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

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

diff --git a/src/jalview/structure/StructureViewSettings.java b/src/jalview/structure/StructureImportSettings.java
similarity index 66%
rename from src/jalview/structure/StructureViewSettings.java
rename to src/jalview/structure/StructureImportSettings.java
index 5880d0f..b23fd53 100644 (file)
--- a/src/jalview/structure/StructureViewSettings.java
+++ b/src/jalview/structure/StructureImportSettings.java
@@ -2,10 +2,8 @@ package jalview.structure;
 
 import jalview.datamodel.DBRefSource;
 
-public class StructureViewSettings
+public class StructureImportSettings
 {
-  private String dbRefType;
-
   /**
    * set to true to add derived sequence annotations (temp factor read from
    * file, or computed secondary structure) to the alignment
@@ -26,15 +24,17 @@ public class StructureViewSettings
 
   private static boolean showSeqFeatures = true;
 
+  private static boolean processHETATMs = false;
+
   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;
+    StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations;
+    StructureImportSettings.predictSecStr = predictSecStr;
+    StructureImportSettings.externalSecondaryStructure = externalSecStr;
+    StructureImportSettings.showSeqFeatures = true;
   }
 
   public static boolean isVisibleChainAnnotation()
@@ -45,7 +45,7 @@ public class StructureViewSettings
   public static void setVisibleChainAnnotation(
           boolean visibleChainAnnotation)
   {
-    StructureViewSettings.visibleChainAnnotation = visibleChainAnnotation;
+    StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation;
   }
 
   public static boolean isPredictSecondaryStructure()
@@ -56,7 +56,7 @@ public class StructureViewSettings
   public static void setPredictSecondaryStructure(
           boolean predictSecondaryStructure)
   {
-    StructureViewSettings.predictSecStr = predictSecondaryStructure;
+    StructureImportSettings.predictSecStr = predictSecondaryStructure;
   }
 
   public static boolean isExternalSecondaryStructure()
@@ -67,7 +67,7 @@ public class StructureViewSettings
   public static void setExternalSecondaryStructure(
           boolean externalSecondaryStructure)
   {
-    StructureViewSettings.externalSecondaryStructure = externalSecondaryStructure;
+    StructureImportSettings.externalSecondaryStructure = externalSecondaryStructure;
   }
 
   public static boolean isShowSeqFeatures()
@@ -77,7 +77,7 @@ public class StructureViewSettings
 
   public static void setShowSeqFeatures(boolean showSeqFeatures)
   {
-    StructureViewSettings.showSeqFeatures = showSeqFeatures;
+    StructureImportSettings.showSeqFeatures = showSeqFeatures;
   }
 
   public static String getCurrentDefaultFormat()
@@ -87,7 +87,17 @@ public class StructureViewSettings
 
   public static void setCurrentDefaultFormat(String currentDefaultFormat)
   {
-    StructureViewSettings.currentDefaultFormat = currentDefaultFormat;
+    StructureImportSettings.currentDefaultFormat = currentDefaultFormat;
+  }
+
+  public static boolean isProcessHETATMs()
+  {
+    return processHETATMs;
+  }
+
+  public static void setProcessHETATMs(boolean processHETATMs)
+  {
+    StructureImportSettings.processHETATMs = processHETATMs;
   }
 
 }