X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;h=c9951f54ed60cc74ca9921e5e52c04a7c9242f4c;hb=afe4b88500a5d61bc8d312909cfdde2b7cdd53df;hp=1fa9e718e625e34f7982bff552ac2fa67aaf89b5;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git
diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 1fa9e71..c9951f5 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -1,27 +1,32 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import javax.swing.JOptionPane;
-
+import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.structure.StructureImportSettings.TFType;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
/**
@@ -39,45 +44,67 @@ public class AssociatePdbFileWithSeq
* @param choice
* @param sequence
*/
- public PDBEntry associatePdbWithSeq(String choice, String protocol,
- SequenceI sequence, boolean prompt)
+ public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
+ SequenceI sequence, boolean prompt,
+ StructureSelectionManagerProvider ssmp)
+ {
+ return associatePdbWithSeq(choice, file, sequence, prompt, ssmp,
+ TFType.DEFAULT, null, true);
+ }
+
+ public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
+ SequenceI sequence, boolean prompt,
+ StructureSelectionManagerProvider ssmp, TFType tft,
+ String paeFilename, boolean doXferSettings)
{
PDBEntry entry = new PDBEntry();
- try
+ StructureFile pdbfile = StructureSelectionManager
+ .getStructureSelectionManager(ssmp)
+ .setMapping(false, new SequenceI[]
+ { sequence }, null, choice, file, tft, paeFilename,
+ doXferSettings);
+ if (pdbfile == null)
{
- MCview.PDBfile pdbfile = new MCview.PDBfile(choice, protocol);
+ // stacktrace already thrown so just return
+ return null;
+ }
+ if (pdbfile.getId() == null)
+ {
+ String reply = null;
- if (pdbfile.id == null)
+ if (prompt)
{
- String reply = null;
-
- if (prompt)
- {
- reply = JOptionPane
- .showInternalInputDialog(
- Desktop.desktop,
- MessageManager.getString("label.couldnt_find_pdb_id_in_file"),
- MessageManager.getString("label.no_pdb_id_in_file"), JOptionPane.QUESTION_MESSAGE);
- }
- if (reply == null)
- {
- return null;
- }
-
- entry.setId(reply);
+ reply = JvOptionPane.showInternalInputDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.couldnt_find_pdb_id_in_file"),
+ MessageManager.getString("label.no_pdb_id_in_file"),
+ JvOptionPane.QUESTION_MESSAGE);
}
- else
+ if (reply == null)
{
- entry.setId(pdbfile.id);
+ return null;
}
- } catch (java.io.IOException ex)
+
+ entry.setId(reply);
+ }
+ else
{
- ex.printStackTrace();
+ entry.setId(pdbfile.getId());
}
+ entry.setType(PDBEntry.Type.FILE);
- entry.setFile(choice);
- sequence.getDatasetSequence().addPDBId(entry);
+ if (pdbfile != null)
+ {
+ entry.setFile(choice);
+ sequence.getDatasetSequence().addPDBId(entry);
+ StructureSelectionManager.getStructureSelectionManager(ssmp)
+ .registerPDBEntry(entry);
+ entry.setStructureFile(pdbfile);
+ }
+ if (tft != null)
+ entry.setProperty("TFType", tft.name());
+ if (paeFilename != null)
+ entry.setProperty("PAEFile", paeFilename);
return entry;
}
-
}