Merge branch 'develop' into task/JAL-2196pdbeProperties

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index ed694f2..f5a0255 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -21,6 +21,7 @@
 package MCview;
 
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
@@ -40,30 +41,24 @@ 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,
-          FileParse source) throws IOException
+  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 +71,7 @@ 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()));
 
@@ -148,7 +144,7 @@ public class PDBfile extends StructureFile
           Atom tmpatom = new Atom(line);
           try
           {
-          tmpchain = findChain(tmpatom.chain);
+            tmpchain = findChain(tmpatom.chain);
             if (tmpatom.resNumIns.trim().equals(lastID))
             {
               // phosphorylated protein - seen both CA and P..
@@ -206,8 +202,6 @@ public class PDBfile extends StructureFile
     markCalcIds();
   }
 
-
-
   /**
    * Process a parsed chain to construct and return a Sequence, and add it to
    * the list of sequences parsed.