X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=025a7a085ef9e69e1845731f57ebbc8156fb7ad4;hb=bdbd32582db88724697211a25b08f9cb8958bcb1;hp=aa928cc81588e1c1552b8e5f48c7c2ec031c5572;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index aa928cc..025a7a0 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,24 +1,27 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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;
import jalview.datamodel.AnnotatedCollectionI;
+import jalview.util.ColorUtils;
import java.awt.Color;
@@ -87,12 +90,16 @@ public class ColourSchemeProperty
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!
@@ -167,6 +174,14 @@ 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;
@@ -240,6 +255,10 @@ public class ColourSchemeProperty
{
index = TCOFFEE;
}
+ else if (cs instanceof RNAHelicesColour)
+ {
+ index = RNAHELIX;
+ }
/*
* else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
*/
@@ -334,6 +353,15 @@ public class ColourSchemeProperty
ret = "T-Coffee Scores";
break;
+
+ case RNAINTERACTION:
+ ret = "RNA Interaction type";
+
+ break;
+ case RNAHELIX:
+ ret = "RNA Helices";
+
+ break;
/*
* case COVARIATION: ret = "Covariation";
*
@@ -388,8 +416,7 @@ public class ColourSchemeProperty
try
{
// fix the launchApp user defined coloursheme transfer bug
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
- "white");
+ UserColourScheme ucs = new UserColourScheme("white");
ucs.parseAppletParameter(name);
} catch (Exception e)
@@ -415,8 +442,7 @@ public class ColourSchemeProperty
* @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(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
@@ -485,10 +511,15 @@ public class ColourSchemeProperty
case TCOFFEE:
cs = new TCoffeeColourScheme(coll);
- // case COVARIATION:
- // cs = new CovariationColourScheme(annotation);
+ break;
- // break;
+ case RNAHELIX:
+ cs = new RNAHelicesColour(coll);
+ break;
+
+ // case COVARIATION:
+ // cs = new CovariationColourScheme(annotation);
+ // break;
case USER_DEFINED:
Color[] col = new Color[24];
@@ -565,4 +596,32 @@ 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] = ColorUtils.generateRandomColor(Color.white);
+ }
+ }
+
}