From 34ce27a9d6276a7bc931ffcc89fb26e78b0b02de Mon Sep 17 00:00:00 2001
From: js2264 <jacquesserizay@gmail.com>
Date: Sat, 2 Sep 2023 14:06:48 +0200
Subject: [PATCH] feat: show method displays strand{12}

---
 R/methods-show.R | 90 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 90 insertions(+)
 create mode 100644 R/methods-show.R

diff --git a/R/methods-show.R b/R/methods-show.R
new file mode 100644
index 0000000..a200140
--- /dev/null
+++ b/R/methods-show.R
@@ -0,0 +1,90 @@
+## Ripped from InteractionSet to add the strand{12} to the print
+setMethod("show", "GInteractions", function(object){
+    .showGInteractions(
+        object, margin="  ", print.seqinfo=TRUE, print.classinfo=TRUE
+    )
+})
+
+#' @importFrom GenomeInfoDb seqinfo
+.showGInteractions <- function(
+    x, margin="", print.seqinfo=FALSE, print.classinfo=FALSE
+) {
+    lx <- length(x)
+    nr <- length(InteractionSet::regions(x))
+    nc <- ncol(mcols(x))
+    if (is.null(nc)) {
+        nc <- 0L
+    }
+    cat(class(x), " object with ",
+        lx, " ", ifelse(lx == 1L, "interaction", "interactions"), " and ",
+        nc, " metadata ", ifelse(nc == 1L, "column", "columns"),
+        ":\n", sep="")
+    out <- S4Vectors::makePrettyMatrixForCompactPrinting(
+        x, .makeNakedMatFromGInteractions
+    )
+    if (print.classinfo) { 
+        .COL2CLASS <- c(
+            seqnames1 = "Rle", ranges1 = "IRanges", strand1 = "Rle", "   "="", 
+            seqnames2="Rle", ranges2="IRanges", strand2 = "Rle"
+        )
+        classinfo <- S4Vectors::makeClassinfoRowForCompactPrinting(x, .COL2CLASS)
+        classinfo[,"   "] <- ""
+        stopifnot(identical(colnames(classinfo), colnames(out)))
+        out <- rbind(classinfo, out)
+    }
+
+    if (nrow(out) != 0L) {
+        rownames(out) <- paste0(margin, rownames(out))
+    }
+
+    print(out, quote=FALSE, right=TRUE, max=length(out))
+    if (print.seqinfo) {
+        cat(margin, "-------\n", sep="")
+        ncr <- ncol(mcols(InteractionSet::regions(x)))
+        if (is.null(ncr)) {
+            ncr <- 0L
+        }
+        cat(
+            margin, "regions: ", nr, " ranges and ", ncr, 
+            " metadata ", ifelse(ncr==1L, "column", "columns"), "\n", sep=""
+        )
+        cat(margin, "seqinfo: ", summary(GenomeInfoDb::seqinfo(x)), "\n", sep="")
+    }
+}
+
+#' @importFrom InteractionSet anchors
+#' @importFrom InteractionSet regions
+#' @importFrom S4Vectors showAsCell
+.makeNakedMatFromGInteractions <- function(x) {
+    lx <- length(x)
+    nc <- ncol(mcols(x))
+    if (is.null(nc)) {
+        nc <- 0L
+    }
+    ans <- cbind(
+        .pasteAnchor(InteractionSet::anchors(x, type="first"), append="1"),
+        "   "=rep.int("---", lx),
+        .pasteAnchor(InteractionSet::anchors(x, type="second"), append="2")
+    )
+    if (nc > 0L) {
+        tmp <- do.call(
+            data.frame, 
+            c(lapply(mcols(x), S4Vectors::showAsCell), list(check.names=FALSE))
+        )
+        ans <- cbind(ans, `|`=rep.int("|", lx), as.matrix(tmp))
+    }
+    ans
+}
+
+#' @importFrom GenomeInfoDb seqnames
+#' @importFrom IRanges ranges
+#' @importFrom BiocGenerics strand
+.pasteAnchor <- function(x, append) {
+    out <- cbind(
+        as.character(GenomeInfoDb::seqnames(x)), 
+        S4Vectors::showAsCell(IRanges::ranges(x)), 
+        as.character(BiocGenerics::strand(x))
+    )
+    colnames(out) <- paste0(c("seqnames", "ranges", "strand"), append)
+    out
+}