/R/SearchBar-GUI.R

  1qsetClass("SearchBar", Qt$QLineEdit, function(gr = NULL, ref = NULL, parent = NULL)
  2{
  3  super(parent)
  4  this$gr <- gr; this$ref <- ref
  5  names <- NULL
  6  metadata <- NULL
  7  if(!is.null(gr)) {
  8    names <- levels(seqnames(gr))
  9    metadata <- unique(unlist(sapply(values(gr),as.character)))
 10  }
 11  namesRef <- NULL
 12  metadataRef <- NULL
 13  if(!is.null(ref)) {
 14    namesRef <- levels(seqnames(ref))
 15    metadataRef <- unique(unlist(sapply(values(ref),as.character)))
 16  }
 17  compVec <- c(names,metadata,namesRef,metadataRef)
 18  if(!is.null(compVec)) {
 19    compVec <- sort(unique(compVec))
 20    comp <- Qt$QCompleter(compVec)
 21    comp$setCaseSensitivity(Qt$Qt$CaseInsensitive)
 22    this$setCompleter(comp)
 23  }
 24
 25  # initialize the GRanges object containing the search range
 26  searchRange <- NULL
 27
 28  # parse the text and update GRanges object when return pressed
 29  qconnect(this, "returnPressed", function() {
 30    parseSearchString(this$text, gr, ref)
 31  })
 32
 33})
 34
 35qsetSignal("rangeChanged", SearchBar)
 36
 37qsetMethod("getSearchRange", SearchBar, function() {
 38  this$searchRange
 39})
 40
 41qsetMethod("setSearchRange", SearchBar, function(newRange) {
 42  this$searchRange <- newRange
 43})
 44
 45qsetMethod("parseSearchString", SearchBar, function(text, gr = NULL, ref = NULL) {
 46  colon <- grepl(":",text,fixed=TRUE)
 47  minus <- grepl("-",text,fixed=TRUE)
 48  plus <- grepl("+",text,fixed=TRUE)
 49  if((!colon) & (minus) ){
 50  start <- as.numeric(unlist(strsplit(text, "-")))[1]
 51  end <- as.numeric(unlist(strsplit(text, "-")))[2]
 52  this$searchRange <- c(start, end)
 53  this$rangeChanged()
 54  }
 55  if(colon & minus) {  # seqname and interval specified
 56    # obtain seqname, start, end
 57    colonIdx <- regexpr(":",text,fixed=TRUE)
 58    minusIdx <- regexpr("-",text,fixed=TRUE)
 59    name <- substr(text,1,colonIdx-1)
 60    start <- as.integer(substr(text,colonIdx+1,minusIdx-1))
 61    end <- as.integer(substr(text,minusIdx+1,nchar(text)))
 62
 63    # return GRanges object with relevant sequence
 64    this$searchRange <- GRanges(seqnames =
 65                     Rle(name, 1),
 66                     ranges =
 67                       IRanges(start = start, end = end),
 68                   )
 69
 70    this$rangeChanged()
 71           
 72  } else if(colon & plus) {  # seqname and center/radius specified
 73    # obtain seqname, start, end
 74    colonIdx <- regexpr(":",text,fixed=TRUE)
 75    plusIdx <- regexpr("+",text,fixed=TRUE)
 76    name <- substr(text,1,colonIdx-1)
 77    center <- as.integer(substr(text,colonIdx+1,plusIdx-1))
 78    radius <- as.integer(substr(text,plusIdx+1,nchar(text)))
 79    start <- center - radius
 80    end <- center + radius
 81
 82    # return GRanges object with relevant sequence
 83    this$searchRange <- GRanges(seqnames =
 84                     Rle(name, 1),
 85                     ranges =
 86                       IRanges(start = start, end = end),
 87                   )
 88
 89    this$rangeChanged()
 90    
 91  } else {
 92    in.names <- NULL
 93    in.metadata <- NULL
 94    if(!is.null(gr)) {
 95      grNames <- levels(seqnames(gr))
 96      in.names <- grep(text,grNames,ignore.case=TRUE)
 97      metaData <- unlist(sapply(values(gr),as.character))
 98      in.metadata <- grep(text,metaData,ignore.case=TRUE)
 99    }
100    in.namesRef <- NULL
101    in.metadataRef <- NULL
102    if(!is.null(ref)) {
103      namesReference <- levels(seqnames(ref))
104      in.namesRef <- grep(text,namesReference,ignore.case=TRUE)
105      metaDataReference <- unlist(sapply(values(ref),as.character))
106      in.metadataRef <- grep(text,metaDataReference,ignore.case=TRUE)
107    }
108    if(length(in.names) > 0) {
109      grSubset <- gr[seqnames(gr) == text]
110      minLoc <- min(IRanges::start(grSubset))
111      maxLoc <- max(IRanges::end(grSubset))
112
113      # return GRanges object with relevant sequence
114      this$searchRange <- GRanges(seqnames =
115                       Rle(text, 1),
116                       ranges =
117                         IRanges(start = minLoc, end = maxLoc),
118                     )
119
120      this$rangeChanged()
121    } else if (length(in.metadataRef) > 0) {
122      matchRows <- in.metadataRef %% dim(values(ref))[1]
123      matchRows[matchRows == 0] <- dim(values(ref))[1]
124      
125      # return GRanges object with matching rows in reference set
126      refSubset <- ref[matchRows]
127      this$searchRange <- refSubset
128
129      this$rangeChanged()
130
131      # change text in search bar to match intervals being displayed
132      setText(base::paste(GenomicRanges::seqnames(refSubset),":",
133                          IRanges::start(refSubset),
134                          "-",IRanges::end(refSubset),collapse="; ",sep=""))
135    } else if (length(in.namesRef) > 0) {
136      refSubset <- ref[seqnames(ref) == text]
137      minLoc <- min(start(refSubset))
138      maxLoc <- max(end(refSubset))
139
140      # return GRanges object with relevant sequence
141      this$searchRange <- GRanges(seqnames =
142                       Rle(text, 1),
143                       ranges =
144                         IRanges(start = minLoc, end = maxLoc),
145                     )
146
147      this$rangeChanged()      
148    } else if (length(in.metadata) > 0) {
149      matchRows <- in.metadata %% dim(values(gr))[1]
150      matchRows[matchRows == 0] <- dim(values(gr))[1]
151      
152      # return GRanges object with matching rows in reference set
153      grSubset <- gr[matchRows]
154      this$searchRange <- grSubset
155
156      this$rangeChanged()
157
158      # change text in search bar to match intervals being displayed
159      setText(base::paste(GenomicRanges::seqnames(grSubset),":",
160                          IRanges::start(grSubset),"-",
161                          IRanges::end(grSubset),collapse="; ",sep=""))
162    } else {
163      setText("")
164      setPlaceholderText("Error: search string not recognized")
165      this$searchRange <- NULL
166    }
167  }
168
169})