Excluded HtmlFile.java dependencies from AppletFomatAdapter

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

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index bc5c219..ee1b151 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -1,6 +1,10 @@
 package jalview.io;
 
 import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.gui.AlignFrame;
+import jalview.json.binding.v1.BioJsAlignmentPojo.JalviewBioJsColorSchemeMapper;
+import jalview.schemes.ColourSchemeI;
 
 import java.io.IOException;
 import java.util.Iterator;
@@ -12,57 +16,134 @@ 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 cs;
+
+  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 = content.val();
+      JSONParser jsonParser = new JSONParser();
+      JSONObject alignmentJsonObj = (JSONObject) jsonParser
+              .parse(alignmentJsonString);
+      JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
+      String bioJsColourScheme = (String) alignmentJsonObj
+              .get("globalColorScheme");
+      cs = getJalviewColorScheme(bioJsColourScheme);
+
+      for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
+              .hasNext();)
+      {
+        JSONObject sequence = sequenceIter.next();
+        String sequcenceString = sequence.get("seq").toString();
+        Sequence seq = new Sequence(sequence.get("name").toString(),
+                sequcenceString, 0, sequcenceString.length());
+
+        JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
+        SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(jsonSeqArray);
+        if (retrievedSeqFeatures != null)
+        {
+          seq.setSequenceFeatures(retrievedSeqFeatures);
+        }
+        seqs.add(seq);
+
+      }
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  public SequenceFeature[] getJalviewSequenceFeatures(
+          JSONArray jsonSeqFeatures)
+  {
+    SequenceFeature[] seqFeatures = null;
+    int count = 0;
+    if (jsonSeqFeatures != null)
+    {
+      seqFeatures = new SequenceFeature[jsonSeqFeatures.size()];
+      for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
+              .hasNext();)
+      {
+
+        SequenceFeature sequenceFeature = new SequenceFeature();
+        JSONObject jsonFeature = seqFeatureItr.next();
+        Long begin = (Long) jsonFeature.get("xStart");
+        Long end = (Long) jsonFeature.get("xEnd");
+        String type = (String) jsonFeature.get("text");
+
+        String color = (String) jsonFeature.get("fillColor");
+
+        sequenceFeature.setBegin(begin.intValue());
+        sequenceFeature.setEnd(end.intValue());
+        sequenceFeature.setType(type);
+        seqFeatures[count++] = sequenceFeature;
+      }
+    }
+    return seqFeatures;
+  }
+
+  public void LoadAlignmentFeatures(AlignFrame af)
+  {
+
+    af.setShowSeqFeatures(true);
+    af.changeColour(cs);
+    af.setMenusForViewport();
+  }
+
+  private ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
+  {
+    ColourSchemeI jalviewColor = null;
+    for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
+            .values())
+    {
+      if (cs.getBioJsName().equals(bioJsColourSchemeName))
+      {
+        jalviewColor = cs.getJvColourScheme();
+        break;
+      }
+    }
+    return jalviewColor;
+  }
+
+  @Override
+  public String print()
+  {
+    throw new UnsupportedOperationException(
+            "Print method of HtmlFile not yet supported!");
+  }
 
 }