X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlFile.java;h=e31e78dcc2551fcf2c80df2059c05d0d10834b07;hb=e60cacff9260c47c12cf34a7e191678cfc97d265;hp=a1882900abd64e3f3ea0f9ac915fd26259a42caf;hpb=13953b6236c6b5de369e3598358d833e07328508;p=jalview.git

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index a188290..e31e78d 100644
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -1,28 +1,54 @@
+/*
+ * 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.
+ */
+
 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 jalview.api.ComplexAlignFile;
+import jalview.api.FeatureSettingsModelI;
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
 
 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
+public class HtmlFile extends AlignFile implements ComplexAlignFile
 {
   public static final String FILE_EXT = "html";
 
   public static final String FILE_DESC = "HTML";
 
-  private ColourSchemeI cs;
+  private String globalColourScheme;
+
+  private boolean showSeqFeatures;
+
+  private ColumnSelection columnSelection;
+
+  private SequenceI[] hiddenSequences;
+
+  private FeaturesDisplayedI displayedFeatures;
 
   public HtmlFile()
   {
@@ -39,10 +65,11 @@ public class HtmlFile extends AlignFile
     super(inFile, type);
   }
 
-  @SuppressWarnings("unchecked")
   @Override
   public void parse() throws IOException
   {
+    Element content = null;
+    Document doc = null;
     try
     {
       StringBuilder htmlData = new StringBuilder();
@@ -51,99 +78,116 @@ public class HtmlFile extends AlignFile
       {
         htmlData.append(currentLine);
       }
+      doc = Jsoup.parse(htmlData.toString());
+    } catch (OutOfMemoryError oom)
+    {
+      errormessage = "Not enough memory to process HTML document";
+      throw new IOException(errormessage);
+    }
 
-      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();)
+    try
+    {
+      boolean contentFromDiv = true;
+      // search for BioJSON data in div element with id seqData
+      content = doc.select("div[id=seqData]").first();
+      if (content == null)
       {
-        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);
+        contentFromDiv = false;
+        // search for BioJSON data in input element with id seqData
+        content = doc.getElementById("seqData");
+      }
 
+      if (content == null)
+      {
+        errormessage = "The html document is not embedded with BioJSON data";
+        throw new IOException(errormessage);
       }
+      JSONFile jsonFile = new JSONFile().parse(new StringReader(
+              contentFromDiv ? content.text() : content.val()));
+      this.seqs = jsonFile.getSeqs();
+      this.seqGroups = jsonFile.getSeqGroups();
+      this.annotations = jsonFile.getAnnotations();
+      this.showSeqFeatures = jsonFile.isShowSeqFeatures();
+      this.globalColourScheme = jsonFile.getGlobalColourScheme();
+      this.hiddenSequences = jsonFile.getHiddenSequences();
+      this.columnSelection = jsonFile.getColumnSelection();
+      this.displayedFeatures = jsonFile.getDisplayedFeatures();
     } catch (Exception e)
     {
-      e.printStackTrace();
+      throw 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();)
-      {
+    throw new UnsupportedOperationException(
+            "Print method of HtmlFile is not supported!");
+  }
+
+  @Override
+  public boolean isShowSeqFeatures()
+  {
+    return showSeqFeatures;
+  }
+
+  public void setShowSeqFeatures(boolean showSeqFeatures)
+  {
+    this.showSeqFeatures = showSeqFeatures;
+  }
 
-        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");
+  @Override
+  public String getGlobalColourScheme()
+  {
+    return globalColourScheme;
+  }
 
-        String color = (String) jsonFeature.get("fillColor");
+  public void setColourScheme(String globalColourScheme)
+  {
+    this.globalColourScheme = globalColourScheme;
+  }
 
-        sequenceFeature.setBegin(begin.intValue());
-        sequenceFeature.setEnd(end.intValue());
-        sequenceFeature.setType(type);
-        seqFeatures[count++] = sequenceFeature;
-      }
-    }
-    return seqFeatures;
+  @Override
+  public ColumnSelection getColumnSelection()
+  {
+    return columnSelection;
+  }
+
+  public void setColumnSelection(ColumnSelection columnSelection)
+  {
+    this.columnSelection = columnSelection;
   }
 
-  public void LoadAlignmentFeatures(AlignFrame af)
+  @Override
+  public SequenceI[] getHiddenSequences()
   {
+    return hiddenSequences;
+  }
 
-    af.setShowSeqFeatures(true);
-    af.changeColour(cs);
-    af.setMenusForViewport();
+  public void setHiddenSequences(SequenceI[] hiddenSequences)
+  {
+    this.hiddenSequences = hiddenSequences;
   }
 
-  private ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
+  @Override
+  public FeaturesDisplayedI getDisplayedFeatures()
   {
-    ColourSchemeI jalviewColor = null;
-    for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
-            .values())
-    {
-      if (cs.getBioJsName().equals(bioJsColourSchemeName))
-      {
-        jalviewColor = cs.getJvColourScheme();
-        break;
-      }
-    }
-    return jalviewColor;
+    return displayedFeatures;
   }
 
+  /**
+   * Returns a descriptor for suitable feature display settings with
+   * <ul>
+   * <li>ResNums or insertions features visible</li>
+   * <li>insertions features coloured red</li>
+   * <li>ResNum features coloured by label</li>
+   * <li>Insertions displayed above (on top of) ResNums</li>
+   * </ul>
+   */
   @Override
-  public String print()
+  public FeatureSettingsModelI getFeatureColourScheme()
   {
-    throw new UnsupportedOperationException(
-            "Print method of HtmlFile not yet supported!");
+    return new PDBFeatureSettings();
   }
 
 }