X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=ebc52aaf0aa0643410590de2c330fd5611782160;hb=f112bc8a75efc4d595f3d5008e13d5e055a4a411;hp=9acc2e7b5438ab8b8db3df2bd46367b5057e64df;hpb=0bec4854366c4bc4608ed0d7dc1506fc6afe2285;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 9acc2e7..ebc52aa 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -23,9 +23,9 @@ package MCview;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
-import jalview.structure.StructureImportSettings;
 import jalview.util.MessageManager;
 
 import java.io.IOException;
@@ -47,17 +47,16 @@ public class PDBfile extends StructureFile
   }
 
   public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
-          boolean externalSecStr, String dataObject, String protocol)
-          throws IOException
+          boolean externalSecStr, String dataObject,
+          DataSourceType sourceType) throws IOException
   {
-    super(false, dataObject, protocol);
+    super(false, dataObject, sourceType);
     addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
     doParse();
   }
 
   public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
-          boolean externalSecStr,
-          FileParse source) throws IOException
+          boolean externalSecStr, FileParse source) throws IOException
   {
     super(false, source);
     addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
@@ -65,7 +64,7 @@ public class PDBfile extends StructureFile
   }
 
   @Override
-  public String print()
+  public String print(SequenceI[] seqs, boolean jvSuffix)
   {
     return null;
   }
@@ -132,8 +131,7 @@ public class PDBfile extends StructureFile
           break;
         }
         if (line.indexOf("ATOM") == 0
-                || (StructureImportSettings.isProcessHETATMs()
-                        && line.indexOf("HETATM") == 0 && !terFlag))
+                || (line.indexOf("HETATM") == 0 && !terFlag))
         {
           terFlag = false;
 
@@ -147,7 +145,7 @@ 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..
@@ -191,9 +189,8 @@ public class PDBfile extends StructureFile
     } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
-      throw new IOException(
-              MessageManager
-                      .getString("exception.outofmemory_loading_pdb_file"));
+      throw new IOException(MessageManager
+              .getString("exception.outofmemory_loading_pdb_file"));
     } catch (NumberFormatException ex)
     {
       if (line != null)
@@ -205,8 +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.
@@ -231,8 +226,8 @@ public class PDBfile extends StructureFile
   public static String relocateCalcId(String calcId,
           Hashtable<String, String> alreadyLoadedPDB) throws Exception
   {
-    int s = CALC_ID_PREFIX.length(), end = calcId
-            .indexOf(CALC_ID_PREFIX, s);
+    int s = CALC_ID_PREFIX.length(),
+            end = calcId.indexOf(CALC_ID_PREFIX, s);
     String between = calcId.substring(s, end - 1);
     return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
             + calcId.substring(end);