JAL-1926 JAL-2106 fix name for flag controlling addition of secondary structure annot...

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index a791558..0ce5f9a 100644 (file)
--- 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 (file)
--- 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 (file)
--- 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()