JAL-2360 code formatting only and if-else changed to switch

[jalview.git] / src / jalview / schemes / ColourSchemeProperty.java

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index e80860e..fc703ba 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * 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 <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;
@@ -86,7 +88,7 @@ public class ColourSchemeProperty
   public static final int COVARIATION = 14;
 
   public static final int TCOFFEE = 15;
-  
+
   public static final int RNAHELIX = 16;
 
   public static final int RNAINTERACTION = 17;
@@ -350,11 +352,11 @@ public class ColourSchemeProperty
       ret = "T-Coffee Scores";
 
       break;
-      
+
     case RNAINTERACTION:
-        ret = "RNA Interaction type";
+      ret = "RNA Interaction type";
 
-        break;
+      break;
     case RNAHELIX:
       ret = "RNA Helices";
 
@@ -413,8 +415,7 @@ 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)
@@ -423,7 +424,7 @@ public class ColourSchemeProperty
         }
       }
     }
-    return getColour(alignment, getColourIndexFromName(name));
+    return getColour(alignment, colindex);
   }
 
   /**
@@ -511,13 +512,13 @@ public class ColourSchemeProperty
     case TCOFFEE:
       cs = new TCoffeeColourScheme(coll);
       break;
-    
+
     case RNAHELIX:
       cs = new RNAHelicesColour(coll);
       break;
-      
-      // case COVARIATION:
-      // cs = new CovariationColourScheme(annotation);
+
+    // case COVARIATION:
+    // cs = new CovariationColourScheme(annotation);
     // break;
 
     case USER_DEFINED:
@@ -536,63 +537,103 @@ public class ColourSchemeProperty
     return cs;
   }
 
+  /**
+   * Returns the Color constant for a given colour name e.g. "pink", or null if
+   * the name is not recognised
+   * 
+   * @param name
+   * @return
+   */
   public static Color getAWTColorFromName(String name)
   {
+    if (name == null)
+    {
+      return null;
+    }
     Color col = null;
     name = name.toLowerCase();
-    if (name.equals("black"))
+
+    // or make a static map; or use reflection on the field name
+    switch (name)
     {
+    case "black":
       col = Color.black;
-    }
-    else if (name.equals("blue"))
-    {
+      break;
+    case "blue":
       col = Color.blue;
-    }
-    else if (name.equals("cyan"))
-    {
+      break;
+    case "cyan":
       col = Color.cyan;
-    }
-    else if (name.equals("darkGray"))
-    {
+      break;
+    case "darkGray":
       col = Color.darkGray;
-    }
-    else if (name.equals("gray"))
-    {
+      break;
+    case "gray":
       col = Color.gray;
-    }
-    else if (name.equals("green"))
-    {
+      break;
+    case "green":
       col = Color.green;
-    }
-    else if (name.equals("lightGray"))
-    {
+      break;
+    case "lightGray":
       col = Color.lightGray;
-    }
-    else if (name.equals("magenta"))
-    {
+      break;
+    case "magenta":
       col = Color.magenta;
-    }
-    else if (name.equals("orange"))
-    {
+      break;
+    case "orange":
       col = Color.orange;
+      break;
+    case "pink":
+      col = Color.pink;
+      break;
+    case "red":
+      col = Color.red;
+      break;
+    case "white":
+      col = Color.white;
+      break;
+    case "yellow":
+      col = Color.yellow;
+      break;
     }
-    else if (name.equals("pink"))
+
+    return col;
+  }
+
+  public static Color rnaHelices[] = null;
+
+  public static void initRnaHelicesShading(int n)
+  {
+    int j = 0;
+    if (rnaHelices == null)
     {
-      col = Color.pink;
+      rnaHelices = new Color[n + 1];
     }
-    else if (name.equals("red"))
+    else if (rnaHelices != null && rnaHelices.length <= n)
     {
-      col = Color.red;
+      Color[] t = new Color[n + 1];
+      System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length);
+      j = rnaHelices.length;
+      rnaHelices = t;
     }
-    else if (name.equals("white"))
+    else
     {
-      col = Color.white;
+      return;
     }
-    else if (name.equals("yellow"))
+    // Generate random colors and store
+    for (; j <= n; j++)
     {
-      col = Color.yellow;
+      rnaHelices[j] = jalview.util.ColorUtils
+              .generateRandomColor(Color.white);
     }
+  }
 
-    return col;
+  /**
+   * delete the existing cached RNA helces colours
+   */
+  public static void resetRnaHelicesShading()
+  {
+    rnaHelices = null;
   }
+
 }