/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.io;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignViewport;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.Objects;
+
+import jalview.api.AlignExportSettingsI;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignExportSettingsAdapter;
+import jalview.datamodel.AlignmentExportData;
import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
-import jalview.gui.SequenceRenderer;
+import jalview.gui.IProgressIndicator;
import jalview.util.MessageManager;
-import java.awt.Color;
-import java.awt.Font;
-import java.io.PrintWriter;
-
-public class HTMLOutput
+public abstract class HTMLOutput implements Runnable
{
- AlignViewport av;
+ protected AlignmentPanel ap;
- SequenceRenderer sr;
+ /*
+ * key for progress or status messages
+ */
+ protected long pSessionId;
- jalview.renderer.seqfeatures.FeatureRenderer fr;
+ /*
+ * (optional) place to write progress messages to
+ */
+ protected IProgressIndicator pIndicator;
- Color color;
+ protected File generatedFile;
- public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
- FeatureRenderer fr1)
- {
- this.av = ap.av;
- this.sr = sr;
+ String _bioJson = null;
- fr = new FeatureRenderer(ap);
- fr.transferSettings(fr1);
+ private String description;
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
- new String[] { "html" }, new String[] { "HTML files" },
- "HTML files");
+ /**
+ * Constructor given an alignment panel (which should not be null)
+ *
+ * @param ap
+ * @param desc
+ */
+ public HTMLOutput(AlignmentPanel ap, String desc)
+ {
+ this.ap = ap;
+ this.pIndicator = ap.alignFrame;
+ this.description = desc;
+ this.pSessionId = System.currentTimeMillis();
+ }
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_as_html"));
- chooser.setToolTipText(MessageManager.getString("action.save"));
+ /**
+ * Gets the BioJSON data as a string, with lazy evaluation (first time called
+ * only). If the output format is configured not to embed BioJSON, returns
+ * null.
+ *
+ * @return
+ */
+ public String getBioJSONData()
+ {
+ if (!isEmbedData())
+ {
+ return null;
+ }
+ if (_bioJson == null)
+ {
+ AlignExportSettingsI options = new AlignExportSettingsAdapter(true);
+ AlignmentExportData exportData = ap.getAlignViewport()
+ .getAlignExportData(options);
+ _bioJson = new FormatAdapter(ap, options).formatSequences(
+ FileFormat.Json, exportData.getAlignment(),
+ exportData.getOmitHidden(), exportData.getStartEndPostions(),
+ ap.getAlignViewport().getAlignment().getHiddenColumns());
+ }
- int value = chooser.showSaveDialog(null);
+ return _bioJson;
+ }
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ /**
+ * 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)
{
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
-
try
{
- PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
- choice));
- out.println("<HTML>");
- out.println("<style type=\"text/css\">");
- out.println("<!--");
- out.print("td {font-family: \"" + av.getFont().getFamily()
- + "\", \"" + av.getFont().getName() + "\", mono; "
- + "font-size: " + av.getFont().getSize() + "px; ");
-
- if (av.getFont().getStyle() == Font.BOLD)
+ isReader = new InputStreamReader(url.openStream());
+ buffReader = new BufferedReader(isReader);
+ String line;
+ String lineSeparator = System.getProperty("line.separator");
+ while ((line = buffReader.readLine()) != null)
{
- out.print("font-weight: BOLD; ");
+ sb.append(line).append(lineSeparator);
}
- if (av.getFont().getStyle() == Font.ITALIC)
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } finally
+ {
+ if (isReader != null)
{
- out.print("font-style: italic; ");
+ isReader.close();
}
- out.println("text-align: center; }");
-
- out.println("-->");
- out.println("</style>");
- out.println("<BODY>");
-
- if (av.getWrapAlignment())
- {
- drawWrappedAlignment(out);
- }
- else
+ if (buffReader != null)
{
- drawUnwrappedAlignment(out);
+ buffReader.close();
}
-
- out.println("\n</body>\n</html>");
- out.close();
- jalview.util.BrowserLauncher.openURL("file:///" + choice);
- } catch (Exception ex)
- {
- ex.printStackTrace();
}
}
+ return sb.toString();
}
- void drawUnwrappedAlignment(PrintWriter out)
+ public static String getImageMapHTML()
{
- out.println("<table border=\"1\"><tr><td>\n");
- out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
+ return new String("<html>\n" + "<head>\n"
+ + "<script language=\"JavaScript\">\n"
+ + "var ns4 = document.layers;\n"
+ + "var ns6 = document.getElementById && !document.all;\n"
+ + "var ie4 = document.all;\n" + "offsetX = 0;\n"
+ + "offsetY = 20;\n" + "var toolTipSTYLE=\"\";\n"
+ + "function initToolTips()\n" + "{\n" + " if(ns4||ns6||ie4)\n"
+ + " {\n"
+ + " if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
+ + " else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
+ + " else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
+ + " if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
+ + " else\n" + " {\n"
+ + " toolTipSTYLE.visibility = \"visible\";\n"
+ + " toolTipSTYLE.display = \"none\";\n" + " }\n"
+ + " document.onmousemove = moveToMouseLoc;\n" + " }\n"
+ + "}\n" + "function toolTip(msg, fg, bg)\n" + "{\n"
+ + " if(toolTip.arguments.length < 1) // hide\n" + " {\n"
+ + " if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
+ + " else toolTipSTYLE.display = \"none\";\n" + " }\n"
+ + " else // show\n" + " {\n"
+ + " if(!fg) fg = \"#555555\";\n"
+ + " if(!bg) bg = \"#FFFFFF\";\n" + " var content =\n"
+ + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
+ + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
+ + " '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
+ + " '\" size=\"-2\"> ' + msg +\n"
+ + " ' </font></td></table></td></table>';\n"
+ + " if(ns4)\n" + " {\n"
+ + " toolTipSTYLE.document.write(content);\n"
+ + " toolTipSTYLE.document.close();\n"
+ + " toolTipSTYLE.visibility = \"visible\";\n" + " }\n"
+ + " if(ns6)\n" + " {\n"
+ + " document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
+ + " toolTipSTYLE.display='block'\n" + " }\n"
+ + " if(ie4)\n" + " {\n"
+ + " document.all(\"toolTipLayer\").innerHTML=content;\n"
+ + " toolTipSTYLE.display='block'\n" + " }\n" + " }\n"
+ + "}\n" + "function moveToMouseLoc(e)\n" + "{\n"
+ + " if(ns4||ns6)\n" + " {\n" + " x = e.pageX;\n"
+ + " y = e.pageY;\n" + " }\n" + " else\n" + " {\n"
+ + " x = event.x + document.body.scrollLeft;\n"
+ + " y = event.y + document.body.scrollTop;\n" + " }\n"
+ + " toolTipSTYLE.left = x + offsetX;\n"
+ + " toolTipSTYLE.top = y + offsetY;\n" + " return true;\n"
+ + "}\n" + "</script>\n" + "</head>\n" + "<body>\n"
+ + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
+ + "<script language=\"JavaScript\"><!--\n"
+ + "initToolTips(); //--></script>\n");
+
+ }
- // ////////////
- SequenceI seq;
- AlignmentI alignment = av.getAlignment();
+ /**
+ * Prompts the user to choose an output file and returns the file path, or
+ * null on Cancel
+ *
+ * @return
+ */
+ public String getOutputFile()
+ {
+ String selectedFile = null;
- // draws the top row, the measure rule
- out.println("<tr><td colspan=\"6\"></td>");
+ // 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());
- int i = 0;
+ jvFileChooser
+ .setDialogTitle(MessageManager.getString("label.save_as_html"));
+ jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
- for (i = 10; i < (alignment.getWidth() - 10); i += 10)
+ int fileChooserOpt = jvFileChooser.showSaveDialog(null);
+ if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
{
- out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
+ Cache.setProperty("LAST_DIRECTORY",
+ jvFileChooser.getSelectedFile().getParent());
+ selectedFile = jvFileChooser.getSelectedFile().getPath();
}
- out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i
- + "<br>|</td>");
- out.println("</tr>");
+ return selectedFile;
+ }
- for (i = 0; i < alignment.getHeight(); i++)
+ protected void setProgressMessage(String message)
+ {
+ if (pIndicator != null && !isHeadless())
{
- seq = alignment.getSequenceAt(i);
-
- String id = seq.getDisplayId(av.getShowJVSuffix());
-
- out.println("<tr><td nowrap>" + id + " </td>");
-
- for (int res = 0; res < seq.getLength(); res++)
- {
- if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
- {
- color = sr.getResidueBoxColour(seq, res);
-
- color = fr.findFeatureColour(color, seq, res);
- }
- else
- {
- color = Color.white;
- }
-
- if (color.getRGB() < -1)
- {
- out.println("<td bgcolor=\"#"
- + jalview.util.Format.getHexString(color) + "\">"
- + seq.getCharAt(res) + "</td>");
- }
- else
- {
- out.println("<td>" + seq.getCharAt(res) + "</td>");
- }
- }
-
- out.println("</tr>");
+ pIndicator.setProgressBar(message, pSessionId);
+ }
+ else
+ {
+ System.out.println(message);
}
-
- // ////////////
- out.println("</table>");
- out.println("</td></tr></table>");
}
- void drawWrappedAlignment(PrintWriter out)
+ /**
+ * Answers true if HTML export is invoke in headless mode or false otherwise
+ *
+ * @return
+ */
+ protected boolean isHeadless()
{
- // //////////////////////////////////
- // / How many sequences and residues can we fit on a printable page?
- AlignmentI al = av.getAlignment();
- SequenceI seq;
- String r;
- String g;
- String b;
-
- out.println("<table border=\"1\"><tr><td>\n");
- out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
+ return System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true");
+ }
- for (int startRes = 0; startRes < al.getWidth(); startRes += av
- .getWrappedWidth())
+ /**
+ * 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())
{
- int endRes = startRes + av.getWrappedWidth();
-
- if (endRes > al.getWidth())
+ /*
+ try
{
- endRes = al.getWidth();
- }
-
- if (av.getScaleAboveWrapped())
+ */
+ jalview.util.BrowserLauncher.openURL("file:///" + getExportedFile());
+ /*
+ } catch (IOException e)
{
- out.println("<tr>");
-
- if (av.getScaleLeftWrapped())
- {
- out.println("<td colspan=\"7\"> </td>");
- }
- else
- {
- out.println("<td colspan=\"6\"> </td>");
- }
-
- for (int i = startRes + 10; i < endRes; i += 10)
- {
- out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
- }
-
- out.println("</tr>");
+ e.printStackTrace();
}
+ */
+ }
+ }
- int startPos, endPos;
- for (int s = 0; s < al.getHeight(); s++)
- {
- out.println("<tr>");
- seq = al.getSequenceAt(s);
-
- startPos = seq.findPosition(startRes);
- endPos = seq.findPosition(endRes) - 1;
-
- String id = seq.getDisplayId(av.getShowJVSuffix());
-
- out.println("<td nowrap>" + id + " </td>");
-
- if (av.getScaleLeftWrapped())
- {
- if (startPos > seq.getEnd() || endPos == 0)
- {
- out.println("<td nowrap> </td>");
- }
- else
- {
- out.println("<td nowrap>" + startPos + " </td>");
- }
- }
-
- for (int res = startRes; res < endRes; res++)
- {
- if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
- {
- color = sr.getResidueBoxColour(seq, res);
-
- color = fr.findFeatureColour(color, seq, res);
- }
- else
- {
- color = Color.white;
- }
-
- if (color.getRGB() < -1)
- {
- out.println("<td bgcolor=\"#"
- + jalview.util.Format.getHexString(color) + "\">"
- + seq.getCharAt(res) + "</td>");
- }
- else
- {
- out.println("<td>" + seq.getCharAt(res) + "</td>");
- }
-
- }
-
- if (av.getScaleRightWrapped()
- && endRes < startRes + av.getWrappedWidth())
- {
- out.println("<td colspan=\""
- + (startRes + av.getWrappedWidth() - endRes) + "\">"
- + " </td>");
- }
+ /**
+ * 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 File getExportedFile()
+ {
+ return generatedFile;
+ }
- if (av.getScaleRightWrapped() && startPos < endPos)
+ public void exportHTML(String outputFile)
+ {
+ setProgressMessage(MessageManager.formatMessage(
+ "status.exporting_alignment_as_x_file", getDescription()));
+ try
+ {
+ if (outputFile == null)
+ {
+ /*
+ * prompt for output file
+ */
+ outputFile = getOutputFile();
+ if (outputFile == null)
{
- out.println("<td nowrap> " + endPos + " </td>");
+ setProgressMessage(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation",
+ getDescription()));
+ return;
}
-
- out.println("</tr>");
- }
-
- if (endRes < al.getWidth())
- {
- out.println("<tr><td height=\"5\"></td></tr>");
}
+ generatedFile = new File(outputFile);
+ } catch (Exception e)
+ {
+ setProgressMessage(MessageManager
+ .formatMessage("info.error_creating_file", getDescription()));
+ e.printStackTrace();
+ return;
}
+ new Thread(this).start();
- out.println("</table>");
- out.println("</table>");
}
- public static String getImageMapHTML()
+ /**
+ * Answers a short description of the image format suitable for display in
+ * messages
+ *
+ * @return
+ */
+ protected final String getDescription()
{
- return new String(
- "<html>\n"
- + "<head>\n"
- + "<script language=\"JavaScript\">\n"
- + "var ns4 = document.layers;\n"
- + "var ns6 = document.getElementById && !document.all;\n"
- + "var ie4 = document.all;\n"
- + "offsetX = 0;\n"
- + "offsetY = 20;\n"
- + "var toolTipSTYLE=\"\";\n"
- + "function initToolTips()\n"
- + "{\n"
- + " if(ns4||ns6||ie4)\n"
- + " {\n"
- + " if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
- + " else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
- + " else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
- + " if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
- + " else\n"
- + " {\n"
- + " toolTipSTYLE.visibility = \"visible\";\n"
- + " toolTipSTYLE.display = \"none\";\n"
- + " }\n"
- + " document.onmousemove = moveToMouseLoc;\n"
- + " }\n"
- + "}\n"
- + "function toolTip(msg, fg, bg)\n"
- + "{\n"
- + " if(toolTip.arguments.length < 1) // hide\n"
- + " {\n"
- + " if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
- + " else toolTipSTYLE.display = \"none\";\n"
- + " }\n"
- + " else // show\n"
- + " {\n"
- + " if(!fg) fg = \"#555555\";\n"
- + " if(!bg) bg = \"#FFFFFF\";\n"
- + " var content =\n"
- + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
- + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
- + " '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
- + " '\" size=\"-2\"> ' + msg +\n"
- + " ' </font></td></table></td></table>';\n"
- + " if(ns4)\n"
- + " {\n"
- + " toolTipSTYLE.document.write(content);\n"
- + " toolTipSTYLE.document.close();\n"
- + " toolTipSTYLE.visibility = \"visible\";\n"
- + " }\n"
- + " if(ns6)\n"
- + " {\n"
- + " document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
- + " toolTipSTYLE.display='block'\n"
- + " }\n"
- + " if(ie4)\n"
- + " {\n"
- + " document.all(\"toolTipLayer\").innerHTML=content;\n"
- + " toolTipSTYLE.display='block'\n"
- + " }\n"
- + " }\n"
- + "}\n"
- + "function moveToMouseLoc(e)\n"
- + "{\n"
- + " if(ns4||ns6)\n"
- + " {\n"
- + " x = e.pageX;\n"
- + " y = e.pageY;\n"
- + " }\n"
- + " else\n"
- + " {\n"
- + " x = event.x + document.body.scrollLeft;\n"
- + " y = event.y + document.body.scrollTop;\n"
- + " }\n"
- + " toolTipSTYLE.left = x + offsetX;\n"
- + " toolTipSTYLE.top = y + offsetY;\n"
- + " return true;\n"
- + "}\n"
- + "</script>\n"
- + "</head>\n"
- + "<body>\n"
- + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
- + "<script language=\"JavaScript\"><!--\n"
- + "initToolTips(); //--></script>\n");
-
+ return description;
}
-}
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff