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JAL_793 implemented embeding source data in exported html
[jalview.git] / src / jalview / io / HtmlSvgOutput.java
diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index 68f9924..64dfc1c 100644 (file)
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -1,9 +1,12 @@
 package jalview.io;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.AnnotationPanel;
+import jalview.gui.Desktop;
 import jalview.gui.FeatureRenderer;
 import jalview.gui.HTMLOptions;
 import jalview.math.AlignmentDimension;
@@ -100,7 +103,8 @@ public class HtmlSvgOutput
 
       String titleSvgData = g1.getSVGDocument();
       String alignSvgData = g2.getSVGDocument();
-      String htmlData = getHtml(titleSvgData, alignSvgData);
+      String jsonData = getJSONData();
+      String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
 
       out.write(htmlData.getBytes());
       out.flush();
@@ -257,18 +261,82 @@ public class HtmlSvgOutput
     return Printable.PAGE_EXISTS;
   }
   
-  private String getHtml(String titleSvg, String alignmentSvg)
+  private String getJSONData()
+  {
+    JSONFile jsonFile = new JSONFile();
+    Alignment al = new Alignment(av.getAlignment().getSequencesArray());
+    jsonFile.seqGroups = av.getAlignment().getGroups();
+    // jsonFile.addAnnotations(al);
+    jsonFile.setDisplayedFeatures(av.getFeaturesDisplayed());
+    Desktop.setCurrentAlignFrame(av.getAlignPanel().alignFrame);
+    for (SequenceI seq : av.getAlignment().getSequences())
+    {
+      jsonFile.seqs.add(seq);
+    }
+
+    // Add non auto calculated annotation to AlignFile
+    for (AlignmentAnnotation annot : av.getAlignment()
+            .getAlignmentAnnotation())
+    {
+      if (annot != null && !annot.autoCalculated)
+      {
+        if (annot.label.equals("PDB.CATempFactor"))
+        {
+          continue;
+        }
+        jsonFile.annotations.add(annot);
+      }
+    }
+
+    // jsonFile.setGlobalColorScheme(av.getGlobalColourScheme());
+    String jsonString = jsonFile.print();
+    System.out.println(">>>>>>>>>>> JSONFile : " + jsonString);
+    return jsonString;
+  }
+
+  private String getHtml(String titleSvg, String alignmentSvg,
+          String jsonData)
   {
     StringBuilder htmlSvg = new StringBuilder();
-    htmlSvg.append("<html><style type=\"text/css\">" + "div.title {"
-            + "height: 100%;" + "width: 9%;" + "float: left;" + "}"
-            + "div.align {" + "height: 100%;" + "width: 91%;"
-            + "overflow: scroll;" + "float: right;" + "}" + "</style>"
-            + "<div style=\"width:100%; height:100%; overflow: hidden\">"
-            + "<div class=\"title\">");
-    htmlSvg.append(titleSvg);
-    htmlSvg.append("</div><div class=\"align\">").append(alignmentSvg);
+    htmlSvg.append("<html>\n");
+    if (jsonData != null)
+    {
+      htmlSvg.append("<input type=\"hidden\" name=\"seqData\" id=\"seqData\" value='"
+              + jsonData + "'>");
+    }
+    htmlSvg.append("\n<style type=\"text/css\"> "
+            + "div.parent{ width:100%;<!-- overflow: auto; -->}\n"
+            + "div.titlex{ width:11%; float: left; }\n"
+            + "div.align{ width:89%; float: right; }\n"
+            + ".sub-category-container {overflow-y: scroll; overflow-x: hidden; width: 100%; height: 100%;}\n"
+            + "object {pointer-events: none;}"
+            + "</style>");
+    htmlSvg.append("<div>");
+    htmlSvg.append(
+"<div class=\"titlex\">");
+    htmlSvg.append(
+"<div class=\"sub-category-container\"> ")
+            .append(titleSvg)
+            .append("</div>")
+            .append("</div>\n\n<!-- ========================================================================================== -->\n\n");
+    htmlSvg.append(
+"<div class=\"align\" >");
+    htmlSvg.append(
+            "<div class=\"sub-category-container\"> <div style=\"overflow-x: scroll;\">")
+            .append(alignmentSvg)
+.append("</div></div>")
+            .append("</div>");
     htmlSvg.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=\"//ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n"
+            + "<script>\n"
+            + "var subCatContainer = $(\".sub-category-container\");\n"
+            + "subCatContainer.scroll(\nfunction() {\n"
+            + "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
+
+    htmlSvg.append("</script></hmtl>");
+
     return htmlSvg.toString();
   }
 }