/*
* 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 java.io.IOException;
import java.util.List;
import org.jsoup.Jsoup;
import org.jsoup.nodes.Document;
import org.jsoup.nodes.Element;
import jalview.api.AlignViewControllerGuiI;
import jalview.schemes.ColourSchemeI;
public class HtmlFile extends AlignFile
{
public static final String FILE_EXT = "html";
public static final String FILE_DESC = "HTML";
private ColourSchemeI colourScheme;
private boolean showSeqFeatures;
private List hiddenColumns;
public HtmlFile()
{
super();
}
public HtmlFile(FileParse source) throws IOException
{
super(source);
}
public HtmlFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
@Override
public void parse() throws IOException
{
try
{
StringBuilder htmlData = new StringBuilder();
String currentLine;
while ((currentLine = nextLine()) != null)
{
htmlData.append(currentLine);
}
Document doc = Jsoup.parse(htmlData.toString());
Element content = doc.getElementById("seqData");
String alignmentJsonString = content.val();
JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
this.seqs = jsonFile.getSeqs();
this.seqGroups = jsonFile.getSeqGroups();
this.annotations = jsonFile.getAnnotations();
this.showSeqFeatures = jsonFile.isShowSeqFeatures();
this.colourScheme = jsonFile.getColourScheme();
this.hiddenColumns = jsonFile.getHiddenColumns();
} catch (Exception e)
{
e.printStackTrace();
}
}
public void applySettingsToAlignmentView(AlignViewControllerGuiI avc)
{
avc.setShowSeqFeatures(isShowSeqFeatures());
avc.changeColour(getColourScheme());
avc.setMenusForViewport();
avc.hideColumns(hiddenColumns);
avc.syncHiddenSequences();
}
@Override
public String print()
{
throw new UnsupportedOperationException(
"Print method of HtmlFile is not supported!");
}
public boolean isShowSeqFeatures()
{
return showSeqFeatures;
}
public void setShowSeqFeatures(boolean showSeqFeatures)
{
this.showSeqFeatures = showSeqFeatures;
}
public ColourSchemeI getColourScheme()
{
return colourScheme;
}
public void setColourScheme(ColourSchemeI colourScheme)
{
this.colourScheme = colourScheme;
}
}