X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FHtmlFile.java;h=a4e9bf4bb15b024746f52691ca8d39086f73e811;hb=refs%2Fheads%2Fmerge%2Fdevelop_JAL-1780_JAL-653_JAL-1892;hp=ee1b151bb874afe82b5132734385255292a952c5;hpb=68c26e8852772be21fdb5b091fa9083d8cdb6eec;p=jalview.git

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index ee1b151..a4e9bf4 100644
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -1,28 +1,51 @@
-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;
-import jalview.datamodel.SequenceFeature;
-import jalview.gui.AlignFrame;
-import jalview.json.binding.v1.BioJsAlignmentPojo.JalviewBioJsColorSchemeMapper;
-import jalview.schemes.ColourSchemeI;
+package jalview.io;
 
 import java.io.IOException;
-import java.util.Iterator;
+import java.io.StringReader;
 
-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
+import jalview.api.ComplexAlignFile;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
+
+public class HtmlFile extends AlignFile implements ComplexAlignFile
 {
-  // public static final String FILE_EXT = "html";
-  //
-  // public static final String FILE_DESC = "HTML";
+  public static final String FILE_EXT = "html";
 
-  private ColourSchemeI cs;
+  public static final String FILE_DESC = "HTML";
+
+  private ColourSchemeI colourScheme;
+
+  private boolean showSeqFeatures;
+
+  private ColumnSelection columnSelection;
+
+  private SequenceI[] hiddenSequences;
 
   public HtmlFile()
   {
@@ -39,111 +62,89 @@ public class HtmlFile extends AlignFile
     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);
-
+      Element content = null;
+      Document doc = null;
+      try {
+    	  StringBuilder htmlData = new StringBuilder();
+          String currentLine;
+          while ((currentLine = nextLine()) != null)
+          {
+            htmlData.append(currentLine);
+          }
+
+          doc = Jsoup.parse(htmlData.toString());
+      } catch (OutOfMemoryError oom) {
+    	  errormessage = "Not enough memory to process HTML document";
+    	  throw new IOException(errormessage);
       }
+      content = doc.getElementById("seqData");
+      
+      JSONFile jsonFile = new JSONFile().parse(new StringReader(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();
     } catch (Exception e)
     {
-      e.printStackTrace();
+      errormessage = "Failed to extract data from HTML document.";
+      throw new IOException("Unexpected exception whilst extracting JSon from HTML.",e);
     }
   }
 
-  public SequenceFeature[] getJalviewSequenceFeatures(
-          JSONArray jsonSeqFeatures)
+
+  @Override
+  public String print()
   {
-    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;
+    throw new UnsupportedOperationException(
+            "Print method of HtmlFile is not supported!");
   }
 
-  public void LoadAlignmentFeatures(AlignFrame af)
+  public boolean isShowSeqFeatures()
   {
+    return showSeqFeatures;
+  }
 
-    af.setShowSeqFeatures(true);
-    af.changeColour(cs);
-    af.setMenusForViewport();
+  public void setShowSeqFeatures(boolean showSeqFeatures)
+  {
+    this.showSeqFeatures = showSeqFeatures;
   }
 
-  private ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
+  public ColourSchemeI getColourScheme()
   {
-    ColourSchemeI jalviewColor = null;
-    for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
-            .values())
-    {
-      if (cs.getBioJsName().equals(bioJsColourSchemeName))
-      {
-        jalviewColor = cs.getJvColourScheme();
-        break;
-      }
-    }
-    return jalviewColor;
+    return colourScheme;
   }
 
-  @Override
-  public String print()
+  public void setColourScheme(ColourSchemeI colourScheme)
   {
-    throw new UnsupportedOperationException(
-            "Print method of HtmlFile not yet supported!");
+    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;
   }
 
 }