+/*
+ * 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentExportData;
import jalview.exceptions.NoFileSelectedException;
-import jalview.gui.AlignViewport;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
-import jalview.json.binding.v1.BioJSReleasePojo;
-import jalview.json.binding.v1.BioJSRepositoryPojo;
+import jalview.json.binding.biojs.BioJSReleasePojo;
+import jalview.json.binding.biojs.BioJSRepositoryPojo;
import jalview.util.MessageManager;
import java.io.BufferedInputStream;
import java.util.Objects;
import java.util.TreeMap;
-
public class BioJsHTMLOutput
{
- private AlignViewport av;
+ private AlignmentViewPanel ap;
private static File currentBJSTemplateFile;
public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.Cache
.getDefault(
"biojs_template_git_repo",
- "https://raw.githubusercontent.com/tcofoegbu/bjs-template/master/package.json");
+ "https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
- public BioJsHTMLOutput(AlignmentPanel ap, FeatureRenderer fr1)
+ public BioJsHTMLOutput(AlignmentViewPanel ap)
{
if (ap != null)
{
- this.av = ap.av;
- av.setFeatureRenderer(new FeatureRenderer(ap));
+ this.ap = ap;
}
}
try
{
String outputFile = getOutputFile();
- String jalviewAlignmentJson = JSONFile.getJSONData(av);
+ // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
+ AlignExportSettingI exportSettings = new AlignExportSettingI()
+ {
+ @Override
+ public boolean isExportHiddenSequences()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportHiddenColumns()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportAnnotations()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportFeatures()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportGroups()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isCancelled()
+ {
+ return false;
+ }
+
+ };
+ AlignmentExportData exportData = jalview.gui.AlignFrame
+ .getAlignmentForExport(JSONFile.FILE_DESC,
+ ap.getAlignViewport(), exportSettings);
+ if (exportData.getSettings().isCancelled())
+ {
+ return;
+ }
+ String jalviewAlignmentJson = new FormatAdapter(ap,
+ exportData.getSettings()).formatSequences(JSONFile.FILE_DESC,
+ exportData.getAlignment(), exportData.getOmitHidden(),
+ exportData.getStartEndPostions(), ap.getAlignViewport()
+ .getColumnSelection());
+
String bioJSTemplateString = getBioJsTemplateAsString();
String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
- .replaceAll(
-"#sequenceData#", jalviewAlignmentJson)
+ .replaceAll("#sequenceData#", jalviewAlignmentJson)
.toString();
PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
{
String selectedFile = null;
JalviewFileChooser jvFileChooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "html" }, new String[]
- { "HTML files" }, "HTML files");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "html" }, new String[] { "HTML files" },
+ "HTML files");
jvFileChooser.setFileView(new JalviewFileView());
- // TODO uncomment when supported by MassageManager
jvFileChooser.setDialogTitle(MessageManager
.getString("label.save_as_biojs_html"));
- jvFileChooser.setDialogTitle("save as BioJs HTML");
jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
int fileChooserOpt = jvFileChooser.showSaveDialog(null);
return selectedFile;
}
-
- public static String getBioJsTemplateAsString()
- throws IOException
+ public static String getBioJsTemplateAsString() throws IOException
{
InputStreamReader isReader = null;
BufferedReader buffReader = null;
try
{
String gitRepoPkgJson = getURLContentAsString(BJS_TEMPLATE_GIT_REPO);
- BioJSRepositoryPojo release = new BioJSRepositoryPojo(
- gitRepoPkgJson);
- syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
- refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
+ if (gitRepoPkgJson != null)
+ {
+ BioJSRepositoryPojo release = new BioJSRepositoryPojo(
+ gitRepoPkgJson);
+ syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
+ refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
+ }
} catch (URISyntaxException e)
{
e.printStackTrace();
}
-
public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
{
for (BioJSReleasePojo bjsRelease : repo.getReleases())