JAL-1541 minor code clean up, and added test for BioJsHTMLOutput

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

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index bc5c219..d507362 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -1,68 +1,100 @@
 package jalview.io;
 
-import jalview.datamodel.Sequence;
+import jalview.gui.AlignFrame;
+import jalview.schemes.ColourSchemeI;
 
 import java.io.IOException;
-import java.util.Iterator;
 
-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!");
-       }
+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;
+
+  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);
+      seqs = jsonFile.seqs;
+      seqGroups = jsonFile.seqGroups;
+      annotations = jsonFile.annotations;
+      showSeqFeatures = jsonFile.isShowSeqFeatures();
+      colourScheme = jsonFile.getColourScheme();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  public void applySettingsToAlignFrame(AlignFrame af)
+  {
+    af.setShowSeqFeatures(isShowSeqFeatures());
+    af.changeColour(getColourScheme());
+    af.setMenusForViewport();
+  }
+
+
+  @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;
+  }
 
 }