStructure(predictSecondaryStructure); + .setProcessSecondaryStructure(predictSecondaryStructure); StructureImportSettings .setExternalSecondaryStructure(externalSecondaryStructure); Object jmf = constructor.newInstance(args); diff --git a/src/jalview/structure/StructureImportSettings.java b/src/jalview/structure/StructureImportSettings.java index 2faca2a..ed53425 100644 --- a/src/jalview/structure/StructureImportSettings.java +++ b/src/jalview/structure/StructureImportSettings.java @@ -13,7 +13,7 @@ public class StructureImportSettings * Set true to predict secondary structure (using JMol for protein, Annotate3D * for RNA) */ - private static boolean predictSecStr = false; + private static boolean processSecStr = false; /** * Set true (with predictSecondaryStructure=true) to predict secondary @@ -33,10 +33,10 @@ public class StructureImportSettings private static StructureFormat currentDefaultFormat = StructureFormat.PDB; public static void addSettings(boolean addAlignmentAnnotations, - boolean predictSecStr, boolean externalSecStr) + boolean processSecStr, boolean externalSecStr) { StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations; - StructureImportSettings.predictSecStr = predictSecStr; + StructureImportSettings.processSecStr = processSecStr; StructureImportSettings.externalSecondaryStructure = externalSecStr; StructureImportSettings.showSeqFeatures = true; } @@ -52,15 +52,15 @@ public class StructureImportSettings StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation; } - public static boolean isPredictSecondaryStructure() + public static boolean isProcessSecondaryStructure() { - return predictSecStr; + return processSecStr; } - public static void setPredictSecondaryStructure( - boolean predictSecondaryStructure) + public static void setProcessSecondaryStructure( + boolean processSecondaryStructure) { - StructureImportSettings.predictSecStr = predictSecondaryStructure; + StructureImportSettings.processSecStr = processSecondaryStructure; } public static boolean isExternalSecondaryStructure() -- 1.7.10.2