+/*
+ * 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.api;
import java.awt.Color;
void setShowUnconserved(boolean showunconserved);
+ /**
+ * @return true if a reference sequence is set and should be displayed
+ */
boolean isDisplayReferenceSeq();
+ /**
+ * @return set the flag for displaying reference sequences when they are
+ * available
+ */
void setDisplayReferenceSeq(boolean displayReferenceSeq);
+ /**
+ * @return true if colourschemes should render according to reference sequence
+ * rather than consensus if available
+ */
boolean isColourByReferenceSeq();
void setSeqNameItalics(boolean default1);
void setRightAlignIds(boolean rightAlignIds);
+ /**
+ * Returns true if annotation panel should be shown below alignment
+ *
+ * @return
+ */
boolean isShowAnnotation();
+ /**
+ * Set flag for whether annotation panel should be shown below alignment
+ *
+ * @param b
+ */
void setShowAnnotation(boolean b);
- void setShowSeqFeaturesHeight(boolean selected);
-
- boolean isShowSequenceFeaturesHeight();
+ void setShowSequenceFeaturesHeight(boolean selected);
+ /**
+ * @return true set flag for deciding if colourschemes should render according
+ * to reference sequence rather than consensus if available
+ */
void setColourByReferenceSeq(boolean colourByReferenceSeq);
Color getTextColour();
boolean isShowColourText();
- boolean isShowSeqFeaturesHeight();
+ boolean isShowSequenceFeaturesHeight();
void setConservationColourSelected(boolean conservationColourSelected);
void setUpperCasebold(boolean upperCasebold);
boolean isUpperCasebold();
-
+
boolean sameStyle(ViewStyleI them);
void setFontName(String name);
*/
void setShowNPFeats(boolean shownpfeats);
+ /**
+ * Get flag to scale protein residues 3 times the width of cDNA bases (only
+ * applicable in SplitFrame views)
+ *
+ * @return
+ */
+ boolean isScaleProteinAsCdna();
+
+ /**
+ * Set flag to scale protein residues 3 times the width of cDNA bases (only
+ * applicable in SplitFrame views)
+ *
+ * @return
+ */
+ void setScaleProteinAsCdna(boolean b);
+
+ /**
+ * Answers true if split screen protein and cDNA use the same font
+ *
+ * @return
+ */
+ boolean isProteinFontAsCdna();
+
+ /**
+ * Set the flag for whether split screen protein and cDNA use the same font
+ *
+ * @return
+ */
+ void setProteinFontAsCdna(boolean b);
}