mungo merge

[jalview.git] / src / jalview / io / gff / Gff2Helper.java

diff --git a/src/jalview/io/gff/Gff2Helper.java b/src/jalview/io/gff/Gff2Helper.java
new file mode 100644 (file)
index 0000000..31303b1
--- /dev/null
+++ b/src/jalview/io/gff/Gff2Helper.java
@@ -0,0 +1,51 @@
+package jalview.io.gff;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+
+public class Gff2Helper extends GffHelperBase
+{
+  /**
+   * GFF2 uses space character to delimit name/value pairs on column 9
+   * 
+   * @param text
+   * @return
+   */
+  public static Map<String, List<String>> parseNameValuePairs(String text)
+  {
+    // TODO: can a value include a comma? if so it will be broken by this
+    return parseNameValuePairs(text, ";", ' ', ",");
+  }
+
+  /**
+   * Return ' ' as the name-value separator used in column 9 attributes.
+   */
+  @Override
+  protected char getNameValueSeparator()
+  {
+    return ' ';
+  }
+
+  /**
+   * Default processing if not overridden is just to construct a sequence
+   * feature
+   */
+  @Override
+  public SequenceFeature processGff(SequenceI seq, String[] gff,
+          AlignmentI align, List<SequenceI> newseqs,
+          boolean relaxedIdMatching) throws IOException
+  {
+    Map<String, List<String>> attributes = null;
+    if (gff.length > ATTRIBUTES_COL)
+    {
+      attributes = parseNameValuePairs(gff[ATTRIBUTES_COL]);
+    }
+    return buildSequenceFeature(gff, attributes);
+  }
+
+}