JAL-1835 made BioJSON embedding to html exports configurable, and trapped import...

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

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index a4e9bf4..4805b8e 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -21,6 +21,12 @@
 
 package jalview.io;
 
+import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
+
 import java.io.IOException;
 import java.io.StringReader;
 
@@ -28,11 +34,6 @@ import org.jsoup.Jsoup;
 import org.jsoup.nodes.Document;
 import org.jsoup.nodes.Element;
 
-import jalview.api.ComplexAlignFile;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
-
 public class HtmlFile extends AlignFile implements ComplexAlignFile
 {
   public static final String FILE_EXT = "html";
@@ -47,6 +48,8 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
 
   private SequenceI[] hiddenSequences;
 
+  private FeaturesDisplayedI displayedFeatures;
+
   public HtmlFile()
   {
     super();
@@ -65,26 +68,33 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
   @Override
   public void parse() throws IOException
   {
+    Element content = null;
+    Document doc = null;
     try
     {
-      Element content = null;
-      Document doc = null;
-      try {
-         StringBuilder htmlData = new StringBuilder();
-          String currentLine;
-          while ((currentLine = nextLine()) != null)
-          {
-            htmlData.append(currentLine);
-          }
-
-          doc = Jsoup.parse(htmlData.toString());
-      } catch (OutOfMemoryError oom) {
-         errormessage = "Not enough memory to process HTML document";
-         throw new IOException(errormessage);
+      StringBuilder htmlData = new StringBuilder();
+      String currentLine;
+      while ((currentLine = nextLine()) != null)
+      {
+        htmlData.append(currentLine);
       }
+      doc = Jsoup.parse(htmlData.toString());
+    } catch (OutOfMemoryError oom)
+    {
+      errormessage = "Not enough memory to process HTML document";
+      throw new IOException(errormessage);
+    }
+
+    try
+    {
       content = doc.getElementById("seqData");
-      
-      JSONFile jsonFile = new JSONFile().parse(new StringReader(content.val()));
+      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()));
       this.seqs = jsonFile.getSeqs();
       this.seqGroups = jsonFile.getSeqGroups();
       this.annotations = jsonFile.getAnnotations();
@@ -92,10 +102,10 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
       this.colourScheme = jsonFile.getColourScheme();
       this.hiddenSequences = jsonFile.getHiddenSequences();
       this.columnSelection = jsonFile.getColumnSelection();
+      this.displayedFeatures = jsonFile.getDisplayedFeatures();
     } catch (Exception e)
     {
-      errormessage = "Failed to extract data from HTML document.";
-      throw new IOException("Unexpected exception whilst extracting JSon from HTML.",e);
+      throw e;
     }
   }
 
@@ -147,4 +157,10 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     this.hiddenSequences = hiddenSequences;
   }
 
+  @Override
+  public FeaturesDisplayedI getDisplayedFeatures()
+  {
+    return displayedFeatures;
+  }
+
 }