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;
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)
{
{
entry.setId(pdbfile.id);
}
+
} catch (java.io.IOException ex)
{
ex.printStackTrace();
entry.setFile(choice);
sequence.getDatasetSequence().addPDBId(entry);
return entry;
+
}
}