X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=0d9c39d26bb497d8e24c2ba52391852b9d1b9ee5;hb=be1666f6c9be6b18051b233abdde85962ac0c89a;hp=f748c967b0188602d9bf18db6fffed4854f374ce;hpb=aebfa57bbc491dfa8c231704a385ed14f6a5e8ae;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index f748c96..0d9c39d 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
@@ -86,14 +89,16 @@ public class ColourSchemeProperty
public static final int TCOFFEE = 15;
- public static final int RNAINTERACTION = 16;
+ 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!
@@ -168,11 +173,14 @@ public class ColourSchemeProperty
{
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;
@@ -246,9 +254,10 @@ public class ColourSchemeProperty
{
index = TCOFFEE;
}
-
-
-
+ else if (cs instanceof RNAHelicesColour)
+ {
+ index = RNAHELIX;
+ }
/*
* else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
*/
@@ -343,11 +352,15 @@ public class ColourSchemeProperty
ret = "T-Coffee Scores";
break;
-
+
case RNAINTERACTION:
- ret = "RNA Interaction type";
+ ret = "RNA Interaction type";
+
+ break;
+ case RNAHELIX:
+ ret = "RNA Helices";
- break;
+ break;
/*
* case COVARIATION: ret = "Covariation";
*
@@ -500,12 +513,13 @@ public class ColourSchemeProperty
case TCOFFEE:
cs = new TCoffeeColourScheme(coll);
break;
-
-
+ case RNAHELIX:
+ cs = new RNAHelicesColour(coll);
+ break;
+
// case COVARIATION:
// cs = new CovariationColourScheme(annotation);
-
// break;
case USER_DEFINED:
@@ -583,4 +597,41 @@ public class ColourSchemeProperty
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;
+ }
+
}