/*
- * 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 2.9)
+ * Copyright (C) 2015 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
+ * 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/>.
+ *
+ * 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 TCOFFEE = 15;
+ public static final int RNAHELIX = 16;
+
+ public static final int RNAINTERACTION = 17;
/**
* index of first colourscheme (includes 'None')
*/
public static final int FIRST_COLOUR = NONE;
- public static final int LAST_COLOUR = NUCLEOTIDE;
+ public static final int LAST_COLOUR = RNAINTERACTION;
/**
* 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 RNAHelicesColour)
+ {
+ index = 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;
+
+ case RNAINTERACTION:
+ ret = "RNA Interaction type";
+
+ break;
+ case RNAHELIX:
+ ret = "RNA Helices";
+
+ break;
/*
* 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 COVARIATION:
// cs = new CovariationColourScheme(annotation);
-
// break;
case USER_DEFINED:
return col;
}
+
+ public static Color rnaHelices[] = null;
+
+ public static void initRnaHelicesShading(int n)
+ {
+ int j = 0;
+ if (rnaHelices == null)
+ {
+ rnaHelices = new Color[n + 1];
+ }
+ else if (rnaHelices != null && rnaHelices.length <= n)
+ {
+ Color[] t = new Color[n + 1];
+ System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length);
+ j = rnaHelices.length;
+ rnaHelices = t;
+ }
+ else
+ {
+ return;
+ }
+ // Generate random colors and store
+ for (; j <= n; j++)
+ {
+ rnaHelices[j] = jalview.util.ColorUtils
+ .generateRandomColor(Color.white);
+ }
+ }
+
+ /**
+ * delete the existing cached RNA helces colours
+ */
+ public static void resetRnaHelicesShading()
+ {
+ rnaHelices = null;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff