X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=58f8ed5b7a35f5b7242e24e8e1602bb4d4c3c860;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=7b7f4b0d47ddd367c58f83a5ced6524335f96c82;hpb=6dd554fdbf34db6b79595d5027159d20225f4894;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 7b7f4b0..58f8ed5 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -63,8 +63,8 @@ public class PDBfile extends jalview.io.AlignFile
    */
   private boolean externalSecondaryStructure = false;
 
-  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecondaryStructure,
-          boolean externalSecStr)
+  public PDBfile(boolean addAlignmentAnnotations,
+          boolean predictSecondaryStructure, boolean externalSecStr)
   {
     super();
     this.visibleChainAnnotation = addAlignmentAnnotations;
@@ -72,9 +72,9 @@ public class PDBfile extends jalview.io.AlignFile
     this.externalSecondaryStructure = externalSecStr;
   }
 
-  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecondaryStructure,
-          boolean externalSecStr, String file, String protocol)
-          throws IOException
+  public PDBfile(boolean addAlignmentAnnotations,
+          boolean predictSecondaryStructure, boolean externalSecStr,
+          String file, String protocol) throws IOException
   {
     super(false, file, protocol);
     this.visibleChainAnnotation = addAlignmentAnnotations;
@@ -83,8 +83,9 @@ public class PDBfile extends jalview.io.AlignFile
     doParse();
   }
 
-  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecondaryStructure,
-          boolean externalSecStr, FileParse source) throws IOException
+  public PDBfile(boolean addAlignmentAnnotations,
+          boolean predictSecondaryStructure, boolean externalSecStr,
+          FileParse source) throws IOException
   {
     super(false, source);
     this.visibleChainAnnotation = addAlignmentAnnotations;
@@ -252,8 +253,7 @@ public class PDBfile extends jalview.io.AlignFile
         processPdbFileWithAnnotate3d(rnaSequences);
       } catch (Exception x)
       {
-        System.err
-                .println("Exceptions when dealing with RNA in pdb file");
+        System.err.println("Exceptions when dealing with RNA in pdb file");
         x.printStackTrace();
 
       }
@@ -339,7 +339,8 @@ public class PDBfile extends jalview.io.AlignFile
   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);
@@ -374,25 +375,24 @@ public class PDBfile extends jalview.io.AlignFile
       Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
       if (cl != null)
       {
-        final Constructor constructor = cl.getConstructor(new Class[]
-        { FileParse.class });
-        final Object[] args = new Object[]
-        { new FileParse(getDataName(), type) };
+        final Constructor constructor = cl
+                .getConstructor(new Class[] { FileParse.class });
+        final Object[] args = new Object[] { new FileParse(getDataName(),
+                type) };
         Object jmf = constructor.newInstance(args);
         AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
-                "getSeqsAsArray", new Class[]
-                {}).invoke(jmf));
-        cl.getMethod("addAnnotations", new Class[]
-        { AlignmentI.class }).invoke(jmf, al);
+                "getSeqsAsArray", new Class[] {}).invoke(jmf));
+        cl.getMethod("addAnnotations", new Class[] { AlignmentI.class })
+                .invoke(jmf, al);
         for (SequenceI sq : al.getSequences())
         {
           if (sq.getDatasetSequence() != null)
           {
-            sq.getDatasetSequence().getPDBId().clear();
+            sq.getDatasetSequence().getAllPDBEntries().clear();
           }
           else
           {
-            sq.getPDBId().clear();
+            sq.getAllPDBEntries().clear();
           }
         }
         replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
@@ -402,8 +402,8 @@ public class PDBfile extends jalview.io.AlignFile
     }
   }
 
-  private void replaceAndUpdateChains(List<SequenceI> prot,
-          AlignmentI al, String pep, boolean b)
+  private void replaceAndUpdateChains(List<SequenceI> prot, AlignmentI al,
+          String pep, boolean b)
   {
     List<List<? extends Object>> replaced = AlignSeq
             .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
@@ -445,27 +445,25 @@ public class PDBfile extends jalview.io.AlignFile
       {
         // TODO: use the PDB ID of the structure if one is available, to save
         // bandwidth and avoid uploading the whole structure to the service
-        Object annotate3d = cl.getConstructor(new Class[]
-        {}).newInstance(new Object[]
-        {});
+        Object annotate3d = cl.getConstructor(new Class[] {}).newInstance(
+                new Object[] {});
         AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
-                new Class[]
-                { FileParse.class }).invoke(annotate3d, new Object[]
-        { new FileParse(getDataName(), type) }));
+                new Class[] { FileParse.class }).invoke(annotate3d,
+                new Object[] { new FileParse(getDataName(), type) }));
         for (SequenceI sq : al.getSequences())
         {
           if (sq.getDatasetSequence() != null)
           {
-            if (sq.getDatasetSequence().getPDBId() != null)
+            if (sq.getDatasetSequence().getAllPDBEntries() != null)
             {
-              sq.getDatasetSequence().getPDBId().clear();
+              sq.getDatasetSequence().getAllPDBEntries().clear();
             }
           }
           else
           {
-            if (sq.getPDBId() != null)
+            if (sq.getAllPDBEntries() != null)
             {
-              sq.getPDBId().clear();
+              sq.getAllPDBEntries().clear();
             }
           }
         }