X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlFile.java;h=a4e9bf4bb15b024746f52691ca8d39086f73e811;hb=refs%2Fheads%2Fmerge%2Fdevelop_JAL-1780_JAL-653_JAL-1892;hp=fd0789311d7cceed503b84604b1180e961bf7230;hpb=e2d6753e8cf3c5eaf8bccf34f4f5e9d651e9cb8e;p=jalview.git

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index fd07893..a4e9bf4 100644
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -1,15 +1,39 @@
-package jalview.io;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 
-import jalview.gui.AlignFrame;
-import jalview.schemes.ColourSchemeI;
+package jalview.io;
 
 import java.io.IOException;
+import java.io.StringReader;
 
 import org.jsoup.Jsoup;
 import org.jsoup.nodes.Document;
 import org.jsoup.nodes.Element;
 
-public class HtmlFile extends AlignFile
+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";
 
@@ -19,6 +43,10 @@ public class HtmlFile extends AlignFile
 
   private boolean showSeqFeatures;
 
+  private ColumnSelection columnSelection;
+
+  private SequenceI[] hiddenSequences;
+
   public HtmlFile()
   {
     super();
@@ -39,42 +67,44 @@ public class HtmlFile extends AlignFile
   {
     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);
-      seqs = jsonFile.seqs;
-      seqGroups = jsonFile.seqGroups;
-      annotations = jsonFile.annotations;
-      showSeqFeatures = jsonFile.isShowSeqFeatures();
-      colourScheme = jsonFile.getColourScheme();
+      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();
+      this.showSeqFeatures = jsonFile.isShowSeqFeatures();
+      this.colourScheme = jsonFile.getColourScheme();
+      this.hiddenSequences = jsonFile.getHiddenSequences();
+      this.columnSelection = jsonFile.getColumnSelection();
     } catch (Exception e)
     {
-      e.printStackTrace();
+      errormessage = "Failed to extract data from HTML document.";
+      throw new IOException("Unexpected exception whilst extracting JSon from HTML.",e);
     }
   }
 
-  public void LoadAlignmentFeatures(AlignFrame af)
-  {
-    af.setShowSeqFeatures(isShowSeqFeatures());
-    af.changeColour(getColourScheme());
-    af.setMenusForViewport();
-  }
-
 
   @Override
   public String print()
   {
     throw new UnsupportedOperationException(
-            "Print method of HtmlFile not yet supported!");
+            "Print method of HtmlFile is not supported!");
   }
 
   public boolean isShowSeqFeatures()
@@ -97,4 +127,24 @@ public class HtmlFile extends AlignFile
     this.colourScheme = colourScheme;
   }
 
+  public ColumnSelection getColumnSelection()
+  {
+    return columnSelection;
+  }
+
+  public void setColumnSelection(ColumnSelection columnSelection)
+  {
+    this.columnSelection = columnSelection;
+  }
+
+  public SequenceI[] getHiddenSequences()
+  {
+    return hiddenSequences;
+  }
+
+  public void setHiddenSequences(SequenceI[] hiddenSequences)
+  {
+    this.hiddenSequences = hiddenSequences;
+  }
+
 }