+ alignment = (Alignment) formatAdapter.readFile(TEST_JSON_FILE,
+ AppletFormatAdapter.FILE, JSONFile.FILE_DESC);
+ jf = (JSONFile) formatAdapter.getAlignFile();
+
+ AlignFrame af = new AlignFrame(alignment, jf.getHiddenSequences(),
+ jf.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures());
+ af.changeColour(jf.getColourScheme());
+ af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures());
+
+
+ formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings);
+ String jsonOutput = formatAdapter.formatSequences(JSONFile.FILE_DESC,
+ af.alignPanel.getAlignment(), false);
+
+ formatAdapter = new AppletFormatAdapter();
+ testAlignment = formatAdapter.readFile(jsonOutput,
+ AppletFormatAdapter.PASTE, JSONFile.FILE_DESC);
+ testJsonFile = (JSONFile) formatAdapter.getAlignFile();
+ // System.out.println(jsonOutput);