From 4e6645f577c44d6ea2d411ef4aacaa3a6c6bbe3e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Thu, 26 Jan 2023 15:00:47 +0100
Subject: [PATCH] app: inputs_metfrag: Predefine metfrag inputs.
* inputs_metfrag: New file.
---
DESCRIPTION | 1 +
R/inputs_metfrag.R | 77 ++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 78 insertions(+)
create mode 100644 R/inputs_metfrag.R
diff --git a/DESCRIPTION b/DESCRIPTION
index 2059e21..6f0ba6c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -46,6 +46,7 @@ Roxygen: list(markdown = TRUE)
Collate:
'base.R'
'resources.R'
+ 'inputs_metfrag.R'
'errors.R'
'mix.R'
'envopts.R'
diff --git a/R/inputs_metfrag.R b/R/inputs_metfrag.R
new file mode 100644
index 0000000..4d84051
--- /dev/null
+++ b/R/inputs_metfrag.R
@@ -0,0 +1,77 @@
+mk_shiny_control <- function(name,fun,args) {
+ content = do.call(what=fun,args=c(list(inputId=name),args))
+ res = list(name=name,
+ fun=fun,
+ content=content)
+ res
+}
+
+INPUTS_METFRAG_NUMERIC = list(mk_shiny_control(name="mf_database_search_relative_mass_deviation",
+ fun="numericInput",
+ args=list(label="Database search relative mass deviation",
+ value=5)),
+ mk_shiny_control(name="mf_fragment_peak_match_absolute_mass_deviation",
+ fun="numericInput",
+ args=list(label="Fragment peak match absolute mass deviation",
+ value=METFRAG_DEFAULT_ABSMASSDEV)),
+ mk_shiny_control(name="mf_fragment_peak_match_relative_mass_deviation",
+ fun="numericInput",
+ args=list(label="Fragment peak match relative mass deviation",
+ value=METFRAG_DEFAULT_RELMASSDEV)),
+ mk_shiny_control(name="mf_maximum_tree_depth",
+ fun="numericInput",
+ args=list(label="MaximumTreeDepth",
+ value=METFRAG_DEFAULT_MAX_TREE_DEPTH)))
+
+INPUTS_METFRAG_SELECT = list(mk_shiny_control(name="mf_pre_processing_candidate_filter",
+ fun="selectInput",
+ args=list(label="Preprocessing candidate filter",
+ choices=shinyscreen:::METFRAG_PREPFLT_CHOICES,
+ selected=shinyscreen:::METFRAG_PREPFLT_DEFAULT,
+ multiple=T)),
+ mk_shiny_control(name="mf_post_processing_candidate_filter",
+ fun="selectInput",
+ args=list(label="Postprocessing candidate filter",
+ choices=shinyscreen:::METFRAG_POSTPFLT_CHOICES,
+ selected=shinyscreen:::METFRAG_POSTPFLT_DEFAULT,
+ multiple=T)),
+ mk_shiny_control(name="mf_metfrag_candidate_writer",
+ fun="selectInput",
+ args=list(label="MetFrag Candidate Writer",
+ choices=shinyscreen:::METFRAG_WRITER_CHOICES,
+ selected=shinyscreen:::METFRAG_DEFAULT_WRITER)),
+ mk_shiny_control(name="mf_database_type",
+ fun="selectInput",
+ args=list(label="Database type",
+ choices=METFRAG_DATABASE_TYPE,
+ selected=METFRAG_DEFAULT_DATABASE_TYPE)),
+ mk_shiny_control(name="mf_local_database",
+ fun="selectInput",
+ args=list(label="Local Database",
+ choices=character(0))),
+ mk_shiny_control(name="mf_local_db_col_ident",
+ fun="selectInput",
+ args=list(label="Select Identifiers",
+ multiple = T,
+ choices=character(0))),
+ mk_shiny_control(name="mf_local_db_col_coll",
+ fun="selectInput",
+ args=list(label="Identifiers for sets of results",
+ multiple = T,
+ choices=character(0))),
+ mk_shiny_control(name="mf_scores_intrinsic",
+ fun="selectInput",
+ args=list(label="Select Scoring Types",
+ choices = METFRAG_INTRINSIC_SCORES,
+ multiple = T,
+ selected = names(METFRAG_DEFAULT_SCORES))),
+ mk_shiny_control(name="mf_local_db_col_scores",
+ fun="selectInput",
+ args=list(label="Select local scoring terms",
+ multiple = T,
+ choices=character(0))))
+
+
+INPUTS_METFRAG = c(INPUTS_METFRAG_NUMERIC, INPUTS_METFRAG_SELECT)
+
+names(INPUTS_METFRAG) = sapply(INPUTS_METFRAG, function(x) x[["name"]])
--
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