X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=fc92cd96b2f400fcb0cc4739d640f6b28df25877;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=518f7ab9c334bce60722ca3c00b9a42d324f8f96;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 518f7ab..fc92cd9 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,28 +1,155 @@
-package jalview.schemes;
-
-public class ColourSchemeProperty {
- String description;
- String className;
- String menuString = null;
-
- public ColourSchemeProperty(String description, String className, String menuString) {
- this.description = new String(description);
- this.className = new String(className);
- if (menuString != null) {
- this.menuString = new String(menuString);
- }
- }
-
- public String getClassName() {
- return className;
- }
- public String getDescription() {
- return description;
- }
- public String getMenuString() {
- return menuString;
- }
- public boolean isMenuItem() {
- return (menuString != null);
- }
-}
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.util.ColorUtils;
+
+import java.awt.Color;
+
+/**
+ * ColourSchemeProperty binds names to hardwired colourschemes and tries to deal
+ * intelligently with mapping unknown names to user defined colourschemes (that
+ * exist or can be created from the string representation of the colourscheme
+ * name - either a hex RGB triplet or a named colour under java.awt.color ). The
+ * 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 class ColourSchemeProperty
+{
+
+ /**
+ * Returns a colour scheme for the given name, with which the given data may
+ * be coloured. The name is not case-sensitive, and may be one of
+ *
+ * - any currently registered colour scheme; Jalview by default
+ * provides
+ *
+ * - Clustal
+ * - Blosum62
+ * - % Identity
+ * - Hydrophobic
+ * - Zappo
+ * - Taylor
+ * - Helix Propensity
+ * - Strand Propensity
+ * - Turn Propensity
+ * - Buried Index
+ * - Nucleotide
+ * - Purine/Pyrimidine
+ * - T-Coffee Scores
+ * - RNA Helices
+ *
+ * - the name of a programmatically added colour scheme
+ * - an AWT colour name e.g. red
+ * - an AWT hex rgb colour e.g. ff2288
+ * - residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow
+ *
+ *
+ * If none of these formats is matched, the string is converted to a colour
+ * using a hashing algorithm. For name "None", returns null.
+ *
+ * @param forData
+ * @param name
+ * @return
+ */
+ public static ColourSchemeI getColourScheme(AnnotatedCollectionI forData,
+ String name)
+ {
+ if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
+ {
+ return null;
+
+ }
+
+ /*
+ * if this is the name of a registered colour scheme, just
+ * create a new instance of it
+ */
+ ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name,
+ forData, null);
+ if (scheme != null)
+ {
+ return scheme;
+ }
+
+ /*
+ * try to parse the string as a residues colour scheme
+ * e.g. A=red;T,G=blue etc
+ * else parse the name as a colour specification
+ * e.g. "red" or "ff00ed",
+ * or failing that hash the name to a colour
+ */
+ UserColourScheme ucs = new UserColourScheme(name);
+ return ucs;
+ }
+
+ 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);
+ }
+ }
+
+ /**
+ * delete the existing cached RNA helices colours
+ */
+ public static void resetRnaHelicesShading()
+ {
+ rnaHelices = null;
+ }
+
+ /**
+ * Returns the name of the colour scheme (or "None" if it is null)
+ *
+ * @param cs
+ * @return
+ */
+ public static String getColourName(ColourSchemeI cs)
+ {
+ return cs == null ? ResidueColourScheme.NONE : cs.getSchemeName();
+ }
+
+}