+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.renderer.seqfeatures;
+import jalview.api.AlignViewportI;
import jalview.api.FeatureRenderer;
import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.SequenceI;
* @param defaultColour
* @param seq
* @param column
- * alignment column position (base zero)
+ * alignment column position (0..)
* @return
*/
public Color findFeatureColour(Color defaultColour, SequenceI seq,
}
}
- Color c = featureRenderer.findFeatureColour(seq, column, g);
+ Color c = featureRenderer.findFeatureColour(seq, column + 1, g);
if (c == null)
{
return defaultColour;
*/
boolean noFeaturesDisplayed()
{
- if (!featureRenderer.getViewport().isShowSequenceFeatures())
+ if (featureRenderer == null)
+ {
+ return true;
+ }
+ AlignViewportI av = featureRenderer.getViewport();
+ if (av.isShowComplementFeatures())
+ {
+ return false;
+ }
+ if (!av.isShowSequenceFeatures())
{
return true;
}