/*
* 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.datamodel.AlignmentExportData;
import jalview.exceptions.NoFileSelectedException;
import jalview.gui.AlignmentPanel;
import jalview.gui.IProgressIndicator;
import jalview.util.MessageManager;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.URL;
import java.util.Objects;
public abstract class HTMLOutput implements Runnable
{
protected AlignmentPanel ap;
protected long pSessionId;
protected IProgressIndicator pIndicator;
protected File generatedFile;
public HTMLOutput(AlignmentPanel ap)
{
if (ap != null)
{
this.ap = ap;
this.pIndicator = ap.alignFrame;
}
}
public String getBioJSONData()
{
return getBioJSONData(null);
}
public String getBioJSONData(AlignExportSettingI exportSettings)
{
if (!isEmbedData())
{
return null;
}
if (exportSettings == null)
{
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(FileFormat.Json, ap.getAlignViewport(),
exportSettings);
String bioJSON = new FormatAdapter(ap, exportData.getSettings())
.formatSequences(FileFormat.Json, exportData.getAlignment(),
exportData.getOmitHidden(),
exportData.getStartEndPostions(), ap.getAlignViewport()
.getAlignment().getHiddenColumns());
return bioJSON;
}
/**
* Read a template file content as string
*
* @param file
* - the file to be read
* @return File content as String
* @throws IOException
*/
public static String readFileAsString(File file) throws IOException
{
InputStreamReader isReader = null;
BufferedReader buffReader = null;
StringBuilder sb = new StringBuilder();
Objects.requireNonNull(file, "File must not be null!");
@SuppressWarnings("deprecation")
URL url = file.toURL();
if (url != null)
{
try
{
isReader = new InputStreamReader(url.openStream());
buffReader = new BufferedReader(isReader);
String line;
String lineSeparator = System.getProperty("line.separator");
while ((line = buffReader.readLine()) != null)
{
sb.append(line).append(lineSeparator);
}
} catch (Exception ex)
{
ex.printStackTrace();
} finally
{
if (isReader != null)
{
isReader.close();
}
if (buffReader != null)
{
buffReader.close();
}
}
}
return sb.toString();
}
public static String getImageMapHTML()
{
return new String("\n" + "\n"
+ "\n" + "\n" + "\n"
+ "\n"
+ "\n");
}
public String getOutputFile() throws NoFileSelectedException
{
String selectedFile = null;
if (pIndicator != null && !isHeadless())
{
pIndicator.setProgressBar(MessageManager.formatMessage(
"status.waiting_for_user_to_select_output_file", "HTML"),
pSessionId);
}
// TODO: JAL-3048 generate html rendered view (requires SvgGraphics and/or
// Jalview HTML rendering system- probably not required for Jalview-JS)
JalviewFileChooser jvFileChooser = new JalviewFileChooser("html",
"HTML files");
jvFileChooser.setFileView(new JalviewFileView());
jvFileChooser
.setDialogTitle(MessageManager.getString("label.save_as_html"));
jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
int fileChooserOpt = jvFileChooser.showSaveDialog(null);
if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
{
jalview.bin.Cache.setProperty("LAST_DIRECTORY",
jvFileChooser.getSelectedFile().getParent());
selectedFile = jvFileChooser.getSelectedFile().getPath();
}
else
{
throw new NoFileSelectedException("No file was selected.");
}
return selectedFile;
}
protected void setProgressMessage(String message)
{
if (pIndicator != null && !isHeadless())
{
pIndicator.setProgressBar(message, pSessionId);
}
else
{
System.out.println(message);
}
}
/**
* Answers true if HTML export is invoke in headless mode or false otherwise
*
* @return
*/
protected boolean isHeadless()
{
return System.getProperty("java.awt.headless") != null
&& System.getProperty("java.awt.headless").equals("true");
}
/**
* This method provides implementation of consistent behaviour which should
* occur before a HTML file export. It MUST be called at the start of the
* exportHTML() method implementation.
*/
protected void exportStarted()
{
pSessionId = System.currentTimeMillis();
}
/**
* This method provides implementation of consistent behaviour which should
* occur after a HTML file export. It MUST be called at the end of the
* exportHTML() method implementation.
*/
protected void exportCompleted()
{
if (isLaunchInBrowserAfterExport() && !isHeadless())
{
try
{
jalview.util.BrowserLauncher
.openURL("file:///" + getExportedFile());
} catch (IOException e)
{
e.printStackTrace();
}
}
}
/**
* if this answers true then BioJSON data will be embedded to the exported
* HTML file otherwise it won't be embedded.
*
* @return
*/
public abstract boolean isEmbedData();
/**
* if this answers true then the generated HTML file is opened for viewing in
* a browser after its generation otherwise it won't be opened in a browser
*
* @return
*/
public abstract boolean isLaunchInBrowserAfterExport();
/**
* handle to the generated HTML file
*
* @return
*/
public abstract File getExportedFile();
/**
* This is the main method to handle the HTML generation.
*
* @param outputFile
* the file path of the generated HTML
*/
public abstract void exportHTML(String outputFile);
}