Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3' into releases/Release_2_...

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index ed694f2..ebc52aa 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -21,7 +21,9 @@
 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.util.MessageManager;
@@ -40,35 +42,29 @@ 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,
+          DataSourceType sourceType) throws IOException
   {
-    super(false, file, protocol);
-    this.visibleChainAnnotation = addAlignmentAnnotations;
-    this.predictSecondaryStructure = predictSecondaryStructure;
-    this.externalSecondaryStructure = externalSecStr;
+    super(false, dataObject, sourceType);
+    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();
   }
 
   @Override
-  public String print()
+  public String print(SequenceI[] seqs, boolean jvSuffix)
   {
     return null;
   }
@@ -76,6 +72,7 @@ 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 +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..
@@ -192,9 +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)
@@ -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.
@@ -232,8 +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);