Merge branch 'develop' into develop_m2_8_1_2

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 1d95f40..829eed7 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -22,11 +22,10 @@ import java.util.*;
 
 import java.awt.*;
 
-
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.*;
+import jalview.ext.jmol.PDBFileWithJmol;
 import jalview.io.FileParse;
-import jalview.ws.jws1.Annotate3D;
 
 public class PDBfile extends jalview.io.AlignFile
 {
@@ -39,12 +38,12 @@ public class PDBfile extends jalview.io.AlignFile
    */
   boolean VisibleChainAnnotation = false;
 
-  public PDBfile(String inFile, String inType) throws Exception
+  public PDBfile(String inFile, String inType) throws IOException
   {
     super(inFile, inType);
   }
 
-  public PDBfile(FileParse source) throws Exception
+  public PDBfile(FileParse source) throws IOException
   {
     super(source);
   }
@@ -54,7 +53,7 @@ public class PDBfile extends jalview.io.AlignFile
     return null;
   }
 
-  public void parse() throws Exception
+  public void parse() throws IOException
   {
     // TODO set the filename sensibly - try using data source name.
     id = safeName(getDataName());
@@ -160,7 +159,9 @@ public class PDBfile extends jalview.io.AlignFile
         PDBEntry entry = new PDBEntry();
         entry.setId(id);
         entry.setProperty(new Hashtable());
-        entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
+        if (((PDBChain)chains.elementAt(i)).id!=null) {
+          entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
+        }
         if (inFile != null)
         {
           entry.setFile(inFile.getAbsolutePath());
@@ -212,6 +213,15 @@ public class PDBfile extends jalview.io.AlignFile
         x.printStackTrace();
         
       };
+      if (prot.size()>0)
+      try {
+        processPdbFileWithJmol(prot);
+      } catch (Exception x)
+      {
+        System.err.println("Exceptions when dealing with RNA in pdb file");
+        x.printStackTrace();
+        
+      };
     } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
@@ -227,14 +237,27 @@ public class PDBfile extends jalview.io.AlignFile
   }
   private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
   {
-    // process prot sequence with Jmol to get annotated alignment. 
-    // replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+    PDBFileWithJmol jmf = new PDBFileWithJmol(new FileParse(getDataName(),type));
+    Alignment al = new Alignment(jmf.getSeqsAsArray());
+    jmf.addAnnotations(al);
+    replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
   }
   private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
 //    System.out.println("this is a PDB format and RNA sequence");
-    Annotate3D an3d = new Annotate3D();
-    AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
-    replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+    // note: we use reflection here so that the applet can compile and run without the HTTPClient bits and pieces needed for accessing Annotate3D web service
+    try {
+    Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
+    if (cl!=null)
+    {
+      // 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[] {});
+      AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor", new Class[] { FileParse.class}).invoke(annotate3d, new Object[] { new FileParse(getDataName(),type)}));
+      replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+    }
+    } catch (ClassNotFoundException x)
+    {
+      //ignore classnotfounds - occurs in applet
+    };
   }
   private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains, AlignmentI al, String dnaOrProtein)
   {
@@ -286,7 +309,9 @@ public class PDBfile extends jalview.io.AlignFile
               ap++;
             }
           }
-          annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+          if (sq.getAnnotation()!=null) {
+            annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+          }
         }
       }
     }