readme improve

README.md

@@ -45,13 +45,13 @@ The user can select the corresponding options.
 
 #### 2.3 Selecting information concerning the baits
 The same way as for the general information, the user can select information about the baits thanks to the dropdown menus.
-The user can select multiple experimental preparations. To do so, it has to increase the number in the spinner. Then, multiple dropdown menu will appear.
-
-The following options can also be typed in:
-- the organism **Tax id**
-- the feature start and end locations
-- the feature xref
-
+The bait organism can be typed in by the user.
+The user can select multiple experimental preparations. To do so, it has to increase the number in the spinner.
+Then, multiple dropdown menu will appear.
+The user can create features by clicking on the corresponding button.
+This action will open a window where the user can create multiple features by increasing the number on the top of it.
+The user can input manually the start and end location of the feature. It can also create multiple cross-references for it (note that the feature xref has to be typed in).
+Once the feature(s) have been created, they will be applied to all the baits.
 
 #### 2.4 Selecting information concerning the preys
 The preys information selection is working the same way as the baits information selection.

src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/jami/xml/InteractionsCreator.java

@@ -29,7 +29,6 @@ public class InteractionsCreator {
     private static int MAX_INTERACTIONS_PER_FILE = 1_000;
     final ExcelFileReader excelFileReader;
     final InteractionWriter interactionWriter;
-//    final UniprotMapperGui uniprotMapperGui;
     final XmlMakerUtils utils = new XmlMakerUtils();
     public final List<XmlInteractionEvidence> xmlModelledInteractions = new ArrayList<>();
     public final List<Map<String, String>> dataList = new ArrayList<>();
@@ -59,7 +58,6 @@ public class InteractionsCreator {
     public InteractionsCreator(ExcelFileReader reader, InteractionWriter writer, Map<String, Integer> columnAndIndex) {
         this.excelFileReader = reader;
         this.interactionWriter = writer;
-//        this.uniprotMapperGui = uniprotMapperGui;
         this.columnAndIndex = columnAndIndex;
         this.publicationId = excelFileReader.publicationId;
     }
@@ -149,7 +147,6 @@ public XmlParticipantEvidence createParticipant(Map<String, String> data) {
         CvTerm xref= terms.get(PARTICIPANT_XREF);
         CvTerm xrefDb = terms.get(PARTICIPANT_XREF_DB);
         CvTerm participantIdentificationMethod = terms.get(PARTICIPANT_IDENTIFICATION_METHOD);
-//        CvTerm participantType = terms.get(PARTICIPANT_TYPE);
 
         String name = Objects.requireNonNull(data.get(PARTICIPANT_NAME.name), "The participant name cannot be null");
         String participantId = data.get(PARTICIPANT_ID.name);
@@ -173,7 +170,9 @@ public XmlParticipantEvidence createParticipant(Map<String, String> data) {
                 break;
             case "nucleic acid":
                 participant = new XmlNucleicAcid(name, organism, uniqueId);
-                CvTerm rnaTerm = utils.fetchTerm("rna");
+                CvTerm rnaTerm = utils.fetchTerm("protein");
+                Annotation annotation = new XmlAnnotation(rnaTerm);
+                participant.getAnnotations().add(annotation);
                 participant.setInteractorType(rnaTerm); //todo: check here
                 break;
             case "molecule":