e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/lib/hCytoBand.c src/hg/lib/hCytoBand.c
index cdb36d61..8084815 100644
--- src/hg/lib/hCytoBand.c
+++ src/hg/lib/hCytoBand.c
@@ -1,167 +1,170 @@
 /* hCytoBand - stuff to help draw chromosomes where we have
  * banding data. */
 
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "hvGfx.h"
 #include "hCommon.h"
 #include "hgColors.h"
 #include "cytoBand.h"
 #include "hCytoBand.h"
 
 
 static char *abbreviatedBandName(struct cytoBand *band, 
 	MgFont *font, int width, boolean isDmel)
 /* Return a string abbreviated enough to fit into space. */
 {
 int textWidth;
 static char string[32];
 
 /* If have enough space, return original chromosome/band. */
 sprintf(string, "%s%s", (isDmel ? "" : skipChr(band->chrom)), band->name);
 textWidth = mgFontStringWidth(font, string);
 if (textWidth <= width)
     return string;
 
 /* Try leaving off chromosome  */
 sprintf(string, "%s", band->name);
 textWidth = mgFontStringWidth(font, string);
 if (textWidth <= width)
     return string;
 
 /* Try leaving off initial letter */
 sprintf(string, "%s", band->name+1);
 textWidth = mgFontStringWidth(font, string);
 if (textWidth <= width)
     return string;
 
 return NULL;
 }
 
 static Color cytoBandColorGiemsa(struct cytoBand *band, 
 	struct hvGfx *hvg, Color aColor, Color bColor,
 	Color *shades, int maxShade)
 /* Figure out color of band based on gieStain field. */
 {
 char *stain = band->gieStain;
 if (startsWith("gneg", stain))
     {
     return shades[1];
     }
 else if (startsWith("gpos", stain))
     {
     int percentage = 100;
     stain += 4;	
     if (isdigit(stain[0]))
         percentage = atoi(stain);
     return shades[hGrayInRange(percentage, -30, 100, maxShade)];
     }
 else if (startsWith("gvar", stain))
     {
     return shades[maxShade];
     }
 else 
     {
     return bColor;
     }
 }
 
 static Color cytoBandColorDmel(struct cytoBand *band, 
 	struct hvGfx *hvg, Color aColor, Color bColor,
 	Color *shades, int maxShade)
 /* Figure out color of band based on D. melanogaster band name: just toggle 
  * color based on subband letter before the number at end of name (number 
  * at end of name gives too much resolution!).  There must be a better way 
  * but the only online refs I've been able to get for these bands are books 
  * and too-old-for-online journal articles... */
 {
 char *lastAlpha = band->name + strlen(band->name) - 1;
 int parity = 0;
 while (isdigit(*lastAlpha) && lastAlpha > band->name)
     lastAlpha--;
 parity = ((*lastAlpha) - 'A') & 0x1;
 if (parity)
     return aColor;
 else 
     return bColor;
 }
 
 Color hCytoBandColor(struct cytoBand *band, struct hvGfx *hvg, boolean isDmel,
 	Color aColor, Color bColor, Color *shades, int maxShade)
 /* Return appropriate color for band. */
 {
 if (isDmel)
      return cytoBandColorDmel(band, hvg, aColor, bColor, shades, maxShade);
 else
      return cytoBandColorGiemsa(band, hvg, aColor, bColor, shades, maxShade);
 }
 
 char *hCytoBandName(struct cytoBand *band, boolean isDmel)
 /* Return name of band.  Returns a static buffer, so don't free result. */
 {
 static char buf[32];
 sprintf(buf, "%s%s", (isDmel ? "" : skipChr(band->chrom)), band->name);
 return buf;
 }
 
 void hCytoBandDrawAt(struct cytoBand *band, struct hvGfx *hvg,
 	int x, int y, int width, int height, boolean isDmel,
 	MgFont *font, int fontPixelHeight, Color aColor, Color bColor,
 	Color *shades, int maxShade)
 /* Draw a single band in appropriate color at given position.  If there's
  * room put in band label. */
 {
 Color col = hCytoBandColor(band, hvg, isDmel, aColor, bColor, shades, maxShade);
 hvGfxBox(hvg, x, y, width, height, col);
 if (height >= mgFontLineHeight(font))
     {
     char *s = abbreviatedBandName(band, font, width, isDmel);
     if (s != NULL)
 	{
 	Color textCol = hvGfxContrastingColor(hvg, col);
 	hvGfxTextCentered(hvg, x, y, width, height, textCol, font, s);
 	}
     }
 }
 
 Color hCytoBandCentromereColor(struct hvGfx *hvg)
 /* Get the color used traditionally to draw centromere */
 {
 return hvGfxFindColorIx(hvg, 150, 50, 50);
 }
 
 void hCytoBandDrawCentromere(struct hvGfx *hvg, int x, int y, 
 	int width, int height, Color bgColor, Color fgColor)
 /* Draw the centromere. */
 {
 struct gfxPoly *poly;
 int xCen = x+width/2, yCen = y+height/2;
 int xEnd = x+width-1, yEnd = y+height-1;
 
 /* Draw box over centromere, may be drawn already with lettering
  * which we don't want. */
 
 hvGfxBox(hvg, x, y, width, height, bgColor);
 
 char *savedHint = hvGfxGetHint(hvg,"fat");
 hvGfxSetHint(hvg,"fat","on");
 
 /* Make up triangle on left of centromere and draw. */
 poly = gfxPolyNew();
 gfxPolyAddPoint(poly, x, y);
 gfxPolyAddPoint(poly, xCen, yCen);
 gfxPolyAddPoint(poly, x, yEnd);
 hvGfxDrawPoly(hvg, poly, fgColor, TRUE);
 gfxPolyFree(&poly);
 
 /* Make up triangle on right of centromere and draw. */
 poly = gfxPolyNew();
 gfxPolyAddPoint(poly, xEnd, y);
 gfxPolyAddPoint(poly, xCen, yCen);
 gfxPolyAddPoint(poly, xEnd, yEnd);
 hvGfxDrawPoly(hvg, poly, fgColor, TRUE);
 gfxPolyFree(&poly);
 
 hvGfxSetHint(hvg,"fat",savedHint);
 }