/*
* 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.FeatureRenderer;
import jalview.datamodel.AlignmentExportData;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.HTMLOptions;
import jalview.math.AlignmentDimension;
import jalview.util.MessageManager;
import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.print.Printable;
import java.awt.print.PrinterException;
import java.io.File;
import java.io.FileOutputStream;
import org.jfree.graphics2d.svg.SVGGraphics2D;
import org.jfree.graphics2d.svg.SVGHints;
public class HtmlSvgOutput
{
AlignViewport av;
FeatureRenderer fr;
AlignmentPanel ap;
public HtmlSvgOutput(File file, AlignmentPanel ap)
{
this.av = ap.av;
this.ap = ap;
fr = ap.cloneFeatureRenderer();
generateHtmlSvgOutput(file);
}
public void generateHtmlSvgOutput(File file)
{
try
{
if (file == null)
{
JalviewFileChooser chooser = getHTMLChooser();
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(ap.alignFrame.getTitle());
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(ap.alignFrame);
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
.getSelectedFile().getParent());
file = chooser.getSelectedFile();
}
else
{
return;
}
}
AlignmentDimension aDimension = ap.getAlignmentDimension();
SVGGraphics2D g1 = new SVGGraphics2D(aDimension.getWidth(),
aDimension.getHeight());
SVGGraphics2D g2 = new SVGGraphics2D(aDimension.getWidth(),
aDimension.getHeight());
String renderStyle = jalview.bin.Cache.getDefault("HTML_RENDERING",
"Prompt each time");
// If we need to prompt, and if the GUI is visible then
// Prompt for rendering style
if (renderStyle.equalsIgnoreCase("Prompt each time")
&& !(System.getProperty("java.awt.headless") != null && System
.getProperty("java.awt.headless").equals("true")))
{
HTMLOptions svgOption = new HTMLOptions();
renderStyle = svgOption.getValue();
if (renderStyle == null || svgOption.cancelled)
{
return;
}
}
if (renderStyle.equalsIgnoreCase("lineart"))
{
g1.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
g2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
}
printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, g1,
g2);
String titleSvgData = g1.getSVGDocument();
String alignSvgData = g2.getSVGDocument();
String jsonData = null;
boolean isEmbbedBioJSON = Boolean.valueOf(jalview.bin.Cache
.getDefault("EXPORT_EMBBED_BIOJSON", "true"));
if (isEmbbedBioJSON)
{
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, av,
exportSettings);
jsonData = new FormatAdapter(ap, exportData.getSettings())
.formatSequences(JSONFile.FILE_DESC,
exportData.getAlignment(),
exportData.getOmitHidden(),
exportData.getStartEndPostions(),
av.getColumnSelection());
}
String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
FileOutputStream out = new FileOutputStream(file);
out.write(htmlData.getBytes());
out.flush();
out.close();
if (!(System.getProperty("java.awt.headless") != null && System
.getProperty("java.awt.headless").equals("true")))
{
jalview.util.BrowserLauncher.openURL("file:///" + file);
}
} catch (Exception e)
{
e.printStackTrace();
}
}
static JalviewFileChooser getHTMLChooser()
{
return new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
new String[] { "html" },
new String[] { "Hypertext Markup Language" },
"Hypertext Markup Language");
}
public int printUnwrapped(int pwidth, int pheight, int pi, Graphics... pg)
throws PrinterException
{
int idWidth = ap.getVisibleIdWidth(false);
FontMetrics fm = ap.getFontMetrics(av.getFont());
int scaleHeight = av.getCharHeight() + fm.getDescent();
pg[0].setColor(Color.white);
pg[0].fillRect(0, 0, pwidth, pheight);
pg[0].setFont(av.getFont());
// //////////////////////////////////
// / How many sequences and residues can we fit on a printable page?
int totalRes = (pwidth - idWidth) / av.getCharWidth();
int totalSeq = (pheight - scaleHeight) / av.getCharHeight() - 1;
int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
// ///////////////////////////
// / Only print these sequences and residues on this page
int startRes;
// ///////////////////////////
// / Only print these sequences and residues on this page
int endRes;
// ///////////////////////////
// / Only print these sequences and residues on this page
int startSeq;
// ///////////////////////////
// / Only print these sequences and residues on this page
int endSeq;
startRes = (pi % pagesWide) * totalRes;
endRes = (startRes + totalRes) - 1;
if (endRes > (av.getAlignment().getWidth() - 1))
{
endRes = av.getAlignment().getWidth() - 1;
}
startSeq = (pi / pagesWide) * totalSeq;
endSeq = startSeq + totalSeq;
if (endSeq > av.getAlignment().getHeight())
{
endSeq = av.getAlignment().getHeight();
}
int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1)
* pheight;
if (av.isShowAnnotation())
{
pagesHigh += ap.getAnnotationPanel().adjustPanelHeight() + 3;
}
pagesHigh /= pheight;
if (pi >= (pagesWide * pagesHigh))
{
return Printable.NO_SUCH_PAGE;
}
// draw Scale
pg[1].translate(0, 0);
ap.getScalePanel().drawScale(pg[1], startRes, endRes, pwidth - idWidth,
scaleHeight);
pg[1].translate(-idWidth, scaleHeight);
// //////////////
// Draw the ids
Color currentColor = null;
Color currentTextColor = null;
pg[0].translate(0, scaleHeight);
pg[0].setFont(ap.getIdPanel().getIdCanvas().getIdfont());
SequenceI seq;
for (int i = startSeq; i < endSeq; i++)
{
seq = av.getAlignment().getSequenceAt(i);
if ((av.getSelectionGroup() != null)
&& av.getSelectionGroup().getSequences(null).contains(seq))
{
currentColor = Color.gray;
currentTextColor = Color.black;
}
else
{
currentColor = av.getSequenceColour(seq);
currentTextColor = Color.black;
}
pg[0].setColor(currentColor);
pg[0].fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth,
av.getCharHeight());
pg[0].setColor(currentTextColor);
int xPos = 0;
if (av.isRightAlignIds())
{
fm = pg[0].getFontMetrics();
xPos = idWidth
- fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix()))
- 4;
}
pg[0].drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
(((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
- (av.getCharHeight() / 5));
}
pg[0].setFont(av.getFont());
pg[0].translate(idWidth, 0);
// draw main sequence panel
pg[1].translate(idWidth, 0);
ap.getSeqPanel().seqCanvas.drawPanel(pg[1], startRes, endRes, startSeq,
endSeq, 0);
if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
{
// draw annotation label - need to offset for current scroll position
int offset = -ap.getAlabels().getScrollOffset();
pg[0].translate(0, offset);
pg[0].translate(-idWidth - 3,
(endSeq - startSeq) * av.getCharHeight() + 3);
ap.getAlabels().drawComponent(pg[0], idWidth);
pg[0].translate(idWidth + 3, 0);
pg[0].translate(0, -offset);
// draw annotation - need to offset for current scroll position
pg[1].translate(0, offset);
pg[1].translate(-idWidth - 3,
(endSeq - startSeq) * av.getCharHeight() + 3);
pg[1].translate(idWidth + 3, 0);
ap.getAnnotationPanel().renderer.drawComponent(
ap.getAnnotationPanel(), av, pg[1], -1, startRes, endRes + 1);
pg[1].translate(0, -offset);
}
return Printable.PAGE_EXISTS;
}
private String getHtml(String titleSvg, String alignmentSvg,
String jsonData)
{
StringBuilder htmlSvg = new StringBuilder();
htmlSvg.append("\n");
if (jsonData != null)
{
htmlSvg.append(" ");
htmlSvg.append("");
htmlSvg.append("