Merge branch 'feature/JAL-3180colourAnnotationMenu' into merge/JAL-3180

[jalview.git] / src / jalview / datamodel / SearchResultMatchI.java

diff --git a/src/jalview/datamodel/SearchResultMatchI.java b/src/jalview/datamodel/SearchResultMatchI.java
index e886bed..661ad6c 100644 (file)
--- a/src/jalview/datamodel/SearchResultMatchI.java
+++ b/src/jalview/datamodel/SearchResultMatchI.java
@@ -1,17 +1,60 @@
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
+/**
+ * An interface that describes one matched region of an alignment, as one
+ * contiguous portion of a single dataset sequence
+ */
 public interface SearchResultMatchI
 {
+  /**
+   * Returns the matched sequence
+   * 
+   * @return
+   */
+  SequenceI getSequence();
 
-  public abstract SequenceI getSequence();
-
-  public abstract int getStart();
-
-  public abstract int getEnd();
+  /**
+   * Returns the start position of the match in the sequence (base 1)
+   * 
+   * @return
+   */
+  int getStart();
 
   /**
-   * Returns the string of characters in the matched region.
+   * Returns the end position of the match in the sequence (base 1)
+   * 
+   * @return
    */
-  public abstract String getCharacters();
+  int getEnd();
 
+  /**
+   * Answers true if this match is for the given sequence and includes (matches
+   * or encloses) the given start-end range
+   * 
+   * @param seq
+   * @param start
+   * @param end
+   * @return
+   */
+  boolean contains(SequenceI seq, int start, int end);
 }
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