JAL-1641 Re-implemented lost changes after sequenceFeature refactor

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

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index 3cb7c3f..aadf246 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -1,17 +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;
 
-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;
@@ -56,68 +49,73 @@ public class HtmlFile extends AlignFile
       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, Integer.valueOf(sequence.get("start")
-                        .toString()), Integer.valueOf(sequence.get("end")
-                        .toString()));
-
-        JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
-        SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(
-                jsonSeqArray, seq);
-        if (retrievedSeqFeatures != null)
-        {
-          seq.setSequenceFeatures(retrievedSeqFeatures);
-        }
-        seqs.add(seq);
 
-      }
+      new JSONFile().parse(alignmentJsonString);
+
+      // 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, Integer.valueOf(sequence.get("start")
+      // .toString()), Integer.valueOf(sequence.get("end")
+      // .toString()));
+      //
+      // JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
+      // SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(
+      // jsonSeqArray, seq);
+      // if (retrievedSeqFeatures != null)
+      // {
+      // seq.setSequenceFeatures(retrievedSeqFeatures);
+      // }
+      // seqs.add(seq);
+      //
+      // }
     } catch (Exception e)
     {
       e.printStackTrace();
     }
   }
 
-  public SequenceFeature[] getJalviewSequenceFeatures(
-          JSONArray jsonSeqFeatures, Sequence seq)
-  {
-    SequenceFeature[] seqFeatures = null;
-    int count = 0;
-    if (jsonSeqFeatures != null)
-    {
-      seqFeatures = new SequenceFeature[jsonSeqFeatures.size()];
-      for (@SuppressWarnings("unchecked")
-      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(seq.findPosition(begin.intValue()));
-        sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
-        sequenceFeature.setType(type);
-        seqFeatures[count++] = sequenceFeature;
-      }
-    }
-    return seqFeatures;
-  }
+  // public SequenceFeature[] getJalviewSequenceFeatures(
+  // JSONArray jsonSeqFeatures, Sequence seq)
+  // {
+  // SequenceFeature[] seqFeatures = null;
+  // int count = 0;
+  // if (jsonSeqFeatures != null)
+  // {
+  // seqFeatures = new SequenceFeature[jsonSeqFeatures.size()];
+  // for (@SuppressWarnings("unchecked")
+  // 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(seq.findPosition(begin.intValue()));
+  // sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
+  // sequenceFeature.setType(type);
+  // seqFeatures[count++] = sequenceFeature;
+  // }
+  // }
+  // return seqFeatures;
+  // }
 
   public void LoadAlignmentFeatures(AlignFrame af)
   {
@@ -127,20 +125,20 @@ public class HtmlFile extends AlignFile
     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;
-  }
+  // 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()