+/*
+ * 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.gui.AlignFrame;
+import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import java.io.IOException;
+import java.io.StringReader;
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";
private boolean showSeqFeatures;
+ private ColumnSelection columnSelection;
+
+ private SequenceI[] hiddenSequences;
+
+ private FeaturesDisplayedI displayedFeatures;
+
public HtmlFile()
{
super();
{
try
{
- StringBuilder htmlData = new StringBuilder();
- String currentLine;
- while ((currentLine = nextLine()) != null)
- {
- htmlData.append(currentLine);
+ 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);
}
-
- Document doc = Jsoup.parse(htmlData.toString());
- Element content = doc.getElementById("seqData");
- String alignmentJsonString = content.val();
-
- JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
- seqs = jsonFile.seqs;
- seqGroups = jsonFile.seqGroups;
- annotations = jsonFile.annotations;
- showSeqFeatures = jsonFile.isShowSeqFeatures();
- colourScheme = jsonFile.getColourScheme();
+ 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();
+ this.displayedFeatures = jsonFile.getDisplayedFeatures();
} 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 void applySettingsToAlignFrame(AlignFrame af)
- {
- af.setShowSeqFeatures(isShowSeqFeatures());
- af.changeColour(getColourScheme());
- af.setMenusForViewport();
- }
-
@Override
public String print()
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;
+ }
+
+ @Override
+ public FeaturesDisplayedI getDisplayedFeatures()
+ {
+ return displayedFeatures;
+ }
+
}