src/jalview/gui/AssociatePdbFileWithSeq.java

   1 package jalview.gui;
   2
   3 import javax.swing.JOptionPane;
   4
   5 import jalview.datamodel.PDBEntry;
   6 import jalview.datamodel.Sequence;
   7 import jalview.datamodel.SequenceI;
   8
   9 /**
  10  * GUI related routines for associating PDB files with sequences
  11  * @author JimP
  12  *
  13  */
  14 public class AssociatePdbFileWithSeq
  15 {
  16
  17 /**
  18  * assocate the given PDB file with
  19  * @param choice
  20  * @param sequence
  21  */
  22   public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt)
  23   {
  24     PDBEntry entry = new PDBEntry();
  25     try
  26     {
  27       MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
  28               protocol);
  29
  30       if (pdbfile.id == null)
  31       {
  32         String reply = null;
  33
  34         if (prompt) { reply = JOptionPane
  35                 .showInternalInputDialog(
  36                         Desktop.desktop,
  37                         "Couldn't find a PDB id in the file supplied."
  38                                 + "Please enter an Id to identify this structure.",
  39                         "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);}
  40         if (reply == null)
  41         {
  42           return null;
  43         }
  44
  45         entry.setId(reply);
  46       }
  47       else
  48       {
  49         entry.setId(pdbfile.id);
  50       }
  51     } catch (java.io.IOException ex)
  52     {
  53       ex.printStackTrace();
  54     }
  55
  56     entry.setFile(choice);
  57     sequence.getDatasetSequence().addPDBId(entry);
  58     return entry;
  59   }
  60
  61 }