+ expectedAnnots.put(alignAnnot.label, alignAnnot);
+
+ expectedColSel.hideColumns(32, 33);
+ expectedColSel.hideColumns(34, 34);
+
+ TEST_SEQ_HEIGHT = expectedSeqs.size();
+ TEST_GRP_HEIGHT = expectedGrps.size();
+ TEST_ANOT_HEIGHT = expectedAnnots.size();
+ TEST_CS_HEIGHT = expectedColSel.getHiddenColumns().size();
+
+ AlignExportSettingI exportSettings = new AlignExportSettingI()
+ {
+ @Override
+ public boolean isExportHiddenSequences()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportHiddenColumns()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportGroups()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportFeatures()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportAnnotations()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isCancelled()
+ {
+ return false;
+ }
+ };
+
+ AppletFormatAdapter formatAdapter = new AppletFormatAdapter();
+ try
+ {
+ alignment = (Alignment) formatAdapter.readFile(TEST_JSON_FILE,
+ DataSourceType.FILE, FileFormat.Json);
+ jf = (JSONFile) formatAdapter.getAlignFile();
+
+ AlignFrame af = new AlignFrame(alignment, jf.getHiddenSequences(),
+ jf.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures());
+ String colourSchemeName = jf.getGlobalColourScheme();
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, alignment);
+ af.changeColour(cs);
+ af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures());
+
+ formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings);
+ String jsonOutput = formatAdapter.formatSequences(FileFormat.Json,
+ af.alignPanel.getAlignment(), false);
+
+ formatAdapter = new AppletFormatAdapter();
+ testAlignment = formatAdapter.readFile(jsonOutput,
+ DataSourceType.PASTE, FileFormat.Json);
+ testJsonFile = (JSONFile) formatAdapter.getAlignFile();
+ // System.out.println(jsonOutput);
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }