Merge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127

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

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index fccc31b..7b79d88 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -30,15 +31,6 @@ import java.util.Map;
 public interface ColourSchemeI
 {
   /**
-   * Returns the colour for the given character. For use when the colour depends
-   * only on the symbol.
-   * 
-   * @param c
-   * @return
-   */
-  Color findColour(char c);
-
-  /**
    * Returns the possibly context dependent colour for the given symbol at the
    * aligned position in the given sequence. For example, the colour may depend
    * on the symbol's relationship to the consensus residue for the column.
@@ -71,12 +63,14 @@ public interface ColourSchemeI
    * new instance for each call to this method, as different instances may have
    * differing shading by consensus or percentage identity applied.
    * 
+   * @param viewport
+   *          - the parent viewport
    * @param sg
-   * @param hiddenRepSequences
+   *          - the collection of sequences to be coloured
    * @return copy of current scheme with any inherited settings transferred
    */
-  ColourSchemeI getInstance(AnnotatedCollectionI sg,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+  ColourSchemeI getInstance(AlignViewportI viewport,
+          AnnotatedCollectionI sg);
 
   /**
    * Answers true if the colour scheme is suitable for the given data, else
@@ -107,4 +101,11 @@ public interface ColourSchemeI
    * @return
    */
   boolean isSimple();
+
+  /**
+   * Answers true if the colour scheme has a colour specified for gaps.
+   * 
+   * @return
+   */
+  boolean hasGapColour();
 }