X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlFile.java;h=e31e78dcc2551fcf2c80df2059c05d0d10834b07;hb=e60cacff9260c47c12cf34a7e191678cfc97d265;hp=bc5c21941ca285ae4351824f82c0447619fb61fc;hpb=50ff87bdae1829a7a7471ec393142ae659b40a11;p=jalview.git

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index bc5c219..e31e78d 100644
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -1,68 +1,193 @@
+/*
+ * 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.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 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 implements ComplexAlignFile
+{
+  public static final String FILE_EXT = "html";
+
+  public static final String FILE_DESC = "HTML";
+
+  private String globalColourScheme;
+
+  private boolean showSeqFeatures;
+
+  private ColumnSelection columnSelection;
+
+  private SequenceI[] hiddenSequences;
+
+  private FeaturesDisplayedI displayedFeatures;
+
+  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
+  {
+    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);
+    }
+
+    try
+    {
+      boolean contentFromDiv = true;
+      // search for BioJSON data in div element with id seqData
+      content = doc.select("div[id=seqData]").first();
+      if (content == null)
+      {
+        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)
+    {
+      throw e;
+    }
+  }
+
+  @Override
+  public String print()
+  {
+    throw new UnsupportedOperationException(
+            "Print method of HtmlFile is not supported!");
+  }
+
+  @Override
+  public boolean isShowSeqFeatures()
+  {
+    return showSeqFeatures;
+  }
+
+  public void setShowSeqFeatures(boolean showSeqFeatures)
+  {
+    this.showSeqFeatures = showSeqFeatures;
+  }
+
+  @Override
+  public String getGlobalColourScheme()
+  {
+    return globalColourScheme;
+  }
+
+  public void setColourScheme(String globalColourScheme)
+  {
+    this.globalColourScheme = globalColourScheme;
+  }
+
+  @Override
+  public ColumnSelection getColumnSelection()
+  {
+    return columnSelection;
+  }
+
+  public void setColumnSelection(ColumnSelection columnSelection)
+  {
+    this.columnSelection = columnSelection;
+  }
+
+  @Override
+  public SequenceI[] getHiddenSequences()
+  {
+    return hiddenSequences;
+  }
+
+  public void setHiddenSequences(SequenceI[] hiddenSequences)
+  {
+    this.hiddenSequences = hiddenSequences;
+  }
+
+  @Override
+  public FeaturesDisplayedI getDisplayedFeatures()
+  {
+    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 FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return new PDBFeatureSettings();
+  }
 
 }