Hidden representatives moved from sequence to viewport

[jalview.git] / src / jalview / datamodel / SequenceI.java

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index eb7cda6..96c6cbf 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,8 +20,6 @@ package jalview.datamodel;
 
 import java.util.*;
 
-import java.awt.*;
-
 
 /**
  * DOCUMENT ME!
@@ -100,7 +98,7 @@ public interface SequenceI
      *
      * @return DOCUMENT ME!
      */
-    public String getSequence();
+    public String getSequenceAsString();
 
     /**
      * DOCUMENT ME!
@@ -110,7 +108,24 @@ public interface SequenceI
      *
      * @return DOCUMENT ME!
      */
-    public String getSequence(int start, int end);
+    public String getSequenceAsString(int start, int end);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public char [] getSequence();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public char [] getSequence(int start, int end);
     /**
      * create a new sequence object from start to end of this sequence
      * @param start int
@@ -174,12 +189,6 @@ public interface SequenceI
      */
     public void deleteChars(int i, int j);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void deleteCharAt(int i);
 
     /**
      * DOCUMENT ME!
@@ -198,21 +207,6 @@ public interface SequenceI
     public void insertCharAt(int i, int length, char c);
 
 
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param c DOCUMENT ME!
-     */
-    public void setColor(Color c);
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color getColor();
-
     /**
      * DOCUMENT ME!
      *
@@ -255,6 +249,8 @@ public interface SequenceI
 
     public void addSequenceFeature(SequenceFeature sf);
 
+    public void deleteFeature(SequenceFeature sf);
+
     public void setDatasetSequence(SequenceI seq);
 
     public SequenceI getDatasetSequence();
@@ -263,10 +259,11 @@ public interface SequenceI
 
     public void addAlignmentAnnotation(AlignmentAnnotation annotation);
 
-    public SequenceGroup getHiddenSequences();
-
-    public void addHiddenSequence(SequenceI seq);
 
-    public void showHiddenSequence(SequenceI seq);
+    /**
+     * Derive a sequence (using this one's dataset or as the dataset)
+     * @return duplicate sequence with valid dataset sequence
+     */
+    public SequenceI deriveSequence();
 
 }