X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=7ad35c3200b2d6d9ef4aa21c90004e2797107de1;hb=7bb1887834cefc1a39ffd5b034b77c7984a13009;hp=bf30ed6175223d7488e179d476817cd35a1070a6;hpb=a97dbd3e6e9707de13f47c66beaa15df8ea24d0e;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index bf30ed6..7ad35c3 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -20,6 +20,8 @@
  */
 package jalview.schemes;
 
+import java.util.Locale;
+
 import jalview.analysis.GeneticCodes;
 
 import java.awt.Color;
@@ -405,6 +407,125 @@ public class ResidueProperties
       Color.white // ' '
   };
 
+  /*
+   * flower, blossom, sunset, ocean colour schemes from geocos.
+   * See https://gecos.biotite-python.org/
+   * https://raw.githubusercontent.com/biotite-dev/biotite/master/src/biotite/sequence/graphics/color_schemes/flower.json
+   * and https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3526-6
+   * (https://doi.org/10.1186/s12859-020-3526-6)
+   */
+  public static final Color[] flower = { new Color(177, 138, 81), // A
+      new Color(131, 191, 241), // R
+      new Color(11, 206, 198), // N
+      new Color(1, 165, 120), // D
+      new Color(255, 87, 1), // C
+      new Color(114, 149, 174), // Q
+      new Color(45, 160, 161), // E
+      new Color(177, 194, 60), // G
+      new Color(1, 148, 249), // H
+      new Color(242, 118, 99), // I
+      new Color(223, 110, 117), // L
+      new Color(127, 195, 215), // K
+      new Color(254, 157, 175), // M
+      new Color(250, 85, 157), // F
+      new Color(79, 163, 42), // P
+      new Color(180, 189, 155), // S
+      new Color(210, 181, 118), // T
+      new Color(255, 45, 237), // W
+      new Color(201, 110, 207), // Y
+      new Color(253, 153, 123), // V
+      Color.white, // B
+      Color.white, // Z
+      Color.white, // X
+      Color.white, // -
+      Color.white, // *
+      Color.white // .
+  };
+
+  public static final Color[] blossom = { new Color(139, 196, 180), // A
+      new Color(252, 149, 2), // R
+      new Color(181, 194, 6), // N
+      new Color(95, 165, 5), // D
+      new Color(8, 147, 254), // C
+      new Color(191, 133, 39), // Q
+      new Color(219, 181, 1), // E
+      new Color(0, 211, 130), // G
+      new Color(255, 87, 1), // H
+      new Color(154, 186, 243), // I
+      new Color(205, 165, 220), // L
+      new Color(254, 165, 39), // K
+      new Color(245, 161, 184), // M
+      new Color(247, 79, 168), // F
+      new Color(16, 214, 49), // P
+      new Color(126, 157, 89), // S
+      new Color(0, 162, 156), // T
+      new Color(254, 8, 251), // W
+      new Color(255, 78, 122), // Y
+      new Color(135, 192, 228), // V
+      Color.white, // B
+      Color.white, // Z
+      Color.white, // X
+      Color.white, // -
+      Color.white, // *
+      Color.white // .
+  };
+
+  public static final Color[] sunset = { new Color(254, 160, 253), // A
+      new Color(133, 116, 106), // R
+      new Color(171, 200, 245), // N
+      new Color(46, 123, 190), // D
+      new Color(252, 12, 254), // C
+      new Color(140, 110, 129), // Q
+      new Color(103, 120, 146), // E
+      new Color(39, 153, 255), // G
+      new Color(219, 197, 142), // H
+      new Color(250, 33, 161), // I
+      new Color(224, 30, 130), // L
+      new Color(222, 190, 204), // K
+      new Color(209, 62, 123), // M
+      new Color(255, 56, 93), // F
+      new Color(87, 102, 249), // P
+      new Color(231, 180, 253), // S
+      new Color(166, 88, 183), // T
+      new Color(255, 55, 1), // W
+      new Color(203, 83, 57), // Y
+      new Color(254, 81, 184), // V
+      Color.white, // B
+      Color.white, // Z
+      Color.white, // X
+      Color.white, // -
+      Color.white, // *
+      Color.white // .
+  };
+
+  public static final Color[] ocean = { new Color(198, 202, 155), // A
+      new Color(12, 160, 168), // R
+      new Color(10, 223, 195), // N
+      new Color(76, 223, 161), // D
+      new Color(198, 129, 54), // C
+      new Color(139, 211, 209), // Q
+      new Color(96, 218, 201), // E
+      new Color(51, 165, 81), // G
+      new Color(0, 207, 254), // H
+      new Color(242, 186, 170), // I
+      new Color(187, 138, 131), // L
+      new Color(64, 160, 144), // K
+      new Color(164, 139, 136), // M
+      new Color(171, 136, 174), // F
+      new Color(175, 211, 101), // P
+      new Color(109, 155, 116), // S
+      new Color(141, 149, 102), // T
+      new Color(117, 138, 238), // W
+      new Color(186, 195, 252), // Y
+      new Color(233, 190, 164), // V
+      Color.white, // B
+      Color.white, // Z
+      Color.white, // X
+      Color.white, // -
+      Color.white, // *
+      Color.white // .
+  };
+
   // Dunno where I got these numbers from
   public static final double[] hyd2 = { 0.62, // A
       0.29, // R
@@ -500,7 +621,8 @@ public class ResidueProperties
 
   public static String STOP = "STOP";
 
-  public static List<String> STOP_CODONS = Arrays.asList("TGA", "TAA", "TAG");
+  public static List<String> STOP_CODONS = Arrays.asList("TGA", "TAA",
+          "TAG");
 
   public static String START = "ATG";
 
@@ -905,47 +1027,51 @@ public class ResidueProperties
     return peptide;
   }
 
-  public static Hashtable<String, String> toDssp3State;
+  /*
+   * lookup of (A-Z) alternative secondary structure symbols'
+   * equivalents in DSSP3 notation
+   */
+  private static char[] toDssp3State;
   static
   {
-    toDssp3State = new Hashtable<>();
-    toDssp3State.put("H", "H");
-    toDssp3State.put("E", "E");
-    toDssp3State.put("C", " ");
-    toDssp3State.put(" ", " ");
-    toDssp3State.put("T", " ");
-    toDssp3State.put("B", "E");
-    toDssp3State.put("G", "H");
-    toDssp3State.put("I", "H");
-    toDssp3State.put("X", " ");
+    toDssp3State = new char[9]; // for 'A'-'I'; extend if needed
+    Arrays.fill(toDssp3State, ' ');
+    toDssp3State['B' - 'A'] = 'E';
+    toDssp3State['E' - 'A'] = 'E';
+    toDssp3State['G' - 'A'] = 'H';
+    toDssp3State['H' - 'A'] = 'H';
+    toDssp3State['I' - 'A'] = 'H';
   }
 
   /**
    * translate from other dssp secondary structure alphabets to 3-state
    * 
-   * @param ssstring
-   * @return ssstring as a three-state secondary structure assignment.
+   * @param ssString
+   * @return ssstring
    */
-  public static String getDssp3state(String ssstring)
+  public static String getDssp3state(String ssString)
   {
-    if (ssstring == null)
+    if (ssString == null)
     {
       return null;
     }
-    StringBuffer ss = new StringBuffer();
-    for (int i = 0; i < ssstring.length(); i++)
+    int lookupSize = toDssp3State.length;
+    int len = ssString.length();
+    char[] trans = new char[len];
+    for (int i = 0; i < len; i++)
     {
-      String ssc = ssstring.substring(i, i + 1);
-      if (toDssp3State.containsKey(ssc))
+      char c = ssString.charAt(i);
+      int index = c - 'A';
+      if (index < 0 || index >= lookupSize)
       {
-        ss.append(toDssp3State.get(ssc));
+        trans[i] = ' ';
       }
       else
       {
-        ss.append(" ");
+        trans[i] = toDssp3State[index];
       }
     }
-    return ss.toString();
+    return new String(trans);
   }
 
   static
@@ -2274,6 +2400,10 @@ public class ResidueProperties
 
   // main method generates perl representation of residue property hash
   // / cut here
+  /**
+   * @j2sIgnore
+   * @param args
+   */
   public static void main(String[] args)
   {
     Hashtable<String, Vector<String>> aaProps = new Hashtable<>();
@@ -2339,7 +2469,7 @@ public class ResidueProperties
         {
           continue;
         }
-        nuc = nuc.toUpperCase();
+        nuc = nuc.toUpperCase(Locale.ROOT);
         if (!result.contains(nuc))
         {
           result.add(nuc);
@@ -2358,7 +2488,7 @@ public class ResidueProperties
         {
           continue;
         }
-        res = res.toUpperCase();
+        res = res.toUpperCase(Locale.ROOT);
         if (!result.contains(res))
         {
           result.add(res);
@@ -2383,7 +2513,7 @@ public class ResidueProperties
       return '0';
     }
     Integer index = ResidueProperties.aa3Hash
-            .get(threeLetterCode.toUpperCase());
+            .get(threeLetterCode.toUpperCase(Locale.ROOT));
     return index == null ? '0' : aa[index].charAt(0);
   }
 }