/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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
+ * 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
+ *
+ * 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.schemes;
* values of the colourscheme constants is important for callers of
* getColourName(int i), since it can be used to enumerate the set of built in
* colours. The FIRST_COLOUR and LAST_COLOUR symbols are provided for this.
- *
+ *
* @author $author$
* @version $Revision$
*/
public static final int COVARIATION = 14;
public static final int TCOFFEE = 15;
+
+ public static final int RNAHELIX = 16;
public static final int RNAINTERACTION = 16;
*/
public static final int FIRST_COLOUR = NONE;
- public static final int LAST_COLOUR = NUCLEOTIDE;
+ public static final int LAST_COLOUR = RNAHELIX;
/**
* DOCUMENT ME!
- *
+ *
* @param name
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public static int getColourIndexFromName(String name)
{
ret = PURINEPYRIMIDINE;
}
-
else if (name.equalsIgnoreCase("RNA Interaction type"))
{
ret = RNAINTERACTION;
}
+ else if (name.equalsIgnoreCase("RNA Helices"))
+ {
+ ret = RNAHELIX;
+ }
// else if (name.equalsIgnoreCase("Covariation"))
// {
// ret = COVARIATION;
/**
* DOCUMENT ME!
- *
+ *
* @param cs
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public static String getColourName(ColourSchemeI cs)
{
index = TCOFFEE;
}
- else if (cs instanceof RNAInteractionColourScheme)
- {
- index = RNAINTERACTION;
- }
+<<<<<<< HEAD
+
+=======
+ else if (cs instanceof RNAHelicesColour)
+ {
+ index = RNAHELIX;
+ }
+>>>>>>> JAL-952_rnahelix
/*
* else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
*/
/**
* DOCUMENT ME!
- *
+ *
* @param index
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public static String getColourName(int index)
ret = "T-Coffee Scores";
break;
+<<<<<<< HEAD
case RNAINTERACTION:
ret = "RNA Interaction type";
break;
+=======
+ case RNAHELIX:
+ ret = "RNA Helices";
+
+ break;
+>>>>>>> JAL-952_rnahelix
/*
* case COVARIATION: ret = "Covariation";
- *
+ *
* break;
*/
case USER_DEFINED:
return ret;
}
+
/**
* retrieve or create colourscheme associated with name
- *
+ *
* @param seqs
* sequences to colour
* @param width
}
/**
- * Construct an instance of ColourSchemeI corresponding to the given colourscheme index
- *
+ * Construct an instance of ColourSchemeI corresponding to the given
+ * colourscheme index
+ *
* @param seqs
* sequences to be coloured by colourscheme
* @param width
* geometry of alignment
* @param index
* colourscheme number
- *
- * @return null or an instance of the colourscheme configured to colour given sequence set
+ *
+ * @return null or an instance of the colourscheme configured to colour given
+ * sequence set
*/
- public static ColourSchemeI getColour(jalview.datamodel.AnnotatedCollectionI coll, int index)
+ public static ColourSchemeI getColour(
+ jalview.datamodel.AnnotatedCollectionI coll, int index)
{
- // TODO 3.0 2.8 refactor signature to take an alignmentI like container so colourschemes based on annotation can be initialised
+ // TODO 3.0 2.8 refactor signature to take an alignmentI like container so
+ // colourschemes based on annotation can be initialised
ColourSchemeI cs = null;
switch (index)
case TCOFFEE:
cs = new TCoffeeColourScheme(coll);
break;
+
+ case RNAHELIX:
+ cs = new RNAHelicesColour(coll);
+ break;
- case RNAINTERACTION:
- cs = new RNAInteractionColourScheme();
- break;
-
- // case COVARIATION:
- // cs = new CovariationColourScheme(annotation);
-
+ // case COVARIATION:
+ // cs = new CovariationColourScheme(annotation);
// break;
case USER_DEFINED: