JAL_793 implemented embeding source data in exported html

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 649aad3..f97a341 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -25,6 +25,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SequenceGroup;
 import jalview.util.MessageManager;
 
 import java.io.File;
@@ -57,7 +58,7 @@ public class AppletFormatAdapter
   public static final String[] READABLE_EXTENSIONS = new String[]
   { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
       "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
-      "jar,jvp", "html" };
+      "jar,jvp", HtmlFile.FILE_EXT };
 
   /**
    * List of readable formats by application in order corresponding to
@@ -65,7 +66,8 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_FNAMES = new String[]
   { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm",
-      "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview", "HTML" };
+      "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview",
+      HtmlFile.FILE_DESC };
 
   /**
    * List of valid format strings for use by callers of the formatSequences
@@ -215,6 +217,7 @@ public class AppletFormatAdapter
     this.inFile = inFile;
     try
     {
+      Alignment al;
       if (format.equals("FASTA"))
       {
         afile = new FastaFile(inFile, type);
@@ -267,19 +270,37 @@ public class AppletFormatAdapter
       {
         afile = new PhylipFile(inFile, type);
       }
-       else if (format.equals(JSONFile.FILE_DESC))
-       {
-       afile = new JSONFile(inFile, type);
-       }
+      else if (format.equals(JSONFile.FILE_DESC))
+      {
+        afile = new JSONFile(inFile, type);
+        al = new Alignment(afile.getSeqsAsArray());
+        afile.addAnnotations(al);
+        for (SequenceGroup sg : afile.getSeqGroups())
+        {
+          al.addGroup(sg);
+        }
+        return al;
+      }
+      else if (format.equals(HtmlFile.FILE_DESC))
+      {
+        afile = new HtmlFile(inFile, type);
+        al = new Alignment(afile.getSeqsAsArray());
+        afile.addAnnotations(al);
+        for (SequenceGroup sg : afile.getSeqGroups())
+        {
+          al.addGroup(sg);
+        }
+        return al;
+      }
       else if (format.equals("RNAML"))
       {
         afile = new RnamlFile(inFile, type);
       }
 
-      Alignment al = new Alignment(afile.getSeqsAsArray());
+      al = new Alignment(afile.getSeqsAsArray());
 
-      afile.addAnnotations(al);
-      afile.addSeqGroups(al);
+      // afile.addAnnotations(al);
+      // afile.addSeqGroups(al);
 
       return al;
     } catch (Exception e)
@@ -344,6 +365,7 @@ public class AppletFormatAdapter
     String type = source.type;
     try
     {
+      Alignment al;
       if (format.equals("FASTA"))
       {
         afile = new FastaFile(source);
@@ -398,14 +420,19 @@ public class AppletFormatAdapter
       {
         afile = new PhylipFile(source);
       }
-       else if (format.equals(JSONFile.FILE_DESC))
-       {
-       afile = new JSONFile(source);
-       }
-      Alignment al = new Alignment(afile.getSeqsAsArray());
-
-      afile.addAnnotations(al);
-      afile.addSeqGroups(al);
+      else if (format.equals(JSONFile.FILE_DESC))
+      {
+        afile = new JSONFile(source);
+        al = new Alignment(afile.getSeqsAsArray());
+        afile.addAnnotations(al);
+        afile.addSeqGroups(al);
+        return al;
+      }
+      else if (format.equals(HtmlFile.FILE_DESC))
+      {
+        afile = new HtmlFile(source);
+      }
+      al = new Alignment(afile.getSeqsAsArray());
 
       return al;
     } catch (Exception e)

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 74410a1..86ec140 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -258,39 +258,14 @@ public class FormatAdapter extends AppletFormatAdapter
   public Alignment readFile(String inFile, String type, String format)
           throws java.io.IOException
   {
-    Alignment al;
-    if (format.equals(JSONFile.FILE_DESC))
-    {
-      afile = new JSONFile(inFile, type);
-      al = new Alignment(afile.getSeqsAsArray());
-      afile.addAnnotations(al);
-      for (SequenceGroup sg : afile.getSeqGroups())
-      {
-        al.addGroup(sg);
-      }
-    }
-    else
-    {
-      al = super.readFile(inFile, type, format);
-    }
+    Alignment al = super.readFile(inFile, type, format);
     return al;
   }
 
   public AlignmentI readFromFile(FileParse source, String format)
           throws java.io.IOException
   {
-    Alignment al;
-    if (format.equals(JSONFile.FILE_DESC))
-    {
-      afile = new JSONFile(source);
-      al = new Alignment(afile.getSeqsAsArray());
-      afile.addAnnotations(al);
-      afile.addSeqGroups(al);
-    }
-    else
-    {
-      al = (Alignment) super.readFromFile(source, format);
-    }
+    Alignment al = (Alignment) super.readFromFile(source, format);
     return al;
   }
 

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index aadf246..7272830 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -11,9 +11,9 @@ import org.jsoup.nodes.Element;
 
 public class HtmlFile extends AlignFile
 {
-  // public static final String FILE_EXT = "html";
-  //
-  // public static final String FILE_DESC = "HTML";
+  public static final String FILE_EXT = "html";
+
+  public static final String FILE_DESC = "HTML";
 
   private ColourSchemeI cs;
 
@@ -32,7 +32,6 @@ public class HtmlFile extends AlignFile
     super(inFile, type);
   }
 
-  @SuppressWarnings("unchecked")
   @Override
   public void parse() throws IOException
   {
@@ -47,98 +46,25 @@ public class HtmlFile extends AlignFile
 
       Document doc = Jsoup.parse(htmlData.toString());
       Element content = doc.getElementById("seqData");
-
       String alignmentJsonString = content.val();
 
-      new JSONFile().parse(alignmentJsonString);
-
-      // JSONParser jsonParser = new JSONParser();
-      // JSONObject alignmentJsonObj = (JSONObject) jsonParser
-      // .parse(alignmentJsonString);
-      // JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
-      // String bioJsColourScheme = (String) alignmentJsonObj
-      // .get("globalColorScheme");
-      // cs = getJalviewColorScheme(bioJsColourScheme);
-      //
-      // for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator();
-      // sequenceIter
-      // .hasNext();)
-      // {
-      // JSONObject sequence = sequenceIter.next();
-      // String sequcenceString = sequence.get("seq").toString();
-      // Sequence seq = new Sequence(sequence.get("name").toString(),
-      // sequcenceString, Integer.valueOf(sequence.get("start")
-      // .toString()), Integer.valueOf(sequence.get("end")
-      // .toString()));
-      //
-      // JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
-      // SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(
-      // jsonSeqArray, seq);
-      // if (retrievedSeqFeatures != null)
-      // {
-      // seq.setSequenceFeatures(retrievedSeqFeatures);
-      // }
-      // seqs.add(seq);
-      //
-      // }
+      JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
+      seqs = jsonFile.seqs;
+      seqGroups = jsonFile.seqGroups;
+      annotations = jsonFile.annotations;
     } catch (Exception e)
     {
       e.printStackTrace();
     }
   }
 
-  // public SequenceFeature[] getJalviewSequenceFeatures(
-  // JSONArray jsonSeqFeatures, Sequence seq)
-  // {
-  // SequenceFeature[] seqFeatures = null;
-  // int count = 0;
-  // if (jsonSeqFeatures != null)
-  // {
-  // seqFeatures = new SequenceFeature[jsonSeqFeatures.size()];
-  // for (@SuppressWarnings("unchecked")
-  // Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator();
-  // seqFeatureItr
-  // .hasNext();)
-  // {
-  //
-  // SequenceFeature sequenceFeature = new SequenceFeature();
-  // JSONObject jsonFeature = seqFeatureItr.next();
-  // Long begin = (Long) jsonFeature.get("xStart");
-  // Long end = (Long) jsonFeature.get("xEnd");
-  // String type = (String) jsonFeature.get("text");
-  // // String color = (String) jsonFeature.get("fillColor");
-  //
-  // sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
-  // sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
-  // sequenceFeature.setType(type);
-  // seqFeatures[count++] = sequenceFeature;
-  // }
-  // }
-  // return seqFeatures;
-  // }
-
   public void LoadAlignmentFeatures(AlignFrame af)
   {
-
-    af.setShowSeqFeatures(true);
-    af.changeColour(cs);
+    af.setShowSeqFeatures(JSONFile.isSeqFeaturesEnabled());
+    af.changeColour(JSONFile.getColourScheme());
     af.setMenusForViewport();
   }
 
-  // private ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
-  // {
-  // ColourSchemeI jalviewColor = null;
-  // for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
-  // .values())
-  // {
-  // if (cs.getBioJsName().equals(bioJsColourSchemeName))
-  // {
-  // jalviewColor = cs.getJvColourScheme();
-  // break;
-  // }
-  // }
-  // return jalviewColor;
-  // }
 
   @Override
   public String print()

diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index 3c9c608..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();
@@ -257,11 +261,50 @@ 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\"> "
+    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"

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index a87f34a..f1089ec 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -133,28 +133,26 @@ public class IdentifyFile
         if ((data.indexOf("# STOCKHOLM") > -1))
         {
           reply = "STH";
-
-          break;
-        }
-        if (data.indexOf("{\"") > -1)
-        {
-          reply = JSONFile.FILE_DESC;
           break;
         }
         // if (data.matches("<(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
         if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
         {
-          reply = "HTML";
+          reply = HtmlFile.FILE_DESC;
           break;
         }
 
         if (data.matches("<(?i)rnaml (\"[^\"]*\"|'[^']*'|[^'\">])*>"))
         {
           reply = "RNAML";
-
           break;
         }
 
+         if (data.indexOf("{\"") > -1)
+         {
+         reply = JSONFile.FILE_DESC;
+         break;
+         }
         if ((data.length() < 1) || (data.indexOf("#") == 0))
         {
           lineswereskipped = true;