Changeset 1590

Timestamp:

Mar 20, 2012, 7:07:31 PM (12 years ago)

Author:

pawels

Message:

added support for 2 channel

File:

• extensions/no.uib.cbu.base.magetabexport/trunk/src/main/java/no/uib/cbu/base/magetabexport/SDRFCreator.java (modified) (2 diffs)

extensions/no.uib.cbu.base.magetabexport/trunk/src/main/java/no/uib/cbu/base/magetabexport/SDRFCreator.java

@@ -175 +175 @@
         }
         
+        
         // add experimental factors
         if (!rba.isAnnotated()) {
@@ -180 +181 @@
                         "Can't retrieve experimental factor(s).");
         }
+        
         for (AnnotationType at : factors) {
+          
           List<AnnotationSnapshot> as = snapMan.findAnnotations(dc, rba, new AnnotationTypeFilter(at), true);
+          
           if (as == null || as.isEmpty()) {
             throw new MageTabException("raw bioassay ["+rba.getName()+"] is not annotated with "+
                 "an experimental factor ["+at.getName()+"].");
-          }
-          if (as.size() > 1) {
+          } 
+          else if (as.size() == 1) {        // one-channel experiment
+            AnnotationSnapshot a = as.get(0);
+            se.addExperimentalFactor(at.getName(), getValueForAnnotation(a));
+          } 
+          else if (as.size() == 2) {        // two-channel experiment
+            // find the correct annotation looking at sample annotation of this SDRFEntry
+            for (AnnotationSnapshot a : as) {   
+              String ann = getValueForAnnotation(a);
+              ItemInfo ii = se.getItems().get(ItemInfo.TYPE.SAMPLE);
+              if (ii != null && ii.getAllCharacteristicsNames().contains(at.getName())) {
+                if (ann.equals(ii.getCharacteristicValue(at.getName()))) {
+                  se.addExperimentalFactor(at.getName(), ann);
+                  break;
+                }
+              }
+            }
+          } else { 
             throw new MageTabException("raw bioassay ["+rba.getName()+"] has multiple annotations "+
                 "of type ["+at.getName()+"].");
           }
-          AnnotationSnapshot a = as.get(0);
-          se.addExperimentalFactor(at.getName(), getValueForAnnotation(a));
+          
+          
         }