label.translation_failed = Translation Failed
label.error_when_translating_sequences_submit_bug_report = Unfortunately, something went wrong when translating your sequences.\nPlease take a look in the Jalview java console\nand submit a bug report including the stacktrace.
label.implementation_error = Implementation error:
-label.automatically_associate_pdb_files_with_sequences_same_name = Do you want to automatically associate the {0} PDB files with sequences in the alignment that have the same name?
-label.automatically_associate_pdb_files_by_name = Automatically Associate PDB files by name
+label.automatically_associate_structure_files_with_sequences_same_name = Do you want to automatically associate the {0} structure file(s) with sequences in the alignment that have the same name?
+label.automatically_associate_structure_files_by_name = Automatically Associate Structure files by name
label.ignore_unmatched_dropped_files_info = <html>Do you want to <em>ignore</em> the {0} files whose names did not match any sequence IDs ?</html>
label.ignore_unmatched_dropped_files = Ignore unmatched dropped files?
label.view_name_original = Original
label.translation_failed = Translation Failed
label.error_when_translating_sequences_submit_bug_report = Desafortunadamente, algo fue mal a la hora de traducir tus secuencias.\nPor favor, revisa la consola Jalview java \ny presenta un informe de error que incluya el seguimiento.
label.implementation_error = Error de implementación:
-label.automatically_associate_pdb_files_with_sequences_same_name = Quieres asociar automáticamente los {0} ficheros PDB con las secuencias del alineamiento que tengan el mismo nombre?
-label.automatically_associate_pdb_files_by_name = Asociar los ficheros PDB por nombre automáticamente
+label.automatically_associate_structure_files_with_sequences_same_name = Quieres asociar automáticamente los {0} ficheros structure con las secuencias del alineamiento que tengan el mismo nombre?
+label.automatically_associate_structure_files_by_name = Asociar los ficheros structure por nombre automáticamente
label.ignore_unmatched_dropped_files_info = Quieres <em>ignorar</em> los {0} ficheros cuyos nombres no coincidan con ningún IDs de las secuencias ?
label.ignore_unmatched_dropped_files = Ignorar los ficheros sin coincidencias?
label.enter_view_name = Introduzca un nombre para la vista
System.out.println("Creating HTML image: " + file);
continue;
}
+ else if (format.equalsIgnoreCase("biojsmsa"))
+ {
+ BioJsHTMLOutput.updateBioJS();
+ try
+ {
+ Thread.sleep(1500);
+ } catch (InterruptedException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel, af);
+ bjs.exportJalviewAlignmentAsBioJsHtmlFile(file);
+ System.out.println("Creating BioJS MSA Viwer HTML file: "
+ + file);
+ continue;
+ }
else if (format.equalsIgnoreCase("imgMap"))
{
af.createImageMap(new File(file), imageName);
+ "-png FILE\tCreate PNG image FILE from alignment.\n"
+ "-svg FILE\tCreate SVG image FILE from alignment.\n"
+ "-html FILE\tCreate HTML file from alignment.\n"
+ + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
+ "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
+ "-eps FILE\tCreate EPS file FILE from alignment.\n"
+ "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
public void bioJSMenuItem_actionPerformed(ActionEvent e)
{
BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
- bjs.exportJalviewAlignmentAsBioJsHtmlFile();
+ bjs.exportJalviewAlignmentAsBioJsHtmlFile(null);
}
public void createImageMap(File file, String image)
}
if (type != null)
{
- if (type.equalsIgnoreCase("PDB"))
+ if (type.equalsIgnoreCase("PDB")
+ || type.equalsIgnoreCase("mmCIF"))
{
filesmatched.add(new Object[] { file, protocol, mtch });
continue;
this,
MessageManager
.formatMessage(
- "label.automatically_associate_pdb_files_with_sequences_same_name",
+ "label.automatically_associate_structure_files_with_sequences_same_name",
new Object[] { Integer
.valueOf(
filesmatched
.size())
.toString() }),
MessageManager
- .getString("label.automatically_associate_pdb_files_by_name"),
+ .getString("label.automatically_associate_structure_files_by_name"),
JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
{
}
}
- public void exportJalviewAlignmentAsBioJsHtmlFile()
+ public void exportJalviewAlignmentAsBioJsHtmlFile(String outputFile)
{
- String outputFile = null;
+ // String outputFile = null;
try
{
- outputFile = getOutputFile();
+ if (outputFile == null)
+ {
+ outputFile = getOutputFile();
+ }
AlignExportSettingI exportSettings = new AlignExportSettingI()
{
@Override
new OOMWarning("Creating Image for " + outputFile, err);
} catch (Exception e)
{
+ if (pIndicator != null && !headless)
+ {
pIndicator.setProgressBar(MessageManager.formatMessage(
"info.error_creating_file", "HTML"), pSessionId);
+ }
e.printStackTrace();
}
}
g2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
}
+ if (av.getWrapAlignment())
+ {
+ printWrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+ g1, g2);
+ }
+ else
+ {
printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
g1, g2);
+ }
String titleSvgData = g1.getSVGDocument();
String alignSvgData = g2.getSVGDocument();
exportData.getStartEndPostions(),
av.getColumnSelection());
}
- String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
+ String htmlData = getHtml(titleSvgData, alignSvgData, jsonData,
+ av.getWrapAlignment());
FileOutputStream out = new FileOutputStream(fileX);
out.write(htmlData.getBytes());
out.flush();
return Printable.PAGE_EXISTS;
}
+ public int printWrapped(int pwidth, int pheight, int pi, Graphics... pg)
+ throws PrinterException
+ {
+ return ap.printWrappedAlignment(pg[1], pwidth, pheight, pi);
+ }
+
private String getHtml(String titleSvg, String alignmentSvg,
- String jsonData)
+ String jsonData, boolean wrapped)
{
StringBuilder htmlSvg = new StringBuilder();
htmlSvg.append("<html>\n");
+ ".facebox_hide { z-index:-100; }\n"
+ ".facebox_overlayBG { background-color: #000; z-index: 99; }");
}
-
htmlSvg.append("</style>");
+ if (!wrapped)
+ {
htmlSvg.append("<div class=\"main-container\" \n>");
htmlSvg.append("<div class=\"titlex\">\n");
htmlSvg.append("<div class=\"sub-category-container\"> \n");
+ "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
htmlSvg.append("</script>\n");
+ }
+ else
+ {
+ htmlSvg.append("<div>\n")
+ .append(alignmentSvg).append("</div>");
+ htmlSvg.append("<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
+ + "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n");
+
+ }
// javascript for launching file in Jalview
git://source.jalview.org / jalview.git / commitdiff