X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=9454cae12b65f3adba5f5fead6759bd7e2430758;hb=c70d42a1afc972ddb3757b9ec4cece3458d396a1;hp=50486f229d9d2bd77bb37ba9a70ae35a416c5ba4;hpb=02d6b4895305788dbf460a6e0334dba93b0b3423;p=jalview.git
diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 50486f2..9454cae 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,9 +1,30 @@
+/*
+ * 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 .
+ * 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.IProgressIndicator;
import jalview.json.binding.biojs.BioJSReleasePojo;
import jalview.json.binding.biojs.BioJSRepositoryPojo;
import jalview.util.MessageManager;
@@ -20,11 +41,16 @@ import java.net.URL;
import java.util.Objects;
import java.util.TreeMap;
-
public class BioJsHTMLOutput
{
private AlignmentViewPanel ap;
+ private long pSessionId;
+
+ private IProgressIndicator pIndicator;
+
+ private boolean headless;
+
private static File currentBJSTemplateFile;
private static TreeMap bioJsMSAVersions;
@@ -40,11 +66,16 @@ public class BioJsHTMLOutput
"biojs_template_git_repo",
"https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
- public BioJsHTMLOutput(AlignmentViewPanel ap)
+ public BioJsHTMLOutput(AlignmentViewPanel ap,
+ IProgressIndicator pIndicator)
{
if (ap != null)
{
this.ap = ap;
+ this.pSessionId = System.currentTimeMillis();
+ this.pIndicator = pIndicator;
+ this.headless = (System.getProperty("java.awt.headless") != null && System
+ .getProperty("java.awt.headless").equals("true"));
}
}
@@ -94,24 +125,17 @@ public class BioJsHTMLOutput
};
AlignmentExportData exportData = jalview.gui.AlignFrame
- .getAlignmentForExport(
-JSONFile.FILE_DESC,
+ .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 bioJSON = 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)
- .toString();
+ .replaceAll("#sequenceData#", bioJSON).toString();
PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
outputFile));
@@ -119,11 +143,18 @@ JSONFile.FILE_DESC,
out.flush();
out.close();
jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
+ if (pIndicator != null && !headless)
+ {
+ pIndicator.setProgressBar(MessageManager.formatMessage(
+ "status.export_complete", "BioJS"), pSessionId);
+ }
} catch (NoFileSelectedException ex)
{
// do noting if no file was selected
} catch (Exception e)
{
+ pIndicator.setProgressBar(MessageManager.formatMessage(
+ "info.error_creating_file", "HTML"), pSessionId);
e.printStackTrace();
}
}
@@ -131,10 +162,17 @@ JSONFile.FILE_DESC,
public String getOutputFile() throws NoFileSelectedException
{
String selectedFile = null;
+ if (pIndicator != null && !headless)
+ {
+ pIndicator.setProgressBar(MessageManager.formatMessage(
+ "status.waiting_for_user_to_select_output_file", "HTML"),
+ pSessionId);
+ }
+
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());
jvFileChooser.setDialogTitle(MessageManager
@@ -150,14 +188,15 @@ JSONFile.FILE_DESC,
}
else
{
+ pIndicator.setProgressBar(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation", "BioJS"),
+ pSessionId);
throw new NoFileSelectedException("No file was selected.");
}
return selectedFile;
}
-
- public static String getBioJsTemplateAsString()
- throws IOException
+ public static String getBioJsTemplateAsString() throws IOException
{
InputStreamReader isReader = null;
BufferedReader buffReader = null;
@@ -235,6 +274,7 @@ JSONFile.FILE_DESC,
{
Thread updateThread = new Thread()
{
+ @Override
public void run()
{
try
@@ -257,7 +297,6 @@ JSONFile.FILE_DESC,
}
-
public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
{
for (BioJSReleasePojo bjsRelease : repo.getReleases())