JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / api / ViewStyleI.java

diff --git a/src/jalview/api/ViewStyleI.java b/src/jalview/api/ViewStyleI.java
index 0313c5c..db82dcf 100644 (file)
--- a/src/jalview/api/ViewStyleI.java
+++ b/src/jalview/api/ViewStyleI.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -79,10 +99,21 @@ public interface ViewStyleI
 
   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);
@@ -95,14 +126,26 @@ public interface ViewStyleI
 
   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();
@@ -117,7 +160,7 @@ public interface ViewStyleI
 
   boolean isShowColourText();
 
-  boolean isShowSeqFeaturesHeight();
+  boolean isShowSequenceFeaturesHeight();
 
   void setConservationColourSelected(boolean conservationColourSelected);
 
@@ -134,7 +177,7 @@ public interface ViewStyleI
   void setUpperCasebold(boolean upperCasebold);
 
   boolean isUpperCasebold();
-  
+
   boolean sameStyle(ViewStyleI them);
 
   void setFontName(String name);