*/
package jalview.api;
-import java.awt.Color;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
import jalview.analysis.Conservation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
/**
* @author jimp
*
*/
void updateGroupAnnotationSettings(boolean applyGlobalSettings,
boolean preserveNewGroupSettings);
-
+
void setSequenceColour(SequenceI seq, Color col);
Color getSequenceColour(SequenceI seq);
/**
* get a copy of the currently visible alignment annotation
- * @param selectedOnly if true - trim to selected regions on the alignment
- * @return an empty list or new alignment annotation objects shown only visible columns trimmed to selected region only
+ *
+ * @param selectedOnly
+ * if true - trim to selected regions on the alignment
+ * @return an empty list or new alignment annotation objects shown only
+ * visible columns trimmed to selected region only
*/
List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
boolean selectedOnly);
* Set whether view should scroll to show the highlighted region of a sequence
*/
void setFollowHighlight(boolean b);
-
- /**
- * Returns a FeatureRenderer instance
- *
- * @return
- */
- public FeatureRenderer getFeatureRenderer();
-
- /**
- * Sets a FeatureRenderer for a viewport
- *
- * @param featureRenderer
- */
- public void setFeatureRenderer(FeatureRenderer featureRenderer);
-
- /**
- * Returns Settings for exporting an Alignment
- *
- * @return
- */
- public AlignExportSettingI getExportSettings();
-
}