X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=baaebc2a1079e85abb541e7d14cee9b8d93df723;hb=5dd663636925f44c6f964fa32fed2f584223b295;hp=bcfcc81fefe6de7f9b7823df0a150d564eabf84f;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index bcfcc81..baaebc2 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -18,8 +18,6 @@
 */
 package jalview.datamodel;
 
-import jalview.util.ShiftList;
-
 import java.util.*;
 
 
@@ -41,12 +39,6 @@ public interface AlignmentI
      */
     public int getWidth();
 
-    /**
-     * Calculates the longest sequence Id of the alignment
-     *
-     * @return Number of characters in longest sequence Id.
-     */
-    public int getMaxIdLength();
 
     /**
      * Calculates if this set of sequences is all the same length
@@ -94,7 +86,7 @@ public interface AlignmentI
     public void setSequenceAt(int i, SequenceI seq);
 
     /**
-     * Deletes a sequence from the alignment.
+     * Deletes a sequence from the alignment
      *
      * @param s Sequence to be deleted.
      */
@@ -107,14 +99,6 @@ public interface AlignmentI
      */
     public void deleteSequence(int i);
 
-    /**
-     * Deletes all residues in every sequence of alignment within given columns.
-     *
-     * @param start Start index of columns to delete.
-     * @param end End index to columns to delete.
-     */
-    public void deleteColumns(SequenceI seqs [], int start, int end);
-
 
     /**
      * Finds sequence in alignment using sequence name as query.
@@ -136,29 +120,6 @@ public interface AlignmentI
      */
     public int findIndex(SequenceI s);
 
-    /**
-    * All sequences will be cut from beginning to given index.
-    *
-    * @param i Remove all residues in sequences up to this column.
-     */
-    public void trimLeft(int i);
-
-    /**
-     * All sequences will be cut from given index.
-     *
-     * @param i Remove all residues in sequences beyond this column.
-     */
-    public void trimRight(int i);
-
-    /**
-     * Removes all columns containing entirely gap characters.
-     */
-    public void removeGaps();
-    /**
-     * remove gaps in alignment - recording any frame shifts in shiftrecord
-     * @param shiftrecord
-     */
-    public void removeGaps(ShiftList shiftrecord);
 
     /**
      * Finds group that given sequence is part of.
@@ -242,12 +203,6 @@ public interface AlignmentI
      */
     public char getGapCharacter();
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getAAFrequency();
 
     /**
      * Returns true if alignment is nucleotide sequence
@@ -273,7 +228,6 @@ public interface AlignmentI
      */
     public boolean padGaps();
 
-    public void adjustSequenceAnnotations();
 
     public HiddenSequences getHiddenSequences();
     /**