JAL-1919 Fixed failing tests, enabled HETATM processing from structure file to be...

[jalview.git] / src / jalview / structure / StructureViewSettings.java

diff --git a/src/jalview/structure/StructureViewSettings.java b/src/jalview/structure/StructureViewSettings.java
deleted file mode 100644 (file)
index 5880d0f..0000000
--- a/src/jalview/structure/StructureViewSettings.java
+++ /dev/null
@@ -1,93 +0,0 @@
-package jalview.structure;
-
-import jalview.datamodel.DBRefSource;
-
-public class StructureViewSettings
-{
-  private String dbRefType;
-
-  /**
-   * set to true to add derived sequence annotations (temp factor read from
-   * file, or computed secondary structure) to the alignment
-   */
-  private static boolean visibleChainAnnotation = false;
-
-  /**
-   * Set true to predict secondary structure (using JMol for protein, Annotate3D
-   * for RNA)
-   */
-  private static boolean predictSecStr = false;
-
-  /**
-   * Set true (with predictSecondaryStructure=true) to predict secondary
-   * structure using an external service (currently Annotate3D for RNA only)
-   */
-  private static boolean externalSecondaryStructure = false;
-
-  private static boolean showSeqFeatures = true;
-
-  private static String currentDefaultFormat = DBRefSource.PDB;
-
-  public static void addSettings(boolean addAlignmentAnnotations,
-          boolean predictSecStr, boolean externalSecStr)
-  {
-    StructureViewSettings.visibleChainAnnotation = addAlignmentAnnotations;
-    StructureViewSettings.predictSecStr = predictSecStr;
-    StructureViewSettings.externalSecondaryStructure = externalSecStr;
-    StructureViewSettings.showSeqFeatures = true;
-  }
-
-  public static boolean isVisibleChainAnnotation()
-  {
-    return visibleChainAnnotation;
-  }
-
-  public static void setVisibleChainAnnotation(
-          boolean visibleChainAnnotation)
-  {
-    StructureViewSettings.visibleChainAnnotation = visibleChainAnnotation;
-  }
-
-  public static boolean isPredictSecondaryStructure()
-  {
-    return predictSecStr;
-  }
-
-  public static void setPredictSecondaryStructure(
-          boolean predictSecondaryStructure)
-  {
-    StructureViewSettings.predictSecStr = predictSecondaryStructure;
-  }
-
-  public static boolean isExternalSecondaryStructure()
-  {
-    return externalSecondaryStructure;
-  }
-
-  public static void setExternalSecondaryStructure(
-          boolean externalSecondaryStructure)
-  {
-    StructureViewSettings.externalSecondaryStructure = externalSecondaryStructure;
-  }
-
-  public static boolean isShowSeqFeatures()
-  {
-    return showSeqFeatures;
-  }
-
-  public static void setShowSeqFeatures(boolean showSeqFeatures)
-  {
-    StructureViewSettings.showSeqFeatures = showSeqFeatures;
-  }
-
-  public static String getCurrentDefaultFormat()
-  {
-    return currentDefaultFormat;
-  }
-
-  public static void setCurrentDefaultFormat(String currentDefaultFormat)
-  {
-    StructureViewSettings.currentDefaultFormat = currentDefaultFormat;
-  }
-
-}