My current work.

BIN-Storing_data.R

@@ -293,6 +293,47 @@ for (ID in pID) {
 #    BUT COPY THE EXACT, COMPLETE  OUTPUT, PASTE IT INTO YOUR SUBMISSION,
 #    AND FORMAT IT CORRECTLY.
 
+# == Submission - Code to add another philosopher to the datamodel:
+
+pID <- autoincrement(philDB$person)
+immanuelKant <- data.frame(id = pID,
+                           name = "Immanuel Kant",
+                           born = "1724",
+                           died = "1804",
+                           school = "Enlightenment Philosophy")
+philDB$person <- rbind(philDB$person, immanuelKant)
+
+bID = autoincrement(philDB$books)
+immanuelKantWork <- data.frame(id = bID,
+                               title = "Critique of Pure Reason",
+                               published = "1781")
+philDB$books <- rbind(philDB$books, immanuelKantWork)
+philDB$works <- rbind(philDB$works, data.frame(id = autoincrement(philDB$works), personID = pID, bookID = bID))
+
+bID = autoincrement(philDB$books)
+immanuelKantWork <- data.frame(id = bID,
+                               title = "Critique of Judgement",
+                               published = "1790")
+philDB$books <- rbind(philDB$books, immanuelKantWork)
+philDB$works <- rbind(philDB$works, data.frame(id = autoincrement(philDB$works), personID = pID, bookID = bID))
+
+# == Submission: Code to list the philosophical schools in alphabetical order as well as their respective books in alphabetical order.
+
+schools <- unique(philDB$person$school)
+schools <- sort(schools)
+
+for (s in schools) {
+  cat(sprintf("%s\n", s))
+  authors = which(philDB$person$school == s)
+  for (author in authors) {
+    works = which(philDB$works$personID == author)
+    for (work in works) {
+      bookId = which(philDB$books$id == philDB$works$bookID[work])
+      cat(sprintf("\t%s - (%s)\n", philDB$books$title[bookId], philDB$books$published[bookId]))
+    }
+  }
+}
+
 
 # =    2  Implementing the protein datamodel  ==================================
 

myScripts/.myProfile.R

@@ -14,7 +14,8 @@
 # ==============================================================================
 # options(stringsAsFactors = FALSE)
 
-myEMail <- "<your-e-mail-address-here>"        # e.g. "u.franklin@utoronto.ca"
+myEMail <- "yh.deng@mail.utoronto.ca"        # e.g. "u.franklin@utoronto.ca"
-myStudentNumber <- <your-student-number-here>  # e.g. 1003141592
+myStudentNumber <- 1005845285  # e.g. 1003141592
+MYSPE <- "Cutaneotrichosporon oleaginosum" 
 
 # [END]

myScripts/CUTOLTaxonomy.json

@@ -0,0 +1,4 @@
+[{
+	"ID": 879819,
+	"species": "Cutaneotrichosporon oleaginosum"}
+]

myScripts/MBP1_CUTOL.json

@@ -0,0 +1,19 @@
+[
+  { "name" : "MBP1_CUTOL",
+    "RefSeqID" : "XP_018278493.1",
+    "UniProtID" : "A0A0J0XLN0",
+    "taxonomyID" : 879819,
+    "sequence" : [
+       "MGKKAAAAGDGGPNTIYKATYSGVPVFEFICRNVAVMRRRSDAYLNATQILKVAGFDKPQRTRVLEREVQ",
+       "KGEHEKVQGGYGKYQGTWVPIERGLALAKQYNVEDLLRPIIDFVPRESVSPPPAPKHAVAPPTKRNKEPK",
+       "PKEGLVPIKSAGVLSGTGRHQTPDSVGEDVESEVMDDMSESQTPSPLNGTSLLPAVDERSIDGMDIDGFS",
+       "MMNGGGHARKRSAAMMDDEDEYEQLKRARGNSAVHTPPPPGQSPRYGGMQHPLTQDEYNDIVLNYFVSEA",
+       "TQIPAVMTNPPYNWDPNGIIDDDHHTALHWAAAMGRTRVIKLLLSAGARIFDKNNLDQTPLMRSVMFTNN",
+       "YDLRKFPEVFELLHRSTLNIDKNNRTVFHHIANLALYKGKTHAARYYMEVILSRLADYPQELADVINFAD",
+       "EDGETALTLAARARSKRIVKALLDHGADPKLRNRDHKSAEDYILEDERFRSSPDVMLNRTQPSAAPRNPT",
+       "SLGAAVFSQGLPPQLYNSEAARLASGPHSSDILQQMQALARSFEAEKLNKERDVLEAKAMLTSIHTEVND",
+       "AGRTLHNLGEQMKPLEAKQGELDGLVERLQSKLQKDLARGARKWKAADEGRENRWKNGDDPSQAGEDYSD",
+       "LPELTAIPDNAEAEEERLRGEIEKMRARRGELVTRLVKAQTQTGTTDKMAQYRRLITAGCGGDINPGEID",
+       "DIVGQLLDMLENEAQSGRPAPPPQAAPSWVTS"]
+  }
+]

myScripts/makeProteinDB.R

@@ -0,0 +1,4 @@
+source("./scripts/ABC-createRefDB.R")
+
+myDB <- dbAddProtein(myDB, jsonlite::fromJSON("./myScripts/MBP1_CUTOL.json"))
+myDB <- dbAddTaxonomy(myDB, jsonlite::fromJSON("./myScripts/CUTOLtaxonomy.json"))

myScripts/myScript.R

@@ -0,0 +1,38 @@
+# myScript.R
+#
+# --- As you work with this file, you can delete the instructions below --------
+# Write your notes and code experiments into this document. Save it
+# from time to time - however I recommend that you do not _commit_
+# your saved version.
+#
+# As long as you do not _commit_ this script to version control,
+# you can _pull_ updated versions of the entire project from GitHub
+# by using the RStudio version control interface. However, once
+# you _commit_ any file in your local version, RStudio will require
+# you to resolve conflicts before you can _pull_ updates.
+# --- As you work with this file, you can delete the instructions above --------
+#
+## Purpose: <...>
+#
+# Version: <...>
+#
+# Date:    <...>
+# Author:  <Name> (<namee@mail.utoronto.ca>)
+#
+# Versions:
+#
+#   <number>    <Features>
+#
+# TODO:
+#   <...>
+#
+# ====================================================================
+
+
+
+
+
+
+
+# [END]
+