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Merge branch 'develop' into trialMerge
[jalview.git]
/
src
/
jalview
/
gui
/
AssociatePdbFileWithSeq.java
diff --git
a/src/jalview/gui/AssociatePdbFileWithSeq.java
b/src/jalview/gui/AssociatePdbFileWithSeq.java
index
d53ddc8
..
ddf38c6
100644
(file)
--- a/
src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/
src/jalview/gui/AssociatePdbFileWithSeq.java
@@
-23,6
+23,8
@@
package jalview.gui;
import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
@@
-43,31
+45,31
@@
public class AssociatePdbFileWithSeq
* @param choice
* @param sequence
*/
* @param choice
* @param sequence
*/
- public PDBEntry associatePdbWithSeq(String choice, String protocol,
+ public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
SequenceI sequence, boolean prompt,
StructureSelectionManagerProvider ssmp)
{
PDBEntry entry = new PDBEntry();
SequenceI sequence, boolean prompt,
StructureSelectionManagerProvider ssmp)
{
PDBEntry entry = new PDBEntry();
- MCview.PDBfile pdbfile = null;
+ StructureFile pdbfile = null;
pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
- .setMapping(false, new SequenceI[]
- { sequence }, null, choice, protocol);
+ .setMapping(false, new SequenceI[] { sequence }, null, choice,
+ file);
if (pdbfile == null)
{
// stacktrace already thrown so just return
return null;
}
if (pdbfile == null)
{
// stacktrace already thrown so just return
return null;
}
- if (pdbfile.id == null)
+ if (pdbfile.getId() == null)
{
String reply = null;
if (prompt)
{
{
String reply = null;
if (prompt)
{
- reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
+ reply = JvOptionPane.showInternalInputDialog(Desktop.desktop,
MessageManager
.getString("label.couldnt_find_pdb_id_in_file"),
MessageManager.getString("label.no_pdb_id_in_file"),
MessageManager
.getString("label.couldnt_find_pdb_id_in_file"),
MessageManager.getString("label.no_pdb_id_in_file"),
- JOptionPane.QUESTION_MESSAGE);
+ JvOptionPane.QUESTION_MESSAGE);
}
if (reply == null)
{
}
if (reply == null)
{
@@
-78,8
+80,9
@@
public class AssociatePdbFileWithSeq
}
else
{
}
else
{
- entry.setId(pdbfile.id);
+ entry.setId(pdbfile.getId());
}
}
+ entry.setType(PDBEntry.Type.FILE);
if (pdbfile != null)
{
if (pdbfile != null)
{