Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

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

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index 73aa5d2..0f5cd55 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -21,17 +21,19 @@
 
 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;
 
 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";
@@ -46,6 +48,8 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
 
   private SequenceI[] hiddenSequences;
 
+  private FeaturesDisplayedI displayedFeatures;
+
   public HtmlFile()
   {
     super();
@@ -66,18 +70,24 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
   {
     try
     {
-      StringBuilder htmlData = new StringBuilder();
-      String currentLine;
-      while ((currentLine = nextLine()) != null)
-      {
-        htmlData.append(currentLine);
+      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);
       }
-
-      Document doc = Jsoup.parse(htmlData.toString());
-      Element content = doc.getElementById("seqData");
-      String alignmentJsonString = content.val();
-
-      JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
+      content = doc.getElementById("seqData");
+      
+      JSONFile jsonFile = new JSONFile().parse(new StringReader(content.val()));
       this.seqs = jsonFile.getSeqs();
       this.seqGroups = jsonFile.getSeqGroups();
       this.annotations = jsonFile.getAnnotations();
@@ -85,9 +95,11 @@ 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)
     {
-      e.printStackTrace();
+      errormessage = "Failed to extract data from HTML document.";
+      throw new IOException("Unexpected exception whilst extracting JSon from HTML.",e);
     }
   }
 
@@ -139,4 +151,10 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     this.hiddenSequences = hiddenSequences;
   }
 
+  @Override
+  public FeaturesDisplayedI getDisplayedFeatures()
+  {
+    return displayedFeatures;
+  }
+
 }