Merge branch 'develop' into menard

[jalview.git] / src / jalview / gui / AssociatePdbFileWithSeq.java

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 6896863..22c891d 100644 (file)
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -18,6 +18,14 @@
 package jalview.gui;
 
 import javax.swing.JOptionPane;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
@@ -31,19 +39,29 @@ import jalview.datamodel.SequenceI;
 public class AssociatePdbFileWithSeq
 {
 
-  /**
-   * assocate the given PDB file with
-   * 
-   * @param choice
-   * @param sequence
-   */
-  public PDBEntry associatePdbWithSeq(String choice, String protocol,
-          SequenceI sequence, boolean prompt)
+/**
+ * assocate the given PDB file with 
+ * @param choice
+ * @param sequence
+ * @throws SAXException 
+ * @throws ParserConfigurationException 
+ * @throws ExceptionFileFormatOrSyntax 
+ * @throws ExceptionLoadingFailed 
+ * @throws ExceptionPermissionDenied 
+ * @throws InterruptedException 
+ * @throws ExceptionUnmatchedClosingParentheses 
+ */
+  public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     PDBEntry entry = new PDBEntry();
     try
     {
-      MCview.PDBfile pdbfile = new MCview.PDBfile(choice, protocol);
+ 
+               System.out.println("This is a annotation PDB");
+       
+       
+      MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
+              protocol);
 
       if (pdbfile.id == null)
       {
@@ -69,6 +87,7 @@ public class AssociatePdbFileWithSeq
       {
         entry.setId(pdbfile.id);
       }
+       
     } catch (java.io.IOException ex)
     {
       ex.printStackTrace();
@@ -77,6 +96,7 @@ public class AssociatePdbFileWithSeq
     entry.setFile(choice);
     sequence.getDatasetSequence().addPDBId(entry);
     return entry;
+    
   }
 
 }