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/hgGenome/usage.c src/hg/hgGenome/usage.c
index 758b5ef..14f2414 100644
--- src/hg/hgGenome/usage.c
+++ src/hg/hgGenome/usage.c
@@ -1,62 +1,65 @@
 /* usage - functions that display helpful usage info text go here. -jk)*/
 
+/* Copyright (C) 2011 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "hPrint.h"
 
 
 void printMainHelp()
 /* Put up main page help info. */
 {
 hPrintf("%s",
 
 "<P>Genome Graphs is a tool for displaying genome-wide data sets such\n"
 "as the results of genome-wide SNP association studies, linkage studies\n"
 "and homozygosity mapping. This section provides line-by-line descriptions\n"
 "of the controls on this page. For more detailed instructions, see the\n"
 "<A HREF=\"../goldenPath/help/hgGenomeHelp.html\" TARGET=\"_blank\">Genome\n"
 "Graphs User's Guide</A>.\n"
 "        <UL>\n"
 "        <LI><B>clade: </B>Specifies which clade the organism is in."
 "        </LI>\n"
 "        <LI><B>genome: </B>Specifies which organism data to use."
 "        </LI>\n"
 "        <LI><B>assembly: </B>Specifies which version of the organism's"
 "        genome sequence to use.\n"
 "        </LI>\n"
 "        <LI><B>graph ... in ...:</B> Selects which graph(s) to display in "
 "        which color."
 "        </LI>\n"
 "        <LI><B>upload: </B> Takes you to a page where you can upload your "
 "        own data.\n"
 "        </LI>\n"
 "        <LI><B>import: </B> Takes you to a page where you can import "
 "        database tables from this assembly.\n"
 "        </LI>\n"
 "        <LI><B>configure: </B> Takes you to a page where you can control "
 "        many aspects of the display including the overall size of the image, "
 "        how many graphs can be drawn, and the chromosome layout."
 "        </LI>\n"
 "        <LI><B>correlate: </B> If more than one graph is selected, takes you "
 "        to a page listing the Pearson's correlation coefficient for each "
 "        pair of graphs."
 "        </LI>\n"
 "        <LI><B>significance threshold: </B> Values above this threshold will "
 "        be considered significant. A light blue line will be drawn across "
 "        the graphs at the significance threshold of the first graph. Regions "
 "        above the threshold will be included in the region list you get with "
 "        the <EM>browse regions</EM> button."
 "        </LI>\n"
 "        <LI><B>browse regions: </B> Takes you to a page with a list of all "
 "        regions above the <EM>significance threshold</EM> on the left, and a "
 "        Genome Browser on the right.  Clicking on a region will move the "
 "        browser's window to that region."
 "        </LI>\n"
 "        <LI><B>sort genes: </B> Opens the Gene Sorter with a filter to "
 "        display only those genes in regions that are above the "
 "        <EM>significance threshold</EM>. If the graph was uploaded using"
 "        markers, then a custom Gene Sorter column with the same name as the "
 "        graph will be created.  This column will list all markers for each "
 "        gene that contain values above the significance threshold."
 "        </LI>\n"
 "        </UL>\n");
 }