From 5eed2b9eb91105550c696147eea8c2888940bf42 Mon Sep 17 00:00:00 2001 From: Susie Date: Wed, 12 Feb 2025 10:26:41 +0000 Subject: [PATCH] readme improve --- README.md | 14 +++++++------- .../mi/xmlmaker/jami/xml/InteractionsCreator.java | 7 +++---- 2 files changed, 10 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 15081b4..3437ad1 100644 --- a/README.md +++ b/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. diff --git a/src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/jami/xml/InteractionsCreator.java b/src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/jami/xml/InteractionsCreator.java index 31c2252..55b2e6d 100644 --- a/src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/jami/xml/InteractionsCreator.java +++ b/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 xmlModelledInteractions = new ArrayList<>(); public final List> dataList = new ArrayList<>(); @@ -59,7 +58,6 @@ public class InteractionsCreator { public InteractionsCreator(ExcelFileReader reader, InteractionWriter writer, Map 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 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 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":