package jalview.io;
+import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+
import java.io.IOException;
-import java.util.List;
+import java.io.StringReader;
import org.jsoup.Jsoup;
import org.jsoup.nodes.Document;
import org.jsoup.nodes.Element;
-import jalview.api.AlignViewControllerGuiI;
-import jalview.schemes.ColourSchemeI;
-
-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 colourScheme;
+ private String globalColourScheme;
private boolean showSeqFeatures;
- private List<int[]> hiddenColumns;
+ private ColumnSelection columnSelection;
+
+ private SequenceI[] hiddenSequences;
+
+ private FeaturesDisplayedI displayedFeatures;
public HtmlFile()
{
@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();
+ 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");
+ }
- JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
+ 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.colourScheme = jsonFile.getColourScheme();
- this.hiddenColumns = jsonFile.getHiddenColumns();
+ this.globalColourScheme = jsonFile.getGlobalColourScheme();
+ this.hiddenSequences = jsonFile.getHiddenSequences();
+ this.columnSelection = jsonFile.getColumnSelection();
+ this.displayedFeatures = jsonFile.getDisplayedFeatures();
} catch (Exception e)
{
- e.printStackTrace();
+ throw e;
}
}
- public void applySettingsToAlignmentView(AlignViewControllerGuiI avc)
- {
- avc.setShowSeqFeatures(isShowSeqFeatures());
- avc.changeColour(getColourScheme());
- avc.setMenusForViewport();
- avc.hideColumns(hiddenColumns);
- avc.syncHiddenSequences();
- }
-
@Override
public String print()
{
this.showSeqFeatures = showSeqFeatures;
}
- public ColourSchemeI getColourScheme()
+ public String getGlobalColourScheme()
{
- return colourScheme;
+ return globalColourScheme;
}
- public void setColourScheme(ColourSchemeI colourScheme)
+ public void setColourScheme(String globalColourScheme)
+ {
+ 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 FeaturesDisplayedI getDisplayedFeatures()
{
- this.colourScheme = colourScheme;
+ return displayedFeatures;
}
}