Merge branch 'develop' into releases/Release_2_11_2_Branch

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

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 09cef92..d55ffbf 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -20,9 +20,10 @@
  */
 package jalview.schemes;
 
+import java.util.Locale;
+
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
 import jalview.util.ColorUtils;
 import jalview.util.StringUtils;
 
@@ -56,18 +57,27 @@ public class UserColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI sg)
+  {
+    return new UserColourScheme(this);
+  }
+
+  /**
+   * Copy constructor
+   * 
+   * @return
+   */
+  protected UserColourScheme(UserColourScheme from)
   {
-    UserColourScheme usc = new UserColourScheme(colors);
-    if (lowerCaseColours != null)
+    this(from.colors);
+    schemeName = from.schemeName;
+    if (from.lowerCaseColours != null)
     {
-      usc.schemeName = schemeName;
-      usc.lowerCaseColours = new Color[lowerCaseColours.length];
-      System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0,
-              lowerCaseColours.length);
+      lowerCaseColours = new Color[from.lowerCaseColours.length];
+      System.arraycopy(from.lowerCaseColours, 0, lowerCaseColours, 0,
+              from.lowerCaseColours.length);
     }
-    return usc;
   }
 
   /**
@@ -207,13 +217,14 @@ public class UserColourScheme extends ResidueColourScheme
             continue;
           }
 
-          if (residue.equals(residue.toLowerCase()))
+          if (residue.equals(residue.toLowerCase(Locale.ROOT)))
           {
             if (lowerCaseColours == null)
             {
               lowerCaseColours = new Color[colors.length];
             }
-            lowerCaseColours[colIndex] = ColorUtils.parseColourString(colour);
+            lowerCaseColours[colIndex] = ColorUtils
+                    .parseColourString(colour);
           }
           else
           {
@@ -223,42 +234,12 @@ public class UserColourScheme extends ResidueColourScheme
       }
     } catch (Exception ex)
     {
-      System.out.println("Error parsing userDefinedColours:\n" + token
-              + "\n" + ex);
+      System.out.println(
+              "Error parsing userDefinedColours:\n" + token + "\n" + ex);
     }
 
   }
 
-  @Override
-  public Color findColour(char c, int j, SequenceI seq)
-  {
-    Color currentColour;
-    int index = ResidueProperties.aaIndex[c];
-
-    if ((threshold == 0) || aboveThreshold(c, j))
-    {
-      if (lowerCaseColours != null && 'a' <= c && c <= 'z')
-      {
-        currentColour = lowerCaseColours[index];
-      }
-      else
-      {
-        currentColour = colors[index];
-      }
-    }
-    else
-    {
-      currentColour = Color.white;
-    }
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
-  }
-
   public void setLowerCaseColours(Color[] lcolours)
   {
     lowerCaseColours = lcolours;
@@ -284,8 +265,8 @@ public class UserColourScheme extends ResidueColourScheme
   }
 
   /**
-   * Answers the customised name of the colour scheme, if it has one, else
-   * "User Defined"
+   * Answers the customised name of the colour scheme, if it has one, else "User
+   * Defined"
    */
   @Override
   public String getSchemeName()
@@ -294,7 +275,7 @@ public class UserColourScheme extends ResidueColourScheme
     {
       return schemeName;
     }
-    return "User Defined";
+    return ResidueColourScheme.USER_DEFINED;
   }
 
   /**
@@ -307,7 +288,7 @@ public class UserColourScheme extends ResidueColourScheme
     /*
      * step 1: build a map from colours to the symbol(s) that have the colour
      */
-    Map<Color, List<String>> colours = new HashMap<Color, List<String>>();
+    Map<Color, List<String>> colours = new HashMap<>();
 
     for (char symbol = 'A'; symbol <= 'Z'; symbol++)
     {
@@ -327,7 +308,7 @@ public class UserColourScheme extends ResidueColourScheme
         c = lowerCaseColours[index];
         if (c != null && !c.equals(Color.white))
         {
-          residue = residue.toLowerCase();
+          residue = residue.toLowerCase(Locale.ROOT);
           if (colours.get(c) == null)
           {
             colours.put(c, new ArrayList<String>());
@@ -340,7 +321,7 @@ public class UserColourScheme extends ResidueColourScheme
     /*
      * step 2: make a list of { A,G,R=12f9d6 } residues/colour specs
      */
-    List<String> residueColours = new ArrayList<String>();
+    List<String> residueColours = new ArrayList<>();
     for (Entry<Color, List<String>> cols : colours.entrySet())
     {
       boolean first = true;
@@ -370,4 +351,10 @@ public class UserColourScheme extends ResidueColourScheme
     Collections.sort(residueColours);
     return StringUtils.listToDelimitedString(residueColours, ";");
   }
+
+  @Override
+  public boolean hasGapColour()
+  {
+    return (findColour(' ') != null);
+  }
 }