a9fbf5bc0936d461782bcb052e288f35cd2770d0
greg
  Thu Feb 2 13:31:07 2012 -0800
Added data format info to the form labels and got rid of the ata formats box since it was redunant.
diff --git src/hg/hgLiftOver/hgLiftOver.c src/hg/hgLiftOver/hgLiftOver.c
index a77c1b7..f2be956 100644
--- src/hg/hgLiftOver/hgLiftOver.c
+++ src/hg/hgLiftOver/hgLiftOver.c
@@ -176,31 +176,31 @@
 cgiSimpleTableFieldStart();
 cgiMakeDoubleVar(HGLFT_MINBLOCKS,(keepSettings) ? minBlocks : chain->minBlocks,6);
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("If thickStart/thickEnd is not mapped, use the closest mapped base:");
 cgiSimpleTableFieldStart();
 cgiMakeCheckBox(HGLFT_FUDGETHICK,(keepSettings) ? fudgeThick : (chain->fudgeThick[0]=='Y'));
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiTableEnd();
 
 /* text box and two buttons (submit, reset) */
-cgiParagraph(" Paste in data:\n");
+cgiParagraph("&nbsp;Paste in data (<a href=\"http://hgwdev.cse.ucsc.edu/FAQ/FAQformat.html#format1\" target=\"_blank\">BED</a> or chrN:start-end formats):\n");
 cgiSimpleTableStart();
 cgiSimpleTableRowStart();
 
 cgiSimpleTableFieldStart();
 cgiMakeTextArea(HGLFT_USERDATA_VAR, cartCgiUsualString(cart, HGLFT_USERDATA_VAR, NULL), 10, 80);
 cgiTableFieldEnd();
 
 /* right element of table is a nested table
  * with two buttons stacked on top of each other */
 cgiSimpleTableFieldStart();
 cgiSimpleTableStart();
 
 cgiSimpleTableRowStart();
 cgiSimpleTableFieldStart();
 cgiMakeSubmitButton();
@@ -208,31 +208,31 @@
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiSimpleTableFieldStart();
 cgiMakeClearButton("mainForm", HGLFT_USERDATA_VAR);
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiTableEnd();
 cgiTableFieldEnd();
 
 cgiTableRowEnd();
 cgiTableEnd();
 
 /* next  row -- file upload controls */
-cgiParagraph("&nbsp;Or upload data from a file:");
+cgiParagraph("&nbsp;Or upload data from a file (<a href=\"http://hgwdev.cse.ucsc.edu/FAQ/FAQformat.html#format1\" target=\"_blank\">BED</a> or chrN:start-end in plain text format):");
 cgiSimpleTableStart();
 cgiSimpleTableRowStart();
 printf("<TD><INPUT TYPE=FILE NAME=\"%s\"></TD>\n", HGLFT_DATAFILE_VAR);
 puts("<TD><INPUT TYPE=SUBMIT NAME=SubmitFile VALUE=\"Submit File\"></TD>\n");
 cgiTableRowEnd();
 cgiTableEnd();
 printf("<input type=\"hidden\" name=\"%s\" value=\"0\">\n",
                         HGLFT_REFRESHONLY_VAR);
 printf("<input type=\"hidden\" name=\"%s\" value=\"%s\">\n", HGLFT_LAST_CHAIN, chainString);
 puts("</FORM>\n");
 
 cartSaveSession(cart);
 puts("</FORM>");
 freeMem(fromOrg);
 freeMem(toOrg);
@@ -292,46 +292,30 @@
 cgiSimpleTableFieldStart();
 printf("%.2f",minBlocks);
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("If thickStart/thickEnd is not mapped, use the closest mapped base:");
 cgiSimpleTableFieldStart();
 printf("%s", fudgeThick ? "on" : "off");
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiTableEnd();
 }
 
-void webDataFormats()
-{
-webNewSection("Data Formats");
-puts("<ul>");
-puts("<LI>");
-puts(
-    "<A HREF=\"../FAQ/FAQformat.html#format1\" TARGET=_blank>"
-    "Browser Extensible Data (BED)</A>\n");
-puts("</LI>");
-puts("<LI>");
-puts("Genomic Coordinate Position<BR>");
-puts("&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; chrN<B>:</B>start<B>-</B>end");
-puts("</LI>");
-puts("</ul>");
-}
-
 void webDownloads()
 {
 webNewSection("Command Line Tool");
 cgiParagraph(
 "To lift genome annotations locally on Linux systems, download the "
 "<A HREF=\"http://hgdownload.cse.ucsc.edu/admin/exe/\">" 
 "<I>liftOver</I></A> executable and the appropriate "
 "<A HREF=\"http://hgdownload.cse.ucsc.edu/downloads.html#liftover\">"
 "chain file</A>."
 " Run <I>liftOver</I> with no arguments to see the usage message.\n");
 }
 
 
 double scoreLiftOverChain(struct liftOverChain *chain,
     char *fromOrg, char *fromDb, char *toOrg, char *toDb,
@@ -551,31 +535,30 @@
         struct lineFile *errFile = lineFileOpen(unmappedTn.forCgi, TRUE);
         puts("<BLOCKQUOTE><PRE>\n");
         while (lineFileNext(errFile, &line, &lineSize))
             puts(line);
         lineFileClose(&errFile);
         puts("</PRE></BLOCKQUOTE>\n");
         }
     puts("<BLOCKQUOTE><PRE>\n");
     puts("Note: &quot;multiple&quot; option is not supported for position format.");
     puts("</PRE></BLOCKQUOTE>\n");
 
     webParamsUsed(minMatch, multiple, minSizeQ, minChainT, minBlocks, fudgeThick);
 
     carefulClose(&unmapped);
     }
-webDataFormats();
 webDownloads();
 cartWebEnd();
 }
 
 /* Null terminated list of CGI Variables we don't want to save
  * permanently. */
 char *excludeVars[] = {"Submit", "submit", "SubmitFile",
                         HGLFT_USERDATA_VAR,
                         HGLFT_DATAFILE_VAR,
                         HGLFT_ERRORHELP_VAR,
                         NULL};
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {