package jalview.io;
-import jalview.api.AlignViewControllerGuiI;
-import jalview.schemes.ColourSchemeI;
-
import java.io.IOException;
import org.jsoup.Jsoup;
import org.jsoup.nodes.Document;
import org.jsoup.nodes.Element;
-public class HtmlFile extends AlignFile
+import jalview.api.ComplexAlignFile;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
+
+public class HtmlFile extends AlignFile implements ComplexAlignFile
{
public static final String FILE_EXT = "html";
private boolean showSeqFeatures;
+ private ColumnSelection columnSelection;
+
+ private SequenceI[] hiddenSequences;
+
public HtmlFile()
{
super();
String alignmentJsonString = content.val();
JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
- seqs = jsonFile.getSeqs();
- seqGroups = jsonFile.getSeqGroups();
- annotations = jsonFile.getAnnotations();
- showSeqFeatures = jsonFile.isShowSeqFeatures();
- colourScheme = jsonFile.getColourScheme();
+ 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();
} catch (Exception e)
{
e.printStackTrace();
}
}
- public void applySettingsToAlignFrame(AlignViewControllerGuiI 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;
+ }
+
}