X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=96c6cbf77d3b845c94ac0a2c6dda6f60ba2f79c9;hb=201b18da026bf92f9cd611e549a9def463583c67;hp=6c9fa2a86a54cc018de263dfa331c3682020cfdd;hpb=0ae0d247aec4361dc0a743d10abd3e9743d6c180;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 6c9fa2a..96c6cbf 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -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
@@ -151,18 +166,18 @@ public interface SequenceI
     public int findIndex(int pos);
 
     /**
-     * DOCUMENT ME!
+     * Returns the sequence position for an alignment position
      *
-     * @param i DOCUMENT ME!
+     * @param i column index in alignment (from 1)
      *
-     * @return DOCUMENT ME!
+     * @return residue number for residue (left of and) nearest ith column
      */
     public int findPosition(int i);
 
     /**
-     * DOCUMENT ME!
+     * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
      *
-     * @return DOCUMENT ME!
+     * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
      */
     public int[] gapMap();
 
@@ -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!
@@ -189,20 +198,14 @@ public interface SequenceI
      */
     public void insertCharAt(int i, char c);
 
-
     /**
      * DOCUMENT ME!
      *
+     * @param i DOCUMENT ME!
      * @param c DOCUMENT ME!
      */
-    public void setColor(Color c);
+    public void insertCharAt(int i, int length, char c);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color getColor();
 
     /**
      * DOCUMENT ME!
@@ -246,6 +249,8 @@ public interface SequenceI
 
     public void addSequenceFeature(SequenceFeature sf);
 
+    public void deleteFeature(SequenceFeature sf);
+
     public void setDatasetSequence(SequenceI seq);
 
     public SequenceI getDatasetSequence();
@@ -254,33 +259,11 @@ public interface SequenceI
 
     public void addAlignmentAnnotation(AlignmentAnnotation annotation);
 
-    public SequenceGroup getHiddenSequences();
-
-    public void addHiddenSequence(SequenceI seq);
-
-    public void showHiddenSequence(SequenceI seq);
-
-    public void changeCase(boolean toUpper, int start, int end);
-
-    public void toggleCase(int start, int end);
-
-  /**
-   * getSubSequence from start to end of sequence
-   * @param start first residue in subSequence
-   * @return SequenceI
-   */
-  public SequenceI getSubSequence(int start);
-  /**
-   * remove all gaps in the sequence
-   * @return number of gaps removed
-   */
-  public int removeGaps();
-  /**
-   * remove all gaps from start to end columns in sequence
-   * @param start 
-   * @param end
-   * @return number of gaps removed
-   */
-  public int removeGaps(int start, int end);
+
+    /**
+     * Derive a sequence (using this one's dataset or as the dataset)
+     * @return duplicate sequence with valid dataset sequence
+     */
+    public SequenceI deriveSequence();
 
 }