X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;h=c9951f54ed60cc74ca9921e5e52c04a7c9242f4c;hb=afe4b88500a5d61bc8d312909cfdde2b7cdd53df;hp=ade341d52436c55d49ac13b75a2ed07c3c2199b9;hpb=c5677e9860106a821a3e6e0429b20ede7b9a732a;p=jalview.git
diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index ade341d..c9951f5 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -1,99 +1,110 @@
-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+/*
+ * 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 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 jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
-import jalview.io.IdentifyFile;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.structure.StructureImportSettings.TFType;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
/**
* GUI related routines for associating PDB files with sequences
+ *
* @author JimP
- *
+ *
*/
public class AssociatePdbFileWithSeq
{
-/**
- * assocate the given PDB file with
- * @param choice
- * @param sequence
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- */
- public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ /**
+ * assocate the given PDB file with
+ *
+ * @param choice
+ * @param sequence
+ */
+ 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)
{
-
- System.out.println("This is a annotation PDB");
-
-
- 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,
- "Couldn't find a PDB id in the file supplied."
- + "Please enter an Id to identify this structure.",
- "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;
-
}
-
}