\r
import jalview.schemes.*;\r
\r
-import jalview.gui.*;\r
-\r
import java.io.*;\r
\r
import java.net.*;\r
*\r
* @param file DOCUMENT ME!\r
*/\r
- public AlignFrame LoadJalviewAlign(String file)\r
+ public AlignFrame LoadJalviewAlign(final String file)\r
{\r
\r
jalview.gui.AlignFrame af = null;\r
\r
object = (JalviewModel) object.unmarshal(in);\r
\r
- af = LoadFromObject(object);\r
+ af = LoadFromObject(object, file);\r
entryCount++;\r
}\r
}\r
while (jarentry != null);\r
}\r
- catch(java.net.UnknownHostException ex)\r
+ catch (final java.net.UnknownHostException ex)\r
{\r
ex.printStackTrace();\r
- System.err.println("Couldn't locate Jalview XML file : " +\r
- ex + "\n");\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Couldn't locate " + file,\r
- "URL not found",\r
- JOptionPane.WARNING_MESSAGE);\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
\r
+ System.err.println("Couldn't locate Jalview XML file : " +\r
+ ex + "\n");\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Couldn't locate " + file,\r
+ "URL not found",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ });\r
}\r
catch (Exception ex)\r
{\r
ex.printStackTrace();\r
- System.err.println("Exception whilst loading jalview XML file : " +\r
- ex + "\n");\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Error loading " + file,\r
- "Error loading Jalview file",\r
- JOptionPane.WARNING_MESSAGE);\r
+ System.err.println("Exception whilst loading jalview XML file : " +\r
+ ex + "\n");\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Error loading " + file,\r
+ "Error loading Jalview file",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ });\r
}\r
\r
return af;\r
}\r
\r
- AlignFrame LoadFromObject(JalviewModel object)\r
+ AlignFrame LoadFromObject(JalviewModel object, String file)\r
{\r
Vector seqids = new Vector();\r
SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
\r
AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());\r
\r
+ af.setFileName(file, "Jalview");\r
+\r
for (int i = 0; i < JSEQ.length; i++)\r
{\r
af.viewport.setSequenceColour(\r
if (groups[i].getConsThreshold() != 0)\r
{\r
jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
- ResidueProperties.propHash, 3, sg.getSequences(false), 0,\r
+ ResidueProperties.propHash, 3, sg.getSequences(null), 0,\r
sg.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, 25);\r