X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FFinderI.java;h=8f6232e25816e7647e132bd44fe23e4212b5104f;hb=7ae11f7f7f00549c6fb3af9ee193dc103a3c8de8;hp=19f6136a3a5740129f0a0869a56ceb22afb7889e;hpb=9b5106c49c8fa0a7269f38ad1825851eb8ba5b85;p=jalview.git
diff --git a/src/jalview/api/FinderI.java b/src/jalview/api/FinderI.java
index 19f6136..8f6232e 100644
--- a/src/jalview/api/FinderI.java
+++ b/src/jalview/api/FinderI.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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 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 Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
+ * If {@code ignoreHidden} is true, then any residues in hidden columns are + * ignored (skipped) when matching, so for example pattern {@code KRT} would + * match sequence {@code KRqmT} (where {@code qm} are in hidden columns). + *
+ * Matches of entirely hidden patterns are not returned. Matches that span + * hidden regions on one or both sides may be returned. * * @param theSearchString * @param caseSensitive * @param searchDescription + * @param ignoreHidden * @return */ void findAll(String theSearchString, boolean caseSensitive, - boolean searchDescription); + boolean searchDescription, boolean ignoreHidden); /** * Finds the next match for the given search string (interpreted as a regular * expression), starting from the position after the last match found. Search * may optionally be case-sensitive, and may optionally including match in - * sequence description (sequence id is always searched). If the viewport has - * an active selection, then the find is restricted to the selection region. + * sequence description (sequence id is always searched). If the viewport has an + * active selection, then the find is restricted to the selection region. * Sequences matched by id or description can be retrieved by getIdMatches(), * and matched residue patterns by getSearchResults(). + *
+ * If {@code ignoreHidden} is true, any hidden residues are skipped (matches may + * span them). If false, they are included for matching purposes. In either + * cases, entirely hidden matches are not returned. * * @param theSearchString * @param caseSensitive * @param searchDescription + * @param ignoreHidden * @return */ void findNext(String theSearchString, boolean caseSensitive, - boolean searchDescription); + boolean searchDescription, boolean ignoreHidden); /** * Returns the (possibly empty) list of sequences matched on sequence name or