JAL-1950 magic keys for different parts of the JSON object

diff --git a/src/jalview/ws/ebi/HmmerJSONProcessor.java b/src/jalview/ws/ebi/HmmerJSONProcessor.java
index 611f99e..4d30b3b 100644 (file)
--- a/src/jalview/ws/ebi/HmmerJSONProcessor.java
+++ b/src/jalview/ws/ebi/HmmerJSONProcessor.java
@@ -77,6 +77,36 @@ public class HmmerJSONProcessor
     }
   }
 
+  // encodings for JSON keys
+  /**
+   * score becomes sequence associated AlignmentAnnotation
+   */
+  private String[] score = { "aliId", "ali_IdCount", "bitscore", "ievalue",
+      "aliSim", "aliSimCount", "aliL", "aliSim", "ievalue", "cevalue" };
+
+  /**
+   * attrib becomes numeric or binary attribute for sequence with respect to
+   * this hmmsearch run
+   */
+  private String[] attrib = { "bias", "oasc", "is_included", "is_reported" };
+
+  /**
+   * name of the hmmsearch query
+   */
+  private String[] label = { "alihmmname" // (query label?)},
+  };
+
+  /**
+   * integer attributes for each
+   */
+  private String[] ipos = { "alihmmfrom", "alihmmto" }, pos_l = {
+      "alimline", "alimodel", "alirfline" };
+
+  /**
+   * positional quantitative annotation encoded as strings.
+   */
+  private String[] pos_nscore = { "alippline" };
+
   //
   // mapping of keys to types of property on sequence
   //