JAL-2145 JAL-1551 formatting

[jalview.git] / src / MCview / PDBfile.java

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index ed694f2..9acc2e7 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -21,9 +21,11 @@
 package MCview;
 
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
+import jalview.structure.StructureImportSettings;
 import jalview.util.MessageManager;
 
 import java.io.IOException;
@@ -40,30 +42,25 @@ public class PDBfile extends StructureFile
           boolean predictSecondaryStructure, boolean externalSecStr)
   {
     super();
-    this.visibleChainAnnotation = addAlignmentAnnotations;
-    this.predictSecondaryStructure = predictSecondaryStructure;
-    this.externalSecondaryStructure = externalSecStr;
+    addSettings(addAlignmentAnnotations, predictSecondaryStructure,
+            externalSecStr);
   }
 
-  public PDBfile(boolean addAlignmentAnnotations,
-          boolean predictSecondaryStructure, boolean externalSecStr,
-          String file, String protocol) throws IOException
+  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+          boolean externalSecStr, String dataObject, String protocol)
+          throws IOException
   {
-    super(false, file, protocol);
-    this.visibleChainAnnotation = addAlignmentAnnotations;
-    this.predictSecondaryStructure = predictSecondaryStructure;
-    this.externalSecondaryStructure = externalSecStr;
+    super(false, dataObject, protocol);
+    addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
     doParse();
   }
 
-  public PDBfile(boolean addAlignmentAnnotations,
-          boolean predictSecondaryStructure, boolean externalSecStr,
+  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+          boolean externalSecStr,
           FileParse source) throws IOException
   {
     super(false, source);
-    this.visibleChainAnnotation = addAlignmentAnnotations;
-    this.predictSecondaryStructure = predictSecondaryStructure;
-    this.externalSecondaryStructure = externalSecStr;
+    addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
     doParse();
   }
 
@@ -76,6 +73,7 @@ public class PDBfile extends StructureFile
   @Override
   public void parse() throws IOException
   {
+    setDbRefType(DBRefSource.PDB);
     // TODO set the filename sensibly - try using data source name.
     setId(safeName(getDataName()));
 
@@ -134,7 +132,8 @@ public class PDBfile extends StructureFile
           break;
         }
         if (line.indexOf("ATOM") == 0
-                || (line.indexOf("HETATM") == 0 && !terFlag))
+                || (StructureImportSettings.isProcessHETATMs()
+                        && line.indexOf("HETATM") == 0 && !terFlag))
         {
           terFlag = false;