# Tests for specific uncovered lines to reach 100% test coverage
# See comments for exact line numbers being tested

# Test 1: R/plot-htna.R lines 150-151 - Matrix input path
test_that("plot_htna works with matrix input", {
  trans_mat <- matrix(c(
    0.7, 0.2, 0.1,
    0.1, 0.6, 0.3,
    0.3, 0.1, 0.6
  ), nrow = 3, byrow = TRUE)
  colnames(trans_mat) <- rownames(trans_mat) <- c("A", "B", "C")

  with_temp_png({
    plot_htna(trans_mat, node_list = list(g1 = c("A", "B"), g2 = c("C")))
  })
})

test_that("plot_htna with matrix without colnames", {
  trans_mat <- matrix(c(
    0.7, 0.2, 0.1,
    0.1, 0.6, 0.3,
    0.3, 0.1, 0.6
  ), nrow = 3, byrow = TRUE)
  # Matrix without colnames will get auto-generated names "1", "2", "3"

  # Test with character group names matching auto-generated names
  with_temp_png({
    plot_htna(trans_mat, node_list = list(g1 = c("1", "2"), g2 = c("3")))
  })
})

# Test 2: R/plot-htna.R line 200 - Circular layout with < 2 groups
# Line 200 checks for circular layout specifically needing at least 2 groups
# But line 139 already checks for 2+ groups in general, so line 200 is unreachable
# with current code structure. The circular layout validation would only trigger
# if bipartite/polygon validations weren't there. Let's test the working circular layout instead.
test_that("plot_htna works with circular layout", {
  trans_mat <- matrix(c(
    0.7, 0.2, 0.1,
    0.1, 0.6, 0.3,
    0.3, 0.1, 0.6
  ), nrow = 3, byrow = TRUE)
  colnames(trans_mat) <- rownames(trans_mat) <- c("A", "B", "C")

  # Test circular layout with 2 groups
  with_temp_png({
    plot_htna(trans_mat, node_list = list(g1 = c("A", "B"), g2 = c("C")), layout = "circular")
  })
})


# Test 3: R/plot-htna.R line 439 - shape_to_pch mapping in legend
test_that("plot_htna legend handles non-standard shapes", {
  trans_mat <- matrix(c(
    0.7, 0.2, 0.1,
    0.1, 0.6, 0.3,
    0.3, 0.1, 0.6
  ), nrow = 3, byrow = TRUE)
  colnames(trans_mat) <- rownames(trans_mat) <- c("A", "B", "C")

  # Use shapes that will trigger the 'else 21' path in line 439
  # "ellipse" is not in the standard shape_to_pch mapping
  with_temp_png({
    plot_htna(trans_mat,
              node_list = list(g1 = c("A"), g2 = c("B"), g3 = c("C")),
              group_shapes = c("ellipse", "pentagon", "hexagon"),
              legend = TRUE)
  })
})

# Test 4: R/plot-htna.R line 643 - outward vector flipping
test_that("plot_htna polygon layout with outward vector flip", {
  # 4-state network, 4 groups in polygon layout to trigger line 643
  trans_mat <- matrix(0.1, nrow = 4, ncol = 4)
  diag(trans_mat) <- 0.7
  colnames(trans_mat) <- rownames(trans_mat) <- c("A", "B", "C", "D")

  with_temp_png({
    plot_htna(trans_mat,
              node_list = list(g1 = c("A"), g2 = c("B"), g3 = c("C"), g4 = c("D")),
              layout = "polygon")
  })
})

# Test 5: R/plot-htna-multi.R line 360 - negative angle normalization
test_that("plot_mtna handles triangle shape with negative angles", {
  skip_if_not_installed("tna")
  # 3-group network to get triangle shape
  trans_mat <- matrix(c(
    0, 0.3, 0.1,
    0.2, 0, 0.3,
    0.1, 0.2, 0
  ), nrow = 3, byrow = TRUE)
  colnames(trans_mat) <- rownames(trans_mat) <- c("A", "B", "C")
  tna_obj <- tna::tna(trans_mat)

  with_temp_png({
    plot_mtna(tna_obj, cluster_list = list(g1 = c("A"), g2 = c("B"), g3 = c("C")))
  })
})

# Test 6: R/plot-htna-multi.R lines 399, 402 - triangle edge_center paths
test_that("plot_mtna triangle edge_center calculation for different angles", {
  skip_if_not_installed("tna")

  trans_mat <- matrix(c(
    0.5, 0.2, 0.3,
    0.3, 0.4, 0.3,
    0.2, 0.3, 0.5
  ), nrow = 3, byrow = TRUE)
  colnames(trans_mat) <- rownames(trans_mat) <- c("X", "Y", "Z")
  tna_obj <- tna::tna(trans_mat)

  with_temp_png({
    plot_mtna(tna_obj,
              cluster_list = list(top = c("X"), left = c("Y"), right = c("Z")),
              node_size = 15)
  })
})

# Test 7: R/plot-htna-multi.R lines 466-467 - zero-length edge offset
test_that("plot_mtna handles self-loops (zero-length edges)", {
  skip_if_not_installed("tna")
  trans_mat <- matrix(c(
    0.5, 0.3, 0.2,
    0.2, 0.6, 0.2,
    0.3, 0.1, 0.6
  ), nrow = 3, byrow = TRUE)
  colnames(trans_mat) <- rownames(trans_mat) <- c("A", "B", "C")
  tna_obj <- tna::tna(trans_mat)

  with_temp_png({
    plot_mtna(tna_obj,
              cluster_list = list(g1 = c("A", "B"), g2 = c("C")))
  })
})

# Test 8: R/plot-htna-multi.R line 598 - max_within == 0 fallback width
test_that("plot_mtna with groups having zero within-group weights", {
  skip_if_not_installed("tna")
  # Matrix where within-group transitions are 0
  trans_mat <- matrix(c(
    0, 0, 0.5, 0.5,
    0, 0, 0.5, 0.5,
    0.5, 0.5, 0, 0,
    0.5, 0.5, 0, 0
  ), nrow = 4, byrow = TRUE)
  colnames(trans_mat) <- rownames(trans_mat) <- c("A", "B", "C", "D")
  tna_obj <- tna::tna(trans_mat)

  with_temp_png({
    plot_mtna(tna_obj,
              cluster_list = list(g1 = c("A", "B"), g2 = c("C", "D")))
  })
})

# Test 9: R/from-qgraph.R lines 21, 27, 33, 39 - RColorBrewer/colorspace fallbacks
# These lines have fallback logic when RColorBrewer/colorspace are not available
# Test by calling the color palette function which uses these fallbacks
test_that("tna_color_palette works with different state counts", {
  skip_if_not_installed("tna")

  # Test different state counts to exercise all switch branches
  # This will hit the appropriate fallback lines if packages aren't available
  colors_2 <- cograph:::tna_color_palette(2)
  expect_length(colors_2, 2)
  expect_true(is.character(colors_2))

  colors_8 <- cograph:::tna_color_palette(8)
  expect_length(colors_8, 8)

  colors_12 <- cograph:::tna_color_palette(12)
  expect_length(colors_12, 12)

  colors_15 <- cograph:::tna_color_palette(15)
  expect_length(colors_15, 15)
})

test_that("tna_color_palette returns valid colors", {
  skip_if_not_installed("tna")

  # Test that colors are valid regardless of which branch is taken
  colors <- cograph:::tna_color_palette(5)
  expect_length(colors, 5)

  # Verify all colors are valid
  for (col in colors) {
    expect_no_error(grDevices::col2rgb(col))
  }
})

# Test 10: R/input-statnet.R line 39 - fallback labels
# This tests the path where network.vertex.names returns NULL or all NA
# The network package typically returns defaults, but our code has a fallback
test_that("parse_statnet handles basic network correctly", {
  skip_if_not_installed("network")

  # Create a basic network - this will exercise the parse_statnet function
  net <- network::network.initialize(3, directed = FALSE)
  network::add.edges(net, tail = c(1, 2), head = c(2, 3))

  result <- cograph:::parse_statnet(net)
  expect_equal(nrow(result$nodes), 3)
  expect_true(all(as.character(result$nodes$label) %in% c("1", "2", "3")))
  expect_true(is.data.frame(result$nodes))
  expect_true(is.data.frame(result$edges))
})

test_that("parse_statnet handles networks with custom vertex names", {
  skip_if_not_installed("network")

  # Create network with custom names
  net <- network::network.initialize(3, directed = FALSE)
  network::add.edges(net, tail = c(1, 2), head = c(2, 3))
  network::set.vertex.attribute(net, "vertex.names", c("A", "B", "C"))

  result <- cograph:::parse_statnet(net)
  expect_equal(as.character(result$nodes$label), c("A", "B", "C"))
})