JAL-1942 JAL-1479 refactored SequenceI.getDBRef/SequenceI.setDBRef to SequenceI.getDB...

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 4039cdd..58611e2 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -20,23 +20,25 @@
  */
 package MCview;
 
-import java.awt.Color;
-import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.FileParse;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
 public class PDBfile extends jalview.io.AlignFile
 {
   private static String CALC_ID_PREFIX = "JalviewPDB";
@@ -63,8 +65,8 @@ 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 +74,9 @@ 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 +85,9 @@ 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;
@@ -93,11 +96,13 @@ public class PDBfile extends jalview.io.AlignFile
     doParse();
   }
 
+  @Override
   public String print()
   {
     return null;
   }
 
+  @Override
   public void parse() throws IOException
   {
     // TODO set the filename sensibly - try using data source name.
@@ -252,8 +257,7 @@ 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();
 
       }
@@ -285,8 +289,8 @@ public class PDBfile extends jalview.io.AlignFile
    */
   protected SequenceI postProcessChain(PDBChain chain)
   {
-    SequenceI dataset = chain.sequence;
-    dataset.setName(id + "|" + dataset.getName());
+    SequenceI pdbSequence = chain.sequence;
+    pdbSequence.setName(id + "|" + pdbSequence.getName());
     PDBEntry entry = new PDBEntry();
     entry.setId(id);
     entry.setType(PDBEntry.Type.PDB);
@@ -305,9 +309,16 @@ public class PDBfile extends jalview.io.AlignFile
       // TODO: decide if we should dump the datasource to disk
       entry.setFile(getDataName());
     }
-    dataset.addPDBId(entry);
+    pdbSequence.addPDBId(entry);
+
+    DBRefEntry sourceDBRef = new DBRefEntry();
+    sourceDBRef.setAccessionId(id);
+    sourceDBRef.setSource(DBRefSource.PDB);
+    sourceDBRef.setStartRes(pdbSequence.getStart());
+    sourceDBRef.setEndRes(pdbSequence.getEnd());
+    pdbSequence.setSourceDBRef(sourceDBRef);
     // PDBChain objects maintain reference to dataset
-    SequenceI chainseq = dataset.deriveSequence();
+    SequenceI chainseq = pdbSequence.deriveSequence();
     seqs.addElement(chainseq);
 
     AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
@@ -339,7 +350,8 @@ 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 +386,24 @@ 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[]
-        { Alignment.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 +413,8 @@ 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 +456,25 @@ 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();
             }
           }
         }