-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
-\r
-\r
- public HTMLOutput(AlignViewport av)\r
- {\r
- SequenceRenderer sr = new SequenceRenderer(av);\r
- Color color;\r
- JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
- chooser.setDialogTitle("Save as HTML");\r
- chooser.setToolTipText("Save");\r
- int value = chooser.showSaveDialog(null);\r
- if(value == JFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.LAST_DIRECTORY = choice;\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
- 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
- out.println("<tr><td nowrap>"+seq.getDisplayId()+" </td>");\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
- 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
- out.println("</table>");\r
- out.println("</td></tr></table>\n</body>\n</html>");\r
-\r
- out.close();\r
-\r
- jalview.util.BrowserLauncher.openURL( "file:///"+choice );\r
- }\r
- catch(Exception ex){ex.printStackTrace();}\r
- }\r
- }\r
-\r
-\r
-}\r
+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(
+ "<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");
+
+ }
+
+ 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);
+ }
+
+ 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);
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff