Index: src/hg/inc/genoLay.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/inc/genoLay.h,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/hg/inc/genoLay.h	20 Feb 2008 00:42:30 -0000	1.4
+++ src/hg/inc/genoLay.h	6 Apr 2009 05:41:20 -0000	1.5
@@ -1,91 +1,95 @@
 /* genoLay - genome layout. Arranges chromosomes so that they
  * tend to fit together nicely on a single page. */
 
 #ifndef GENOLAY_H
 #define GENOLAY_H
 
 #ifndef HVGFX_H
 #include "hvGfx.h"
 #endif
 
 struct genoLayChrom
 /* Information on a chromosome. */
      {
      struct genoLayChrom *next;
      char *fullName;	/* Name of full deal. Set before genoLayNew. */
      char *shortName;	/* Name w/out chr prefix. Set before genoLayNew. */
      int size;		/* Size in bases. Set before genoLayNew. */
      int x,y;		/* Upper left corner pixel coordinates*/
      int width,height; 	/* Pixel width and height */
      };
 
 #define genoLayTwoPerLine "two per line"
 #define genoLayOnePerLine "one per line"
 #define genoLayAllOneLine "all in one line"
 /* The "how" parameter to genoLayNew should be one of these 
  * above three. */
 
 struct genoLay
 /* This has information on how to lay out chromosomes. */
     {
     MgFont *font;			/* Font used for labels */
     struct genoLayChrom *chromList;	/* List of all chromosomes. */
     struct hash *chromHash;		/* Hash of chromosomes. */
     int picWidth;			/* Total picture width */
     int picHeight;			/* Total picture height */
     int margin;				/* Blank area around sides */
     int spaceWidth;			/* Width of a space. */
     struct slRef *leftList;		/* Left chromosomes. */
     struct slRef *rightList;		/* Right chromosomes. */
     struct slRef *bottomList;		/* Sex chromosomes are on bottom. */
     int lineCount;			/* Number of chromosome lines. */
     int leftLabelWidth, rightLabelWidth;/* Pixels for left/right labels */
     int lineHeight;			/* Height for one line */
     int betweenChromHeight;		/* Height between chromosomes. */
     int betweenChromOffsetY;		/* Start of area between chroms. */
     int chromHeight;			/* Height of chromosome ideograms. */
     int chromOffsetY;			/* Start of chromosome ideograms. */
     int totalHeight;			/* Total width/height in pixels */
     double basesPerPixel;		/* Bases per pixel */
     double pixelsPerBase;		/* Pixels per base. */
     char *how;				/* How parameter from genoLayNew. */
     boolean allOneLine;			/* True if draw all on one line. */
     };
 
 void genoLayDump(struct genoLay *gl);
 /* Print out info on genoLay */
 
 int genoLayChromCmpName(const void *va, const void *vb);
 /* Compare two chromosome names so as to sort numerical part
  * by number.. */
 
+struct genoLayChrom *genoLayDbChromsExt(struct sqlConnection *conn, 
+	boolean withRandom, boolean abortOnErr);
+/* Get chrom info list. */
+
 struct genoLayChrom *genoLayDbChroms(struct sqlConnection *conn, 
 	boolean withRandom);
 /* Get chrom info list. */
 
 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.  The how
  * parameter should be one of the string constants defined above. */
 
 void genoLayDrawChromLabels(struct genoLay *gl, struct hvGfx *hvg, int color);
 /* Draw chromosomes labels in image */
 
 void genoLayDrawSimpleChroms(struct genoLay *gl,
 	struct hvGfx *hvg, int color);
 /* Draw boxes for all chromosomes in given 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 */
 /* Draw boxes for all chromosomes in given color */
 
 #endif /* GENOLAY_H */
 

