Merge branch 'feature/JAL-3187linkedFeatures' into feature/JAL-3251biotypedMappings

[jalview.git] / src / jalview / api / FinderI.java

diff --git a/src/jalview/api/FinderI.java b/src/jalview/api/FinderI.java
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+++ b/src/jalview/api/FinderI.java
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+package jalview.api;
+
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceI;
+
+import java.util.List;
+
+/**
+ * An interface for searching for a pattern in an aligment
+ */
+public interface FinderI
+{
+
+  /**
+   * Performs a find for the given search string (interpreted as a regular
+   * expression). 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. Sequences matched by id or description can be retrieved
+   * by getIdMatches(), and matched residue patterns by getSearchResults().
+   * 
+   * @param theSearchString
+   * @param caseSensitive
+   * @param searchDescription
+   * @return
+   */
+  void findAll(String theSearchString, boolean caseSensitive,
+          boolean searchDescription);
+
+  /**
+   * 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.
+   * Sequences matched by id or description can be retrieved by getIdMatches(),
+   * and matched residue patterns by getSearchResults().
+   * 
+   * @param theSearchString
+   * @param caseSensitive
+   * @param searchDescription
+   * @return
+   */
+  void findNext(String theSearchString, boolean caseSensitive,
+          boolean searchDescription);
+
+  /**
+   * Returns the (possibly empty) list of sequences matched on sequence name or
+   * description
+   * 
+   * @return
+   */
+  List<SequenceI> getIdMatches();
+
+  /**
+   * Answers the search results (possibly empty) from the last search
+   * 
+   * @return
+   */
+  SearchResultsI getSearchResults();
+
+}
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