+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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.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";
+ 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 ColourSchemeI cs;
+ private FeaturesDisplayedI displayedFeatures;
public HtmlFile()
{
super(inFile, type);
}
- @SuppressWarnings("unchecked")
@Override
public void parse() throws IOException
{
+ Element content = null;
+ Document doc = null;
try
{
StringBuilder htmlData = new StringBuilder();
{
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, 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);
+ 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, Sequence seq)
+ @Override
+ public String print()
{
- SequenceFeature[] seqFeatures = null;
- int count = 0;
- if (jsonSeqFeatures != null)
- {
- seqFeatures = new SequenceFeature[jsonSeqFeatures.size()];
- for (@SuppressWarnings("unchecked")
- Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
- .hasNext();)
- {
+ throw new UnsupportedOperationException(
+ "Print method of HtmlFile is not supported!");
+ }
- 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 boolean isShowSeqFeatures()
+ {
+ return showSeqFeatures;
}
- public void LoadAlignmentFeatures(AlignFrame af)
+ public void setShowSeqFeatures(boolean showSeqFeatures)
{
+ this.showSeqFeatures = showSeqFeatures;
+ }
- af.setShowSeqFeatures(true);
- af.changeColour(cs);
- af.setMenusForViewport();
+ public String getGlobalColourScheme()
+ {
+ return globalColourScheme;
}
- private ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
+ public void setColourScheme(String globalColourScheme)
{
- ColourSchemeI jalviewColor = null;
- for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
- .values())
- {
- if (cs.getBioJsName().equals(bioJsColourSchemeName))
- {
- jalviewColor = cs.getJvColourScheme();
- break;
- }
- }
- return jalviewColor;
+ this.globalColourScheme = globalColourScheme;
+ }
+
+ 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;
}
@Override
- public String print()
+ public FeaturesDisplayedI getDisplayedFeatures()
{
- throw new UnsupportedOperationException(
- "Print method of HtmlFile not yet supported!");
+ return displayedFeatures;
}
}
git://source.jalview.org / jalview.git / blobdiff