JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index d507362..0d0fae9 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -1,15 +1,40 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ */
+
 package jalview.io;
 
-import jalview.gui.AlignFrame;
+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;
 
-public class HtmlFile extends AlignFile
+public class HtmlFile extends AlignFile implements ComplexAlignFile
 {
   public static final String FILE_EXT = "html";
 
@@ -19,6 +44,12 @@ public class HtmlFile extends AlignFile
 
   private boolean showSeqFeatures;
 
+  private ColumnSelection columnSelection;
+
+  private SequenceI[] hiddenSequences;
+
+  private FeaturesDisplayedI displayedFeatures;
+
   public HtmlFile()
   {
     super();
@@ -37,6 +68,8 @@ public class HtmlFile extends AlignFile
   @Override
   public void parse() throws IOException
   {
+    Element content = null;
+    Document doc = null;
     try
     {
       StringBuilder htmlData = new StringBuilder();
@@ -45,31 +78,46 @@ public class HtmlFile extends AlignFile
       {
         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();
+    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");
+      }
 
-      JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
-      seqs = jsonFile.seqs;
-      seqGroups = jsonFile.seqGroups;
-      annotations = jsonFile.annotations;
-      showSeqFeatures = jsonFile.isShowSeqFeatures();
-      colourScheme = jsonFile.getColourScheme();
+      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.hiddenSequences = jsonFile.getHiddenSequences();
+      this.columnSelection = jsonFile.getColumnSelection();
+      this.displayedFeatures = jsonFile.getDisplayedFeatures();
     } catch (Exception e)
     {
-      e.printStackTrace();
+      throw e;
     }
   }
 
-  public void applySettingsToAlignFrame(AlignFrame af)
-  {
-    af.setShowSeqFeatures(isShowSeqFeatures());
-    af.changeColour(getColourScheme());
-    af.setMenusForViewport();
-  }
-
-
   @Override
   public String print()
   {
@@ -97,4 +145,30 @@ 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;
+  }
+
+  @Override
+  public FeaturesDisplayedI getDisplayedFeatures()
+  {
+    return displayedFeatures;
+  }
+
 }