JAL-653 GFF new/refactored helper classes

[jalview.git] / src / jalview / io / gff / GffHelperI.java

diff --git a/src/jalview/io/gff/GffHelperI.java b/src/jalview/io/gff/GffHelperI.java
new file mode 100644 (file)
index 0000000..3d9dc6f
--- /dev/null
+++ b/src/jalview/io/gff/GffHelperI.java
@@ -0,0 +1,44 @@
+package jalview.io.gff;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+import java.util.List;
+
+/**
+ * An interface to described common functionality of different flavours of GFF
+ * 
+ * @author gmcarstairs
+ *
+ */
+public interface GffHelperI
+{
+
+  final String RENAME_TOKEN = "$RENAME_TO$";
+
+  /**
+   * Process one GFF feature line
+   * 
+   * @param seq
+   *          the sequence with which this feature is associated
+   * @param gffColumns
+   *          the GFF column data
+   * @param align
+   *          the alignment we are adding GFF to
+   * @param newseqs
+   *          any new sequences referenced by the GFF
+   * @param relaxedIdMatching
+   *          if true, match word tokens in sequence names
+   * @return a SequenceFeature if one should be created, else null
+   * @throws IOException
+   */
+  SequenceFeature processGff(SequenceI seq, String[] gffColumns,
+          AlignmentI align,
+          List<SequenceI> newseqs, boolean relaxedIdMatching)
+          throws IOException;
+
+  // java 8 will allow static methods in interfaces:
+  // static boolean recognises(String [] columns);
+}