X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=5fb16d6050add60b4ea8e80f6b3c6e743286c927;hb=0669bcd76c254141146c1fc2628812c782571c0b;hp=2abb1f8c5096c7de4e7dcca3510225daba0c8a74;hpb=f3f90b8d541ef383d4f1d4cb3c1947200d6983ed;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 2abb1f8..5fb16d6 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -5,16 +5,16 @@
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General License
+ * modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General License for more details.
+ * PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General License
+ * You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
@@ -358,6 +358,8 @@ public interface AlignmentI extends AnnotatedCollectionI
HiddenSequences getHiddenSequences();
+ HiddenColumns getHiddenColumns();
+
/**
* Compact representation of alignment
*
@@ -579,12 +581,31 @@ public interface AlignmentI extends AnnotatedCollectionI
AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
/**
- * Calculate the visible start and end index of an alignment. The result is
- * returned an int array where: int[0] = startIndex, and int[1] = endIndex.
+ * Set the hidden columns collection on the alignment
*
- * @param hiddenCols
- * @return
+ * @param cols
+ */
+ public void setHiddenColumns(HiddenColumns cols);
+
+ /**
+ * 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 int[] getVisibleStartAndEndIndex(List hiddenCols);
+ public HiddenColumns propagateInsertions(SequenceI profileseq,
+ AlignmentView input);
}