[Nomi Harris <nomi@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chadoxml
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv1627/apollo/dataadapter/chadoxml

Modified Files:
	ChadoXmlAdapter.java 
Log Message:

Now that we're treating one-level annots as one-levels (rather than
promoting them to three levels), we expect them to be identified as such
in the tiers file:
number_of_levels : 1
If the user has an out-of-date tiers file without this line for a
one-level type, the one-level annot will not show up.  Pop up a warning.


Index: ChadoXmlAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chadoxml/ChadoXmlAdapter.java,v
retrieving revision 1.84
retrieving revision 1.85
diff -C2 -d -r1.84 -r1.85
*** ChadoXmlAdapter.java	18 Dec 2005 05:12:48 -0000	1.84
--- ChadoXmlAdapter.java	19 Dec 2005 22:10:22 -0000	1.85
***************
*** 622,642 ****
      }
  
      // If annot is unstranded, it won't show up--temporarily force it onto a strand.
      forceStrandIfNeeded(annot);
  
-     // Apollo expects annotations to have transcripts, even those that shouldn't,
-     // like transposable_element.  In GAME XML, even transposable_elements have
-     // fake transcripts, like this:
-     // <annotation id="TE19303">
-     //   <feature_set id="TE19303-RA">
-     // Apollo shouldn't make that assumption, but because it does, we may need
-     // to construct these fake transcripts (and exons) for annotations that are
-     // missing them.  (And then when we write out those annots in Chado XML,
-     // we need to make sure not to write the fake transcript!)
-     //
-     // 11/2005: Apollo can now handle one-level annots, so no need to make
-     // fake transcripts.
-     //    makeFakeTranscriptIfNeeded(annot, curation);
- 
      // If annot doesn't have a name, use its ID as a name
      // (need a name for it to display as a label).
--- 622,636 ----
      }
  
+     // Now that we're treating one-level annots as one-levels (rather than
+     // promoting them to three levels), we expect them to be identified as such
+     // in the tiers file:
+     // number_of_levels : 1
+     // If the user has an out-of-date tiers file without this line for a
+     // one-level type, the one-level annot will not show up.  Pop up a warning.
+     warnIfOneLevelDiscrepancy(annot);
+     
      // If annot is unstranded, it won't show up--temporarily force it onto a strand.
      forceStrandIfNeeded(annot);
  
      // If annot doesn't have a name, use its ID as a name
      // (need a name for it to display as a label).
***************
*** 649,652 ****
--- 643,662 ----
    }
  
+   /** Now that we're treating one-level annots as one-levels (rather than
+     * promoting them to three levels), we expect them to be identified as such
+     * in the tiers file:
+     * number_of_levels : 1
+     * If the user has an out-of-date tiers file without this line for a
+     * one-level type, the one-level annot will not show up.  Pop up a warning. */
+   private void warnIfOneLevelDiscrepancy(SeqFeature annot) {
+     if ((annot.getFeatures() == null || annot.getFeatures().size() == 0)) {
+       FeatureProperty fp = Config.getPropertyScheme().getFeatureProperty(annot.getFeatureType());
+       if (fp.getNumberOfLevels() != 1) {
+         // errorDialog prints the message to stderr if we're running in command-line mode
+         apollo.util.IOUtil.errorDialog("Annotation " + annot.getName() + " is one-level, but type " + annot.getFeatureType() + "\ndoes not have 'number_of_levels: 1' in tiers file " + Config.getStyle().getTiersFile() + ".\nEither the data is buggy or your tiers file is out of date.");
+       }
+     }
+   }
+ 
    /** Wordy chadoXML way to store feature type is
        <type_id>       <cvterm>        <cv_id>          <cv>            <name>SO</name>          </cv>        </cv_id>