X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=2d5b23dfa343f3b55284a07b944c6df4563a896e;hb=refs%2Fheads%2Ffeature%2FJAL-3468featureDescriptionEllipsis;hp=518f7ab9c334bce60722ca3c00b9a42d324f8f96;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 518f7ab..2d5b23d 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,28 +1,158 @@
-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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.api.AlignViewportI;
+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
+   * <ul>
+   * <li>any currently registered colour scheme; Jalview by default
+   * provides</li>
+   * <ul>
+   * <li>Clustal</li>
+   * <li>Blosum62</li>
+   * <li>% Identity</li>
+   * <li>Hydrophobic</li>
+   * <li>Zappo</li>
+   * <li>Taylor</li>
+   * <li>Helix Propensity</li>
+   * <li>Strand Propensity</li>
+   * <li>Turn Propensity</li>
+   * <li>Buried Index</li>
+   * <li>Nucleotide</li>
+   * <li>Purine/Pyrimidine</li>
+   * <li>T-Coffee Scores</li>
+   * <li>RNA Helices</li>
+   * </ul>
+   * <li>the name of a programmatically added colour scheme</li>
+   * <li>an AWT colour name e.g. red</li>
+   * <li>an AWT hex rgb colour e.g. ff2288</li>
+   * <li>residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li>
+   * </ul>
+   * 
+   * 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(AlignViewportI view,
+          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,
+            view,
+            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();
+  }
+
+}