-package jalview.io;\r
-\r
-import jalview.gui.*;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import java.awt.*;\r
-import javax.swing.*;\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-\r
-public class HTMLOutput\r
-{\r
- AlignViewport av;\r
- SequenceRenderer sr;\r
- Color color;\r
-\r
- public HTMLOutput(AlignViewport av)\r
- {\r
- this.av = av;\r
- sr = new SequenceRenderer(av);\r
- JalviewFileChooser chooser = new JalviewFileChooser(\r
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
- new String[]{"html"},\r
- new String[]{"HTML files"},\r
- "HTML files");\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save as HTML");\r
- chooser.setToolTipText("Save");\r
- int value = chooser.showSaveDialog(null);\r
- if(value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());\r
- try{\r
- PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(choice));\r
- out.println("<HTML>");\r
- out.println("<style type=\"text/css\">");\r
- out.println("<!--");\r
- out.print("td {font-family: \""+av.getFont().getFamily()+"\", \""+av.getFont().getName()+ "\", mono; "\r
- +"font-size: "+av.getFont().getSize()+"px; ");\r
-\r
-\r
- if (av.getFont().getStyle() == Font.BOLD)\r
- out.print("font-weight: BOLD; ");\r
-\r
- if (av.getFont().getStyle() == Font.ITALIC)\r
- out.print("font-style: italic; ");\r
-\r
- out.println("text-align: center; }");\r
-\r
- out.println("-->");\r
- out.println("</style>");\r
- out.println("<BODY>");\r
-\r
-\r
- if(av.getWrapAlignment())\r
- drawWrappedAlignment(out);\r
- else\r
- drawUnwrappedAlignment(out);\r
-\r
- out.println("\n</body>\n</html>");\r
- out.close();\r
- jalview.util.BrowserLauncher.openURL( "file:///"+choice );\r
- }\r
- catch(Exception ex){ex.printStackTrace();}\r
- }\r
- }\r
-\r
- void drawUnwrappedAlignment(PrintWriter out)\r
- {\r
-\r
- out.println("<table border=\"1\"><tr><td>\n");\r
- out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
-\r
-\r
- //////////////\r
- SequenceGroup [] groups;\r
- SequenceI seq;\r
- ColourSchemeI cs = null;\r
- AlignmentI alignment = av.getAlignment();\r
- String r,g,b;\r
-\r
- // draws the top row, the measure rule\r
- out.println("<tr><td colspan=\"6\"></td>");\r
- int i=0;\r
- for(i=10; i<alignment.getWidth()-10; i+=10)\r
- out.println("<td colspan=\"9\">"+i+"<br>|</td><td></td>");\r
-\r
- out.println("<td colspan=\"3\"></td><td colspan=\"3\">"+i+"<br>|</td>");\r
- out.println("</tr>");\r
-\r
- for (i = 0; i < alignment.getHeight(); i++)\r
- {\r
- seq = alignment.getSequenceAt(i);\r
- groups = alignment.findAllGroups( seq );\r
- if(av.getShowFullId())\r
- out.println("<tr><td nowrap>"+seq.getDisplayId()+" </td>");\r
- else\r
- out.println("<tr><td nowrap>"+seq.getName()+" </td>");\r
-\r
-\r
-\r
- for (int res = 0; res < seq.getLength(); res++)\r
- {\r
- cs = av.getGlobalColourScheme();\r
-\r
- if(groups!=null)\r
- {\r
- for (int k = 0; k < groups.length; k++)\r
- if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)\r
- {\r
- cs = groups[k].cs;\r
- break;\r
- }\r
- }\r
-\r
-\r
- color = sr.getResidueBoxColour(cs, seq, res);\r
-\r
- if(color.getRGB()<-1)\r
- {\r
- out.println("<td bgcolor=\"#"\r
- + jalview.util.Format.getHexString(color)\r
- + "\">"+seq.getCharAt(res)+"</td>");\r
- }\r
- else\r
- out.println("<td>"+seq.getCharAt(res)+"</td>");\r
-\r
- }\r
-\r
- out.println("</tr>");\r
- }\r
- //////////////\r
- out.println("</table>");\r
- out.println("</td></tr></table>");\r
-\r
- }\r
-\r
- void drawWrappedAlignment(PrintWriter out)\r
- {\r
- ////////////////////////////////////\r
- /// How many sequences and residues can we fit on a printable page?\r
- AlignmentI al = av.getAlignment();\r
- SequenceGroup [] groups;\r
- SequenceI seq;\r
- ColourSchemeI cs = null;\r
- String r,g,b;\r
-\r
- out.println("<table border=\"1\"><tr><td>\n");\r
- out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
-\r
- for(int startRes=0; startRes<al.getWidth(); startRes+=av.getChunkWidth())\r
- {\r
-\r
- int endRes = startRes+av.getChunkWidth();\r
- if(endRes>al.getWidth())\r
- endRes = al.getWidth();\r
-\r
- out.println("<tr>");\r
- out.println("<td colspan=\"6\"> </td>");\r
- for (int i = startRes+10; i < endRes; i += 10)\r
- out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
-\r
- // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +\r
- // "<br>|</td>");\r
- out.println("</tr>");\r
-\r
-\r
-\r
- for (int s = 0; s < al.getHeight(); s++)\r
- {\r
- out.println("<tr>");\r
- seq = al.getSequenceAt(s);\r
- groups = al.findAllGroups( seq );\r
- if(av.getShowFullId())\r
- out.println("<td nowrap>"+seq.getDisplayId()+" </td>");\r
- else\r
- out.println("<td nowrap>"+seq.getName()+" </td>");\r
-\r
- for (int res = startRes; res < endRes; res++)\r
- {\r
- cs = av.getGlobalColourScheme();\r
- if(groups!=null)\r
- {\r
- for (int k = 0; k < groups.length; k++)\r
- if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)\r
- {\r
- cs = groups[k].cs;\r
- break;\r
- }\r
- }\r
-\r
- color = sr.getResidueBoxColour(cs, seq, res);\r
-\r
- if(color.getRGB()<-1)\r
- {\r
- r = Integer.toHexString(color.getRed());\r
- if(r.length()<2)\r
- r = "0"+r;\r
- g = Integer.toHexString(color.getGreen());\r
- if(g.length()<2)\r
- g = "0"+g;\r
- b = Integer.toHexString(color.getBlue());\r
- if(b.length()<2)\r
- b = "0"+b;\r
- out.println("<td bgcolor=\"#"+ r + g + b + "\">"+seq.getCharAt(res)+"</td>");\r
- }\r
- else\r
- out.println("<td>"+seq.getCharAt(res)+"</td>");\r
-\r
- }\r
-\r
- out.println("</tr>");\r
-\r
- }\r
- if(endRes<al.getWidth())\r
- out.println("<tr><td height=\"5\"></td></tr>");\r
-\r
-\r
-\r
- }\r
-\r
- out.println("</table>");\r
- out.println("</table>");\r
-\r
-\r
-\r
- }\r
-\r
-\r
-}\r
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+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.IProgressIndicator;
+import jalview.util.MessageManager;
+
+public abstract class HTMLOutput implements Runnable
+{
+ protected AlignmentPanel ap;
+
+ /*
+ * key for progress or status messages
+ */
+ protected long pSessionId;
+
+ /*
+ * (optional) place to write progress messages to
+ */
+ protected IProgressIndicator pIndicator;
+
+ protected File generatedFile;
+
+ String _bioJson = null;
+
+ private String description;
+
+ /**
+ * 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();
+ }
+
+ /**
+ * 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());
+ }
+
+ 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("<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");
+
+ }
+
+ /**
+ * Prompts the user to choose an output file and returns the file path, or
+ * null on Cancel
+ *
+ * @return
+ */
+ public String getOutputFile()
+ {
+ String selectedFile = null;
+
+ // 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)
+ {
+ Cache.setProperty("LAST_DIRECTORY",
+ jvFileChooser.getSelectedFile().getParent());
+ selectedFile = jvFileChooser.getSelectedFile().getPath();
+ }
+
+ 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 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 File getExportedFile()
+ {
+ return generatedFile;
+ }
+
+ 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)
+ {
+ setProgressMessage(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation",
+ getDescription()));
+ return;
+ }
+ }
+ generatedFile = new File(outputFile);
+ } catch (Exception e)
+ {
+ setProgressMessage(MessageManager
+ .formatMessage("info.error_creating_file", getDescription()));
+ e.printStackTrace();
+ return;
+ }
+ new Thread(this).start();
+
+ }
+
+ /**
+ * Answers a short description of the image format suitable for display in
+ * messages
+ *
+ * @return
+ */
+ protected final String getDescription()
+ {
+ return description;
+ }
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff