JAL-1760 JAL-1641 Serialisation of Hidden Seqs and Cols in JSON output. Added ability...

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

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index bc5c219..3dd937d 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -1,68 +1,126 @@
-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.datamodel.Sequence;
+package jalview.io;
 
 import java.io.IOException;
-import java.util.Iterator;
+import java.util.List;
 
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
 import org.jsoup.Jsoup;
 import org.jsoup.nodes.Document;
 import org.jsoup.nodes.Element;
 
-public class HtmlFile extends AlignFile {
-       public static final String FILE_EXT = "html";
-
-       public static final String FILE_DESC = "HTML";
-
-       public HtmlFile() {
-               super();
-       }
-
-       public HtmlFile(FileParse source) throws IOException {
-               super(source);
-       }
-
-       public HtmlFile(String inFile, String type) throws IOException {
-               super(inFile, type);
-       }
-
-       @SuppressWarnings("unchecked")
-       @Override
-       public void parse() throws IOException {
-               try {
-                       StringBuilder htmlData = new StringBuilder();
-                       String currentLine;
-                       while ((currentLine = nextLine()) != null) {
-                               htmlData.append(currentLine);
-                       }
-
-                       Document doc = Jsoup.parse(htmlData.toString());
-                       Element content = doc.getElementById("seqData");
-                       
-                       String alignmentJsonString = "{\"seqs\":" + content.val() + "}";
-                       JSONParser jsonParser = new JSONParser();
-                       JSONObject alignmentJsonObj = (JSONObject) jsonParser.parse(alignmentJsonString);
-                       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
-
-                       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter.hasNext();) {
-                               JSONObject sequence = sequenceIter.next();
-                               System.out.println(sequence.get("id").toString() + " " + sequence.get("name"));
-                               String sequcenceString = sequence.get("seq").toString();
-                               Sequence seq = new Sequence(sequence.get("name").toString(), sequcenceString, 0, sequcenceString.length());
-                               seqs.add(seq);
-
-                       }
-               } catch (Exception e) {
-                       e.printStackTrace();
-               }
-       }
-
-       @Override
-       public String print() {
-               throw new UnsupportedOperationException("Print method of HtmlFile not yet supported!");
-       }
+import jalview.api.AlignViewControllerGuiI;
+import jalview.schemes.ColourSchemeI;
+
+public class HtmlFile extends AlignFile
+{
+  public static final String FILE_EXT = "html";
+
+  public static final String FILE_DESC = "HTML";
+
+  private ColourSchemeI colourScheme;
+
+  private boolean showSeqFeatures;
+
+  private List<int[]> hiddenColumns;
+
+  public HtmlFile()
+  {
+    super();
+  }
+
+  public HtmlFile(FileParse source) throws IOException
+  {
+    super(source);
+  }
+
+  public HtmlFile(String inFile, String type) throws IOException
+  {
+    super(inFile, type);
+  }
+
+  @Override
+  public void parse() throws IOException
+  {
+    try
+    {
+      StringBuilder htmlData = new StringBuilder();
+      String currentLine;
+      while ((currentLine = nextLine()) != null)
+      {
+        htmlData.append(currentLine);
+      }
+
+      Document doc = Jsoup.parse(htmlData.toString());
+      Element content = doc.getElementById("seqData");
+      String alignmentJsonString = content.val();
+
+      JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
+      this.seqs = jsonFile.getSeqs();
+      this.seqGroups = jsonFile.getSeqGroups();
+      this.annotations = jsonFile.getAnnotations();
+      this.showSeqFeatures = jsonFile.isShowSeqFeatures();
+      this.colourScheme = jsonFile.getColourScheme();
+      this.hiddenColumns = jsonFile.getHiddenColumns();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  public void applySettingsToAlignmentView(AlignViewControllerGuiI avc)
+  {
+    avc.setShowSeqFeatures(isShowSeqFeatures());
+    avc.changeColour(getColourScheme());
+    avc.setMenusForViewport();
+    avc.hideColumns(hiddenColumns);
+    avc.syncHiddenSequences();
+  }
+
+  @Override
+  public String print()
+  {
+    throw new UnsupportedOperationException(
+            "Print method of HtmlFile is not supported!");
+  }
+
+  public boolean isShowSeqFeatures()
+  {
+    return showSeqFeatures;
+  }
+
+  public void setShowSeqFeatures(boolean showSeqFeatures)
+  {
+    this.showSeqFeatures = showSeqFeatures;
+  }
+
+  public ColourSchemeI getColourScheme()
+  {
+    return colourScheme;
+  }
+
+  public void setColourScheme(ColourSchemeI colourScheme)
+  {
+    this.colourScheme = colourScheme;
+  }
 
 }