handle alpha colors in CLI heatmaps

Both TwoColorHeatMap and ThreeColorHeatMap CLI should also handle alpha channel color values so that CLI mimics GUI functionality (#66).

Both CLI contain lines that validate alpha value as numeric 0 to 255 and update the color's alpha channel. Their flags are related to the letter "t" for transparency.

Also contains bug fix in ThreeColorHM such that more than one color can be specified in a single call (before there was a restriction imposed for one color being changed at a time).

TwoColorHM was also adjusted to avoid redundancy. The check for custom color being selected occurred more than once so the hexcode decoding block was moved.

Author: owlang

src/cli/Figure_Generation/ThreeColorHeatMapCLI.java

@@ -76,7 +76,7 @@ static class MaxGroup {
 	@Option(names = {"-0", "--include-zeros"}, description = "used with `-p` flag, indicating exclusion of zero values when calculating percentile thresholds")
 	private boolean includeZeros = false;
 
-	@ArgGroup(multiplicity = "0..1", heading = "%nSelect heatmap colors:%n")
+	@ArgGroup(multiplicity = "0..1", exclusive=false, heading = "%nSelect heatmap colors:%n")
 	private ColorGroup color = new ColorGroup();
 	static class ColorGroup {
 		@Option(names = {"-cn", "--color-min"}, description = "Color indicating minimum values (default=YELLOW) For custom color: type hexadecimal string to represent colors (e.g. \"FF0000\" is hexadecimal for red).\n See <http://www.javascripter.net/faq/rgbtohex.htm> for some color options with their corresponding hex strings.\n")
@@ -88,7 +88,20 @@ static class ColorGroup {
 		@Option(names = {"-ca", "--color-nan"}, description = "Color indicating not-a-number values (default=GRAY) For custom color: type hexadecimal string to represent colors (e.g. \"FF0000\" is hexadecimal for red).\n See <http://www.javascripter.net/faq/rgbtohex.htm> for some color options with their corresponding hex strings.\n")
 		private String nan = null;
 	}
-
+	
+	@ArgGroup(multiplicity = "0..1", exclusive=false, heading = "%nSelect transparency of heatmap colors (alpha channel):%n")
+	private AlphaGroup alpha = new AlphaGroup();
+	static class AlphaGroup {
+		@Option(names = {"-tn", "--transparent-min"}, description = "Value indicating transparency of minimum values, 0 to 255 (default=255)\n")
+		private int min = 255;
+		@Option(names = {"-td", "--transparent-mid"}, description = "Value indicating transparency of middle values, 0 to 255  (default=255)\n")
+		private int mid = 255;
+		@Option(names = {"-tx", "--transparent-max"}, description = "Value indicating transparency of maximum values, 0 to 255  (default=255)\n")
+		private int max = 255;
+		@Option(names = {"-ta", "--transparent-nan"}, description = "Value indicating transparency of not-a-number values, 0 to 255  (default=255)\n")
+		private int nan = 255;
+	}
+	
 	String scaleType = "treeview";
 	//Colors from JavaTreeview microarray software
 	Color CMAX = new Color(254,255,0,255);
@@ -217,6 +230,16 @@ private String validateInput() throws IOException {
 			System.err.println("Decoding NaN color: 0x" + color.nan);
 			CNAN = Color.decode("0x" + color.nan);
 		}
+		// check that Alpha channel/transparency values are formatted properly and decode/assign colors
+		if (alpha.max<0 || alpha.max>255) { r += "(!)Alpha/transparency value for higher values (max) must be a numeric 0 to 255\n"; }
+		else { CMAX = new Color(CMAX.getRed(), CMAX.getGreen(), CMAX.getBlue(), alpha.max); }
+		if (alpha.mid<0 || alpha.mid>255) { r += "(!)Alpha/transparency value for middling values (mid) must be a numeric 0 to 255\n"; }
+		else { CMID = new Color(CMID.getRed(), CMID.getGreen(), CMID.getBlue(), alpha.mid); }
+		if (alpha.min<0 || alpha.min>255) { r += "(!)Alpha/transparency value for lower values(min) must be a numeric 0 to 255\n"; }
+		else { CMIN = new Color(CMIN.getRed(), CMIN.getGreen(), CMIN.getBlue(), alpha.min); }
+		if (alpha.nan<0 || alpha.nan>255) { r += "(!)Alpha/transparency value for invalid/non-numeric values(NaN) must be a numeric 0 to 255\n"; }
+		else { CNAN = new Color(CNAN.getRed(), CNAN.getGreen(), CNAN.getBlue(), alpha.nan); }
+		
 		// assign vals for contrast thresholds and set bools
 		if(maxGroup.percentile!=null) {
 			MAX = maxGroup.percentile;

src/cli/Figure_Generation/TwoColorHeatMapCLI.java

@@ -56,7 +56,6 @@ public class TwoColorHeatMapCLI implements Callable<Integer> {
 
 	@ArgGroup(exclusive = true, multiplicity = "0..1", heading = "%nSelect heatmap color:%n\t@|fg(red) (select no more than one of these options)|@%n")
 	private ColorGroup color = new ColorGroup();
-
 	static class ColorGroup {
 		@Option(names = { "--black" }, description = "Use the color black for generating the heatmap (default)")
 		private boolean black = false;
@@ -68,6 +67,9 @@ static class ColorGroup {
 				"--color" }, description = "For custom color: type hexadecimal string to represent colors (e.g. \"FF0000\" is hexadecimal for red).\n See <http://www.javascripter.net/faq/rgbtohex.htm> for some color options with their corresponding hex strings.\n")
 		private String custom = null;
 	}
+	@Option(names = { "-t",
+				"--transparent" }, description = "Value indicating transparency of heatmap, 0 to 255  (default=255)\\n")
+	private int alpha = 255;
 
 	String scaleType = "treeview";
 	Color MAXCOLOR = Color.BLACK;
@@ -140,14 +142,7 @@ private String validateInput() throws IOException {
 		if (compression < 1 || compression > 4) {
 			r += "(!)Compression must be integer 1-4. Please select from the available compression types.";
 		}
-		// check that hex string is formatted properly
-		if (color.custom != null) {
-			Pattern hexColorPat = Pattern.compile("[0-9A-Fa-f]{6}");
-			Matcher m = hexColorPat.matcher(color.custom);
-			if (!m.matches()) {
-				r += "(!)Color must be formatted as a hexidecimal String!\n\tExpected input string format: \"[0-9A-Fa-f]{6}\"";
-			}
-		}
+
 		// check scaling is valid input
 		if (absolute == -999 && percentile == -999) {
 			absolute = 10;
@@ -169,8 +164,16 @@ private String validateInput() throws IOException {
 			MAXCOLOR = Color.BLUE;
 		} else if (color.custom != null) {
 			System.err.println("Decoding color: 0x" + color.custom);
-			MAXCOLOR = Color.decode("0x" + color.custom);
+			// check that hex string is formatted properly
+			Pattern hexColorPat = Pattern.compile("[0-9A-Fa-f]{6}");
+			Matcher m = hexColorPat.matcher(color.custom);
+			if (!m.matches()) {
+				r += "(!)Color must be formatted as a hexidecimal String!\n\tExpected input string format: \"[0-9A-Fa-f]{6}\"";
+			} else { MAXCOLOR = Color.decode("0x" + color.custom); }
 		}
+		// check that Alpha channel/transparency values are formatted properly and decode/assign colors
+		if (alpha<0 || alpha>255) { r += "(!)Alpha/transparency value for higher values (max) must be a numeric 0 to 255\n"; }
+		else { MAXCOLOR = new Color(MAXCOLOR.getRed(), MAXCOLOR.getGreen(), MAXCOLOR.getBlue(), alpha); }
 
 		return (r);
 	}