533112afe2a2005e80cdb1f82904ea65032d4302
braney
  Sat Oct 2 11:37:34 2021 -0700
split hg/lib into two separate libaries, one only used by the cgis

diff --git src/hg/lib/genoLay.c src/hg/lib/genoLay.c
deleted file mode 100644
index 417d7b4..0000000
--- src/hg/lib/genoLay.c
+++ /dev/null
@@ -1,564 +0,0 @@
-/* genoLay - genome layout. Arranges chromosomes so that they
- * tend to fit together nicely on a single page. */
-
-/* Copyright (C) 2014 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
-
-#include "common.h"
-#include "hash.h"
-#include "jksql.h"
-#include "vGfx.h"
-#include "cytoBand.h"
-#include "hCytoBand.h"
-#include "genoLay.h"
-
-
-void genoLayDump(struct genoLay *gl)
-/* Print out info on genoLay */
-{
-struct genoLayChrom *chrom;
-struct slRef *left, *right, *ref;
-int total;
-printf("gl: lineCount %d, leftLabelWidth %d, rightLabelWidth %d, basesPerPixel %f<BR>\n",
-	gl->lineCount, gl->leftLabelWidth, gl->rightLabelWidth, gl->basesPerPixel);
-for (left = gl->leftList, right = gl->rightList; left != NULL || right != NULL;)
-    {
-    total=0;
-    if (left != NULL)
-	{
-	chrom = left->val;
-	printf("%s@%d,%d[%d] %d ----  ", chrom->fullName, chrom->x, chrom->y, chrom->width, chrom->size);
-	total += chrom->size;
-        left = left->next;
-	}
-    if (right != NULL)
-	{
-	chrom = right->val;
-	printf("%d  %s@%d,%d[%d]", chrom->size, chrom->fullName, chrom->x, chrom->y, chrom->width);
-	total += chrom->size;
-        right = right->next;
-	}
-    printf(" : %d<BR>", total);
-    }
-total=0;
-for (ref = gl->bottomList; ref != NULL; ref = ref->next)
-    {
-    chrom = ref->val;
-    total += chrom->size;
-    printf("%s@%d,%d[%d] %d ...  ", chrom->fullName, chrom->x, chrom->y, chrom->width, chrom->size);
-    }
-printf(" : %d<BR>", total);
-}
-
-int genoLayChromCmpName(const void *va, const void *vb)
-/* Compare two chromosome names so as to sort numerical part
- * by number.. */
-{
-const struct genoLayChrom *a = *((struct genoLayChrom **)va);
-const struct genoLayChrom *b = *((struct genoLayChrom **)vb);
-char *aName = a->shortName, *bName = b->shortName;
-if (isdigit(aName[0]))
-    {
-    if (isdigit(bName[0]))
-	{
-	int diff = atoi(aName) - atoi(bName);
-	if (diff == 0)
-	    diff = strcmp(skipNumeric(aName), skipNumeric(bName));
-	return diff;
-	}
-    else
-        return -1;
-    }
-else if (isdigit(bName[0]))
-    return 1;
-else
-    return strcmp(aName, bName);
-}
-
-struct genoLayChrom *genoLayDbChromsExt(struct sqlConnection *conn, 
-	boolean withRandom, boolean abortOnErr)
-/* Get chrom info list. */
-{
-struct sqlResult *sr;
-char **row;
-struct genoLayChrom *chrom, *chromList = NULL;
-sr = sqlGetResult(conn, NOSQLINJ "select chrom,size from chromInfo");
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    char *name = row[0];
-    if (withRandom || 
-        (
-        (startsWith("chr", name))
-     && (!startsWith("chrUn", name))
-     && (!sameString("chrM", name))
-     && (!strchr(name, '_'))   // avoiding _random and _hap*
-	)
-       )
-	{
-	AllocVar(chrom);
-	chrom->fullName = cloneString(name);
-	chrom->shortName = chrom->fullName+3;
-	chrom->size = sqlUnsigned(row[1]);
-	slAddHead(&chromList, chrom);
-	}
-    }
-if (chromList == NULL)
-    {
-    if (abortOnErr)
-    	errAbort("No chromosomes found in chromInfo.");
-    return NULL;
-    }
-int count = slCount(chromList);
-if (count > 500)
-    {
-    if (abortOnErr)
-	errAbort("Sorry, cannot do genome layout on an assembly "
-    	    "with too many (%d) chromosomes exceeds 500. "
-    	    "Please select another organism or assembly.", count);
-    }
-slReverse(&chromList);
-slSort(&chromList, genoLayChromCmpName);
-return chromList;
-}
-
-struct genoLayChrom *genoLayDbChroms(struct sqlConnection *conn, 
-	boolean withRandom)
-/* Get chrom info list. */
-{
-return genoLayDbChromsExt(conn, withRandom, TRUE);
-}
-
-
-static void separateSexChroms(struct slRef *in,
-	struct slRef **retAutoList, struct slRef **retSexList)
-/* Separate input chromosome list into sex and non-sex chromosomes. */
-{
-struct slRef *autoList = NULL, *sexList = NULL, *ref, *next;
-
-for (ref = in; ref != NULL; ref = next)
-    {
-    struct genoLayChrom *chrom = ref->val;
-    char *name = chrom->shortName;
-    next = ref->next;
-    if (sameWord(name, "X") || sameWord(name, "Y") || sameWord(name, "Z")
-    	|| sameWord(name, "W"))
-	{
-	slAddHead(&sexList, ref);
-	}
-    else
-        {
-	slAddHead(&autoList, ref);
-	}
-    }
-slReverse(&sexList);
-slReverse(&autoList);
-*retAutoList = autoList;
-*retSexList = sexList;
-}
-
-struct genoLay *genoLayNew(struct genoLayChrom *chromList,
-	MgFont *font, int picWidth, int betweenChromHeight,
-	int minLeftLabelWidth, int minRightLabelWidth,
-	char *how)
-/* Figure out layout.  For human and most mammals this will be
- * two columns with sex chromosomes on bottom.  This is complicated
- * by the platypus having a bunch of sex chromosomes. */
-{
-int margin = 3;
-struct slRef *refList = NULL, *ref, *left, *right;
-struct genoLayChrom *chrom;
-struct genoLay *gl;
-int autoCount, halfCount, bases;
-int leftLabelWidth=0, rightLabelWidth=0, labelWidth;
-int spaceWidth = mgFontCharWidth(font, ' ');
-int extraLabelPadding = 0;
-int autosomeOtherPixels=0, sexOtherPixels=0;
-int autosomeBasesInLine=0;	/* Maximum bases in a line for autosome. */
-int sexBasesInLine=0;		/* Bases in line for sex chromsome. */
-double sexBasesPerPixel, autosomeBasesPerPixel, basesPerPixel;
-int pos = margin;
-int y = 0;
-int fontHeight = mgFontLineHeight(font);
-int chromHeight = fontHeight;
-int lineHeight = chromHeight + betweenChromHeight;
-boolean allOneLine = FALSE;
-
-refList = refListFromSlList(chromList);
-
-/* Allocate genoLay object and fill in simple fields. */
-AllocVar(gl);
-gl->chromList = chromList;
-gl->chromHash = hashNew(0);
-gl->font = font;
-gl->picWidth = picWidth;
-gl->margin = margin;
-gl->spaceWidth = spaceWidth;
-gl->lineHeight = lineHeight;
-gl->betweenChromHeight = betweenChromHeight;
-gl->betweenChromOffsetY = 0;
-gl->chromHeight = chromHeight;
-gl->chromOffsetY = lineHeight - chromHeight;
-
-
-/* Save chromosomes in hash too, for easy access */
-for (chrom = chromList; chrom != NULL; chrom = chrom->next)
-    hashAdd(gl->chromHash, chrom->fullName, chrom);
-
-if (sameString(how, genoLayOnePerLine))
-    {
-    gl->leftList = refList;
-    }
-else if (sameString(how, genoLayAllOneLine))
-    {
-    gl->bottomList = refList;
-    allOneLine = TRUE;
-    }
-else
-    {
-    /* Put sex chromosomes on bottom, and rest on left. */
-    separateSexChroms(refList, &refList, &gl->bottomList);
-    autoCount = slCount(refList);
-    gl->leftList = refList;
-
-    /* If there are a lot of chromosomes, then move later
-     * (and smaller) chromosomes to a new right column */
-    if (autoCount > 12)
-	{
-	halfCount = (autoCount+1)/2;
-	ref = slElementFromIx(refList, halfCount-1);
-	gl->rightList = ref->next;
-	ref->next = NULL;
-	slReverse(&gl->rightList);
-	}
-    }
-
-if (allOneLine)
-    {
-    unsigned long totalBases = 0, bStart=0, bEnd;
-    int chromCount = 0, chromIx=0;
-    for (ref = gl->bottomList; ref != NULL; ref = ref->next)
-        {
-	chrom = ref->val;
-	totalBases += chrom->size;
-	chromCount += 1;
-	}
-    int availablePixels = picWidth - minLeftLabelWidth - minRightLabelWidth
-       - 2*margin - (chromCount-1);
-    double basesPerPixel = (double)totalBases/availablePixels;
-    gl->picHeight = 2*margin + lineHeight + fontHeight;
-    for (ref = gl->bottomList; ref != NULL; ref = ref->next)
-        {
-	chrom = ref->val;
-	bEnd = bStart + chrom->size;
-	int pixStart = round(bStart / basesPerPixel);
-	int pixEnd = round(bEnd / basesPerPixel);
-	chrom->width = pixEnd - pixStart;
-	chrom->height = lineHeight;
-	chrom->x = pixStart + margin + chromIx + minLeftLabelWidth;
-	chrom->y = 0;
-	chromIx += 1;
-	bStart = bEnd;
-	}
-    gl->lineCount = 1;
-    gl->picHeight = 2*margin + lineHeight + fontHeight + 1;
-    gl->allOneLine = TRUE;
-    gl->leftLabelWidth = minLeftLabelWidth;
-    gl->rightLabelWidth = minRightLabelWidth;
-    gl->basesPerPixel = basesPerPixel;
-    gl->pixelsPerBase = 1.0/basesPerPixel;
-    }
-else
-    {
-    /* Figure out space needed for autosomes. */
-    left = gl->leftList;
-    right = gl->rightList;
-    while (left || right)
-	{
-	bases = 0;
-	if (left)
-	    {
-	    chrom = left->val;
-	    labelWidth = mgFontStringWidth(font, chrom->shortName) + spaceWidth;
-	    if (leftLabelWidth < labelWidth)
-		leftLabelWidth = labelWidth;
-	    bases = chrom->size;
-	    left = left->next;
-	    }
-	if (right)
-	    {
-	    chrom = right->val;
-	    labelWidth = mgFontStringWidth(font, chrom->shortName) + spaceWidth;
-	    if (rightLabelWidth < labelWidth)
-		rightLabelWidth = labelWidth;
-	    bases += chrom->size;
-	    right = right->next;
-	    }
-	if (autosomeBasesInLine < bases)
-	    autosomeBasesInLine = bases;
-	gl->lineCount += 1;
-	}
-
-    /* Figure out space needed for bottom chromosomes. */
-    if (gl->bottomList)
-	{
-	gl->lineCount += 1;
-	sexOtherPixels = spaceWidth + 2*margin;
-	for (ref = gl->bottomList; ref != NULL; ref = ref->next)
-	    {
-	    chrom = ref->val;
-	    sexBasesInLine += chrom->size;
-	    labelWidth = mgFontStringWidth(font, chrom->shortName) + spaceWidth;
-	    if (ref == gl->bottomList )
-		{
-		if (leftLabelWidth < labelWidth)
-		    leftLabelWidth  = labelWidth;
-		sexOtherPixels = leftLabelWidth;
-		}
-	    else if (ref->next == NULL)
-		{
-		if (rightLabelWidth < labelWidth)
-		    rightLabelWidth  = labelWidth;
-		sexOtherPixels += rightLabelWidth + spaceWidth;
-		}
-	    else
-		{
-		sexOtherPixels += labelWidth + spaceWidth;
-		}
-	    }
-	}
-
-    /* Do some adjustments if side labels are bigger than needed for
-     * chromosome names. */
-    if (leftLabelWidth < minLeftLabelWidth)
-	{
-	extraLabelPadding += (minLeftLabelWidth - leftLabelWidth);
-	leftLabelWidth = minLeftLabelWidth;
-	}
-    if (rightLabelWidth < minRightLabelWidth)
-	{
-	extraLabelPadding += (minRightLabelWidth - rightLabelWidth);
-	rightLabelWidth = minRightLabelWidth;
-	}
-    sexOtherPixels += extraLabelPadding;
-
-    /* Figure out the number of bases needed per pixel. */
-    autosomeOtherPixels = 2*margin + spaceWidth + leftLabelWidth + rightLabelWidth;
-    basesPerPixel = autosomeBasesPerPixel 
-	    = autosomeBasesInLine/(picWidth-autosomeOtherPixels);
-    if (gl->bottomList)
-	{
-	sexBasesPerPixel = sexBasesInLine/(picWidth-sexOtherPixels);
-	if (sexBasesPerPixel > basesPerPixel)
-	    basesPerPixel = sexBasesPerPixel;
-	}
-
-    /* Save positions and sizes of some things in layout structure. */
-    gl->leftLabelWidth = leftLabelWidth;
-    gl->rightLabelWidth = rightLabelWidth;
-    gl->basesPerPixel = basesPerPixel;
-    gl->pixelsPerBase = 1.0/basesPerPixel;
-
-    /* Set pixel positions for left autosomes */
-    for (ref = gl->leftList; ref != NULL; ref = ref->next)
-	{
-	chrom = ref->val;
-	chrom->x = leftLabelWidth + margin;
-	chrom->y = y;
-	chrom->width = round(chrom->size/basesPerPixel);
-	chrom->height = lineHeight;
-	y += lineHeight;
-	}
-
-    /* Set pixel positions for right autosomes */
-    y = 0;
-    for (ref = gl->rightList; ref != NULL; ref = ref->next)
-	{
-	chrom = ref->val;
-	chrom->width = round(chrom->size/basesPerPixel);
-	chrom->height = lineHeight;
-	chrom->x = picWidth - margin - rightLabelWidth - chrom->width;
-	chrom->y = y;
-	y += lineHeight;
-	}
-    gl->picHeight = 2*margin + lineHeight * gl->lineCount;
-    y = gl->picHeight - margin - lineHeight;
-
-    /* Set pixel positions for sex chromosomes */
-    for (ref = gl->bottomList; ref != NULL; ref = ref->next)
-	{
-	chrom = ref->val;
-	chrom->y = y;
-	chrom->width = round(chrom->size/basesPerPixel);
-	chrom->height = lineHeight;
-	if (ref == gl->bottomList)
-	    chrom->x = leftLabelWidth + margin;
-	else if (ref->next == NULL)
-	    chrom->x = picWidth - margin - rightLabelWidth - chrom->width;
-	else
-	    chrom->x = 2*spaceWidth+mgFontStringWidth(font,chrom->shortName) + pos;
-	pos = chrom->x + chrom->width;
-	}
-    }
-return gl;
-}
-
-static void leftLabel(struct hvGfx *hvg, struct genoLay *gl,
-	struct genoLayChrom *chrom, int yOffset, int fontHeight,
-	int color)
-/* Draw a chromosome with label on left. */
-{
-hvGfxTextRight(hvg, gl->margin, chrom->y + yOffset, 
-    chrom->x - gl->margin - gl->spaceWidth, fontHeight, color,
-    gl->font, chrom->shortName);
-}
-
-static void rightLabel(struct hvGfx *hvg, struct genoLay *gl,
-	struct genoLayChrom *chrom, int yOffset, int fontHeight, 
-	int color)
-/* Draw a chromosome with label on left. */
-{
-hvGfxText(hvg, chrom->x + chrom->width + gl->spaceWidth,
-	chrom->y + yOffset, 
-	color, gl->font, chrom->shortName);
-}
-
-static void midLabel(struct hvGfx *hvg, struct genoLay *gl,
-	struct genoLayChrom *chrom, int yOffset, int fontHeight, 
-	int color)
-/* Draw a chromosome with label on left. */
-{
-MgFont *font = gl->font;
-int textWidth = mgFontStringWidth(font, chrom->shortName);
-hvGfxTextRight(hvg, chrom->x - textWidth - gl->spaceWidth, 
-    chrom->y + yOffset, 
-    textWidth, fontHeight, color,
-    font, chrom->shortName);
-}
-
-void genoLayDrawChromLabels(struct genoLay *gl, struct hvGfx *hvg, int color)
-/* Draw chromosomes labels in image */
-{
-struct slRef *ref;
-struct genoLayChrom *chrom;
-int pixelHeight = mgFontPixelHeight(gl->font);
-if (gl->allOneLine)
-    {
-    int yOffset = gl->chromOffsetY + gl->chromHeight + 1;
-
-    for (ref = gl->bottomList; ref != NULL; ref = ref->next)
-	{
-	chrom = ref->val;
-	hvGfxTextCentered(hvg, chrom->x, yOffset, chrom->width, pixelHeight, color, gl->font,
-		chrom->shortName);
-	}
-    }
-else
-    {
-    int yOffset = gl->chromOffsetY + gl->chromHeight - pixelHeight;
-
-    /* Draw chromosome labels. */
-    for (ref = gl->leftList; ref != NULL; ref = ref->next)
-	leftLabel(hvg, gl, ref->val, yOffset, pixelHeight, color);
-    for (ref = gl->rightList; ref != NULL; ref = ref->next)
-	rightLabel(hvg, gl, ref->val, yOffset, pixelHeight, color);
-    for (ref = gl->bottomList; ref != NULL; ref = ref->next)
-	{
-	chrom = ref->val;
-	if (ref == gl->bottomList)
-	    leftLabel(hvg, gl, chrom, yOffset, pixelHeight, color);
-	else if (ref->next == NULL)
-	    rightLabel(hvg, gl, chrom, yOffset, pixelHeight, color);
-	else
-	    midLabel(hvg, gl, chrom, yOffset, pixelHeight, color);
-	}
-    }
-}
-
-void genoLayDrawSimpleChroms(struct genoLay *gl,
-	struct hvGfx *hvg, int color)
-/* Draw boxes for all chromosomes in given color */
-{
-int height = gl->chromHeight;
-int yOffset = gl->chromOffsetY;
-struct genoLayChrom *chrom;
-for (chrom = gl->chromList; chrom != NULL; chrom = chrom->next)
-    hvGfxBox(hvg, chrom->x, chrom->y + yOffset, 
-	chrom->width, height, color);
-
-}
-
-void genoLayDrawBandedChroms(struct genoLay *gl, struct hvGfx *hvg, char *db,
-	struct sqlConnection *conn, Color *shadesOfGray, int maxShade, 
-	int defaultColor)
-/* Draw chromosomes with centromere and band glyphs. 
- * Get the band data from the database.  If the data isn't
- * there then draw simple chroms in default color instead */
-{
-char *bandTable = "cytoBandIdeo";
-int yOffset = gl->chromOffsetY;
-genoLayDrawSimpleChroms(gl, hvg, defaultColor);
-if (sqlTableExists(conn, bandTable) && !gl->allOneLine)
-    {
-    int centromereColor = hCytoBandCentromereColor(hvg);
-    double pixelsPerBase = 1.0/gl->basesPerPixel;
-    int height = gl->chromHeight;
-    int innerHeight = gl->chromHeight-2;
-    struct genoLayChrom *chrom;
-    boolean isDmel = hCytoBandDbIsDmel(db);
-    boolean bColor = hvGfxFindColorIx(hvg, 200, 150, 150);
-    int fontPixelHeight = mgFontPixelHeight(gl->font);
-    for (chrom = gl->chromList; chrom != NULL; chrom = chrom->next)
-	{
-	struct sqlResult *sr;
-	char **row;
-	char query[256];
-	int cenX1=BIGNUM, cenX2=0;
-	int y = chrom->y + yOffset;
-
-	/* Fetch bands from database and draw them. */
-	sqlSafef(query, sizeof(query), "select * from %s where chrom='%s'",
-		bandTable, chrom->fullName);
-	sr = sqlGetResult(conn, query);
-	while ((row = sqlNextRow(sr)) != NULL)
-	    {
-	    struct cytoBand band;
-	    int x1, x2;
-	    cytoBandStaticLoad(row, &band);
-	    x1 = pixelsPerBase*band.chromStart;
-	    x2 = pixelsPerBase*band.chromEnd;
-	    if (sameString(band.gieStain, "acen"))
-		{
-		/* Centromere is represented as two adjacent bands.
-		 * We'll just record the extents of it here, and draw it
-		 * in one piece later. */
-		if (x1 < cenX1)
-		    cenX1 = x1;
-		if (x2 > cenX2)
-		    cenX2 = x2;
-		}
-	    else
-		{
-		/* Draw band */
-		hCytoBandDrawAt(&band, hvg, x1+chrom->x, y+1, x2-x1, innerHeight, 
-			isDmel, gl->font, fontPixelHeight, MG_BLACK, bColor,
-		    shadesOfGray, maxShade);
-		}
-	    }
-	sqlFreeResult(&sr);
-
-	/* Draw box around chromosome */
-	hvGfxBox(hvg, chrom->x, y, chrom->width, 1, MG_BLACK);
-	hvGfxBox(hvg, chrom->x, y+height-1, chrom->width, 1, MG_BLACK);
-	hvGfxBox(hvg, chrom->x, y, 1, height, MG_BLACK);
-	hvGfxBox(hvg, chrom->x+chrom->width-1, y, 1, height, MG_BLACK);
-
-	/* Draw centromere if we found one. */
-	if (cenX2 > cenX1)
-	    {
-	    hCytoBandDrawCentromere(hvg, cenX1+chrom->x, y, cenX2-cenX1, height,
-	       MG_WHITE, centromereColor);
-	    }
-	}
-    }
-}
-