package jalview.io;
import jalview.api.ComplexAlignFile;
+import jalview.api.FeatureSettingsModelI;
import jalview.api.FeaturesDisplayedI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import java.io.IOException;
private boolean showSeqFeatures;
- private ColumnSelection columnSelection;
+ private HiddenColumns hiddenColumns;
private SequenceI[] hiddenSequences;
super(source);
}
- public HtmlFile(String inFile, String type) throws IOException
+ public HtmlFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
@Override
this.showSeqFeatures = jsonFile.isShowSeqFeatures();
this.globalColourScheme = jsonFile.getGlobalColourScheme();
this.hiddenSequences = jsonFile.getHiddenSequences();
- this.columnSelection = jsonFile.getColumnSelection();
+ this.hiddenColumns = jsonFile.getHiddenColumns();
this.displayedFeatures = jsonFile.getDisplayedFeatures();
} catch (Exception e)
{
}
@Override
- public String print()
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
throw new UnsupportedOperationException(
"Print method of HtmlFile is not supported!");
}
+ @Override
public boolean isShowSeqFeatures()
{
return showSeqFeatures;
this.showSeqFeatures = showSeqFeatures;
}
+ @Override
public String getGlobalColourScheme()
{
return globalColourScheme;
this.globalColourScheme = globalColourScheme;
}
- public ColumnSelection getColumnSelection()
+ @Override
+ public HiddenColumns getHiddenColumns()
{
- return columnSelection;
+ return hiddenColumns;
}
- public void setColumnSelection(ColumnSelection columnSelection)
+ public void setHiddenColumns(HiddenColumns hidden)
{
- this.columnSelection = columnSelection;
+ this.hiddenColumns = hidden;
}
+ @Override
public SequenceI[] getHiddenSequences()
{
return hiddenSequences;
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();
+ }
+
}