X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlSvgOutput.java;h=c8d6975f3bbf4520a49efd0b1188a22e79dacdfc;hb=6e314387a9cf3c422388cd8b8315811ee58621f0;hp=464385826989c2c469e8b14df13a86ca87f1e6a6;hpb=cca50cb3aee94f3ed1a5e504d45b8d8b665f8c5b;p=jalview.git diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java index 4643858..c8d6975 100644 --- a/src/jalview/io/HtmlSvgOutput.java +++ b/src/jalview/io/HtmlSvgOutput.java @@ -1,10 +1,11 @@ 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.AnnotationPanel; -import jalview.gui.FeatureRenderer; import jalview.gui.HTMLOptions; import jalview.math.AlignmentDimension; import jalview.util.MessageManager; @@ -27,22 +28,22 @@ public class HtmlSvgOutput FeatureRenderer fr; AlignmentPanel ap; - AnnotationPanel annotationPanel; - public HtmlSvgOutput(AlignmentPanel ap) + public HtmlSvgOutput(File file, AlignmentPanel ap) { - - this.av = ap.av; - this.ap = ap; - this.annotationPanel = ap.getAnnotationPanel(); - generateHtmlSvgOutput(); + this.av = ap.av; + this.ap = ap; + fr = ap.cloneFeatureRenderer(); + generateHtmlSvgOutput(file); } - public void generateHtmlSvgOutput() + public void generateHtmlSvgOutput(File file) { - File file = null; try { + if (file == null) + { + JalviewFileChooser chooser = getHTMLChooser(); chooser.setFileView(new jalview.io.JalviewFileView()); chooser.setDialogTitle(ap.alignFrame.getTitle()); @@ -55,6 +56,7 @@ public class HtmlSvgOutput .getSelectedFile().getParent()); file = chooser.getSelectedFile(); } + } AlignmentDimension aDimension = ap.getAlignmentDimension(); SVGGraphics2D g1 = new SVGGraphics2D(aDimension.getWidth(), @@ -89,17 +91,71 @@ public class HtmlSvgOutput } printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, g1, g2); - FileOutputStream out = new FileOutputStream(file); String titleSvgData = g1.getSVGDocument(); String alignSvgData = g2.getSVGDocument(); - String htmlData = getHtml(titleSvgData, alignSvgData); + 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(); @@ -247,18 +303,361 @@ public class HtmlSvgOutput return Printable.PAGE_EXISTS; } - private String getHtml(String titleSvg, String alignmentSvg) + private String getHtml(String titleSvg, String alignmentSvg, + String jsonData) { StringBuilder htmlSvg = new StringBuilder(); - htmlSvg.append("" - + "
" - + "
"); + htmlSvg.append("\n"); + if (jsonData != null) + { + htmlSvg.append("  "); + htmlSvg.append(""); + htmlSvg.append("
" + + jsonData + "
"); + htmlSvg.append("
 "); + } + htmlSvg.append("\n"); + htmlSvg.append("
"); + htmlSvg.append("
\n"); + htmlSvg.append("
\n"); htmlSvg.append(titleSvg); - htmlSvg.append("
").append(alignmentSvg); htmlSvg.append("
"); + htmlSvg.append("
\n\n\n\n"); + htmlSvg.append("
"); + htmlSvg.append( + "
") + .append(alignmentSvg) +.append("
") + .append("
"); + htmlSvg.append("
"); + + htmlSvg.append("\n" + + "\n" + + "\n"); + + // javascript for launching file in Jalview + + htmlSvg.append("\n"); + htmlSvg.append(""); return htmlSvg.toString(); } }