JAL-2322 Refactored unified architecture for data + html exporting for SVG & BioJS...

[jalview.git] / src / jalview / io / HtmlFile.java

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index 4805b8e..e31e78d 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -22,10 +22,10 @@
 package jalview.io;
 
 import jalview.api.ComplexAlignFile;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
 
 import java.io.IOException;
 import java.io.StringReader;
@@ -40,7 +40,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
 
   public static final String FILE_DESC = "HTML";
 
-  private ColourSchemeI colourScheme;
+  private String globalColourScheme;
 
   private boolean showSeqFeatures;
 
@@ -87,19 +87,28 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
 
     try
     {
-      content = doc.getElementById("seqData");
+      boolean contentFromDiv = true;
+      // search for BioJSON data in div element with id seqData
+      content = doc.select("div[id=seqData]").first();
+      if (content == null)
+      {
+        contentFromDiv = false;
+        // search for BioJSON data in input element with id seqData
+        content = doc.getElementById("seqData");
+      }
+
       if (content == null)
       {
         errormessage = "The html document is not embedded with BioJSON data";
         throw new IOException(errormessage);
       }
-      JSONFile jsonFile = new JSONFile().parse(new StringReader(content
-              .val()));
+      JSONFile jsonFile = new JSONFile().parse(new StringReader(
+              contentFromDiv ? content.text() : content.val()));
       this.seqs = jsonFile.getSeqs();
       this.seqGroups = jsonFile.getSeqGroups();
       this.annotations = jsonFile.getAnnotations();
       this.showSeqFeatures = jsonFile.isShowSeqFeatures();
-      this.colourScheme = jsonFile.getColourScheme();
+      this.globalColourScheme = jsonFile.getGlobalColourScheme();
       this.hiddenSequences = jsonFile.getHiddenSequences();
       this.columnSelection = jsonFile.getColumnSelection();
       this.displayedFeatures = jsonFile.getDisplayedFeatures();
@@ -109,7 +118,6 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     }
   }
 
-
   @Override
   public String print()
   {
@@ -117,6 +125,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
             "Print method of HtmlFile is not supported!");
   }
 
+  @Override
   public boolean isShowSeqFeatures()
   {
     return showSeqFeatures;
@@ -127,16 +136,18 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     this.showSeqFeatures = showSeqFeatures;
   }
 
-  public ColourSchemeI getColourScheme()
+  @Override
+  public String getGlobalColourScheme()
   {
-    return colourScheme;
+    return globalColourScheme;
   }
 
-  public void setColourScheme(ColourSchemeI colourScheme)
+  public void setColourScheme(String globalColourScheme)
   {
-    this.colourScheme = colourScheme;
+    this.globalColourScheme = globalColourScheme;
   }
 
+  @Override
   public ColumnSelection getColumnSelection()
   {
     return columnSelection;
@@ -147,6 +158,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     this.columnSelection = columnSelection;
   }
 
+  @Override
   public SequenceI[] getHiddenSequences()
   {
     return hiddenSequences;
@@ -163,4 +175,19 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     return displayedFeatures;
   }
 
+  /**
+   * Returns a descriptor for suitable feature display settings with
+   * <ul>
+   * <li>ResNums or insertions features visible</li>
+   * <li>insertions features coloured red</li>
+   * <li>ResNum features coloured by label</li>
+   * <li>Insertions displayed above (on top of) ResNums</li>
+   * </ul>
+   */
+  @Override
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return new PDBFeatureSettings();
+  }
+
 }