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file format enum wip changes
[jalview.git]
/
src
/
jalview
/
io
/
BioJsHTMLOutput.java
diff --git
a/src/jalview/io/BioJsHTMLOutput.java
b/src/jalview/io/BioJsHTMLOutput.java
index
9454cae
..
0ebebc2
100644
(file)
--- a/
src/jalview/io/BioJsHTMLOutput.java
+++ b/
src/jalview/io/BioJsHTMLOutput.java
@@
-24,7
+24,9
@@
import jalview.api.AlignExportSettingI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentExportData;
import jalview.exceptions.NoFileSelectedException;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentExportData;
import jalview.exceptions.NoFileSelectedException;
+import jalview.gui.AlignFrame;
import jalview.gui.IProgressIndicator;
import jalview.gui.IProgressIndicator;
+import jalview.gui.OOMWarning;
import jalview.json.binding.biojs.BioJSReleasePojo;
import jalview.json.binding.biojs.BioJSRepositoryPojo;
import jalview.util.MessageManager;
import jalview.json.binding.biojs.BioJSReleasePojo;
import jalview.json.binding.biojs.BioJSRepositoryPojo;
import jalview.util.MessageManager;
@@
-81,10
+83,10
@@
public class BioJsHTMLOutput
public void exportJalviewAlignmentAsBioJsHtmlFile()
{
public void exportJalviewAlignmentAsBioJsHtmlFile()
{
+ String outputFile = null;
try
{
try
{
- String outputFile = getOutputFile();
- // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
+ outputFile = getOutputFile();
AlignExportSettingI exportSettings = new AlignExportSettingI()
{
@Override
AlignExportSettingI exportSettings = new AlignExportSettingI()
{
@Override
@@
-124,11
+126,11
@@
public class BioJsHTMLOutput
}
};
}
};
- AlignmentExportData exportData = jalview.gui.AlignFrame
- .getAlignmentForExport(JSONFile.FILE_DESC,
+ AlignmentExportData exportData = AlignFrame
+ .getAlignmentForExport(FileFormat.Json,
ap.getAlignViewport(), exportSettings);
String bioJSON = new FormatAdapter(ap, exportData.getSettings())
ap.getAlignViewport(), exportSettings);
String bioJSON = new FormatAdapter(ap, exportData.getSettings())
- .formatSequences(JSONFile.FILE_DESC, exportData
+ .formatSequences(FileFormat.Json, exportData
.getAlignment(), exportData.getOmitHidden(),
exportData.getStartEndPostions(), ap
.getAlignViewport().getColumnSelection());
.getAlignment(), exportData.getOmitHidden(),
exportData.getStartEndPostions(), ap
.getAlignViewport().getColumnSelection());
@@
-151,6
+153,11
@@
public class BioJsHTMLOutput
} catch (NoFileSelectedException ex)
{
// do noting if no file was selected
} catch (NoFileSelectedException ex)
{
// do noting if no file was selected
+ } catch (OutOfMemoryError err)
+ {
+ System.out.println("########################\n" + "OUT OF MEMORY "
+ + outputFile + "\n" + "########################");
+ new OOMWarning("Creating Image for " + outputFile, err);
} catch (Exception e)
{
pIndicator.setProgressBar(MessageManager.formatMessage(
} catch (Exception e)
{
pIndicator.setProgressBar(MessageManager.formatMessage(