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.BufferedReader;
-import java.io.File;
import java.io.IOException;
-import java.io.InputStreamReader;
import java.io.StringReader;
-import java.net.URL;
-import java.util.Objects;
import org.jsoup.Jsoup;
import org.jsoup.nodes.Document;
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 ColumnSelection getColumnSelection()
+ public HiddenColumns getHiddenColumns()
{
- return columnSelection;
+ return hiddenColumns;
}
- public void setColumnSelection(ColumnSelection columnSelection)
+ public void setHiddenColumns(HiddenColumns hidden)
{
- this.columnSelection = columnSelection;
+ this.hiddenColumns = hidden;
}
@Override
return new PDBFeatureSettings();
}
- /**
- * Read a template file content as string
- *
- * @param file
- * - the file to be read
- * @return File content as String
- * @throws IOException
- */
- public static String readFileAsString(File file) throws IOException
- {
- InputStreamReader isReader = null;
- BufferedReader buffReader = null;
- StringBuilder sb = new StringBuilder();
- Objects.requireNonNull(file, "File must not be null!");
- @SuppressWarnings("deprecation")
- URL url = file.toURL();
- if (url != null)
- {
- try
- {
- isReader = new InputStreamReader(url.openStream());
- buffReader = new BufferedReader(isReader);
- String line;
- String lineSeparator = System.getProperty("line.separator");
- while ((line = buffReader.readLine()) != null)
- {
- sb.append(line).append(lineSeparator);
- }
-
- } catch (Exception ex)
- {
- ex.printStackTrace();
- } finally
- {
- if (isReader != null)
- {
- isReader.close();
- }
-
- if (buffReader != null)
- {
- buffReader.close();
- }
- }
- }
- return sb.toString();
- }
-
}