+/*
+ * 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();
+ }
}
git://source.jalview.org / jalview.git / blobdiff