X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=5fb16d6050add60b4ea8e80f6b3c6e743286c927;hb=dc3dd2e76d340b0577259c4e9d64372a1c126aee;hp=b076ea78c41264265241eb0c79d258f2fe27b977;hpb=621b23ed6783d2c4c7caaf6d58151217b2fa4f1d;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index b076ea7..5fb16d6 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -24,7 +24,6 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import java.util.function.Consumer;
 
 /**
  * Data structure to hold and manipulate a multiple sequence alignment
@@ -581,8 +580,32 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 
+  /**
+   * Set the hidden columns collection on the alignment
+   * 
+   * @param cols
+   */
   public void setHiddenColumns(HiddenColumns cols);
 
-  public void forEachSequence(Consumer<SequenceI> c, int start, int end);
+  /**
+   * Set the first sequence as representative and hide its insertions. Typically
+   * used when loading JPred files.
+   */
+  public void setupJPredAlignment();
+
+  /**
+   * Add gaps into the sequences aligned to profileseq under the given
+   * AlignmentView
+   * 
+   * @param profileseq
+   *          sequence in al which sequences are aligned to
+   * @param input
+   *          alignment view where sequence corresponding to profileseq is first
+   *          entry
+   * @return new HiddenColumns for new alignment view, with insertions into
+   *         profileseq marked as hidden.
+   */
+  public HiddenColumns propagateInsertions(SequenceI profileseq,
+          AlignmentView input);
 
 }