JAL-1925 update source version in license

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

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index e847c58..6673446 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -21,6 +21,11 @@
 
 package jalview.io;
 
+import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+
 import java.io.IOException;
 import java.io.StringReader;
 
@@ -28,18 +33,13 @@ 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";
 
   public static final String FILE_DESC = "HTML";
 
-  private ColourSchemeI colourScheme;
+  private String globalColourScheme;
 
   private boolean showSeqFeatures;
 
@@ -47,6 +47,8 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
 
   private SequenceI[] hiddenSequences;
 
+  private FeaturesDisplayedI displayedFeatures;
+
   public HtmlFile()
   {
     super();
@@ -65,6 +67,8 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
   @Override
   public void parse() throws IOException
   {
+    Element content = null;
+    Document doc = null;
     try
     {
       StringBuilder htmlData = new StringBuilder();
@@ -73,24 +77,46 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
       {
         htmlData.append(currentLine);
       }
+      doc = Jsoup.parse(htmlData.toString());
+    } catch (OutOfMemoryError oom)
+    {
+      errormessage = "Not enough memory to process HTML document";
+      throw new IOException(errormessage);
+    }
 
-      Document doc = Jsoup.parse(htmlData.toString());
-      Element content = doc.getElementById("seqData");
-      JSONFile jsonFile = new JSONFile().parse(new StringReader(content.val()));
+    try
+    {
+      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(
+              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();
     } catch (Exception e)
     {
-      e.printStackTrace();
+      throw e;
     }
   }
 
-
   @Override
   public String print()
   {
@@ -108,14 +134,14 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     this.showSeqFeatures = showSeqFeatures;
   }
 
-  public ColourSchemeI getColourScheme()
+  public String getGlobalColourScheme()
   {
-    return colourScheme;
+    return globalColourScheme;
   }
 
-  public void setColourScheme(ColourSchemeI colourScheme)
+  public void setColourScheme(String globalColourScheme)
   {
-    this.colourScheme = colourScheme;
+    this.globalColourScheme = globalColourScheme;
   }
 
   public ColumnSelection getColumnSelection()
@@ -138,4 +164,10 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     this.hiddenSequences = hiddenSequences;
   }
 
+  @Override
+  public FeaturesDisplayedI getDisplayedFeatures()
+  {
+    return displayedFeatures;
+  }
+
 }