void advFilterRemakeTextVar(struct column *col, char *varName, int size)
/* Make a text field of given name and size filling it in with
* the existing value if any. */
{
char *var = advFilterName(col, varName);
cartMakeTextVar(cart, var, NULL, size);
}
void userSettingsSaveForm(struct userSettings *us)
/* Put up controls that let user name and save the current
* set. */
{
char buf[1024];
struct hashEl *list = cartFindPrefix(us->cart, us->savePrefix);
safef(buf, sizeof(buf), "Save %s", us->formTitle);
makeTitle(buf, NULL);
/* Start form/save session/print title. */
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" NAME=\"usForm\" METHOD=GET>\n");
cartSaveSession(us->cart);
/* Put up controls that are always there. */
hPrintf("Please name this setup:\n");
cartMakeTextVar(us->cart, us->nameVar, "", 16);
hPrintf(" ");
cgiMakeButton(us->formVar, "save");
hPrintf(" ");
cgiMakeButton(us->formVar, "cancel");
/* Put up additional controls if have saved settings already. */
if (list != NULL)
{
struct dyString *js = newDyString(0);
htmlHorizontalLine();
slSort(&list, hashElCmp);
hPrintf("Existing Setups:");
dyStringPrintf(js, "document.usForm.%s.value=", us->nameVar);
dyStringPrintf(js, "document.usForm.%s.options", us->listDisplayVar);
dyStringPrintf(js, "[document.usForm.%s.selectedIndex].value;", us->listDisplayVar);
hPrintf("<SELECT NAME=\"%s\" SIZE=%d onchange=\"%s\">",
us->listDisplayVar, slCount(list), js->string);
printLabelList(us, list);
hPrintf("</SELECT>\n");
cgiMakeButton(us->formVar, "delete existing setup");
}
/* Cleanup. */
hPrintf("</FORM>\n");
slFreeList(&list);
}
static void showTableFilterControlRow(struct fieldedTable *table, struct cart *cart,
char *varPrefix, int maxLenField, struct hash *suggestHash)
/* Assuming we are in table already drow control row.
* The suggestHash is keyed by field name. If something is there we'll assume
* it's value is slName list of suggestion values */
{
/* Include javascript and style we need */
webIncludeResourceFile("jquery-ui.css");
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("jquery.plugins.js", NULL);
jsIncludeFile("jquery-ui.js", NULL);
jsIncludeFile("jquery.watermark.js", NULL);
int i;
printf("<TR>");
for (i=0; i<table->fieldCount; ++i)
{
char *field = table->fields[i];
char varName[256];
safef(varName, sizeof(varName), "%s_f_%s", varPrefix, field);
webPrintLinkCellStart();
#ifdef MAKES_TOO_WIDE
/* Print out input control. As you can see from all the commented out bits
* this part has been a challenge. We'd like to make the input cell fit the
* table size, but if we do it with style it makes whole table wider. */
char *oldVal = cartUsualString(cart, varName, "");
printf("<input type=\"text\" name=\"%s\" style=\"display:table-cell; width=100%%\""
" value=\"%s\">", varName, oldVal);
#endif /* MAKES_TOO_WIDE */
/* Approximate size of input control in characters */
int size = fieldedTableMaxColChars(table, i);
if (size > maxLenField)
size = maxLenField;
#ifdef ACTUALLY_WORKS
/* This way does work last I checked and is just a line of code.
* Getting an id= property on the input tag though isn't possible this way. */
cartMakeTextVar(cart, varName, "", size + 1);
#endif
/* Print input control getting previous value from cart. Set an id=
* so auto-suggest can find this control. */
char *oldVal = cartUsualString(cart, varName, "");
printf("<INPUT TYPE=TEXT NAME=\"%s\" id=\"%s\" SIZE=%d VALUE=\"%s\">\n",
varName, varName, size+1, oldVal);
/* Write out javascript to initialize autosuggest on control */
printWatermark(varName, " filter ");
if (suggestHash != NULL)
{
struct slName *suggestList = hashFindVal(suggestHash, field);
if (suggestList != NULL)
{
printSuggestScript(varName, suggestList);
}
}
webPrintLinkCellEnd();
}
printf("</TR>");
}
void uploadPage()
/* Put up initial upload page. */
{
char *oldFileName = cartUsualString(cart, hggUploadFile "__filename", "");
cartWebStart(cart, database, "Upload Data to Genome Graphs");
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=\"POST\" ENCTYPE=\"multipart/form-data\">");
cartSaveSession(cart);
hPrintf("name of data set: ");
cartMakeTextVar(cart, hggDataSetName, "", 16);
hPrintf("<BR>");
hPrintf("description: ");
cartMakeTextVar(cart, hggDataSetDescription, "", 64);
hPrintf("<BR>\n");
hPrintf("file format: ");
cgiMakeDropList(hggFormatType, formatNames, ArraySize(formatNames),
cartUsualString(cart, hggFormatType, formatNames[0]));
hPrintf("<BR>\n");
hPrintf(" markers are: ");
cgiMakeDropList(hggMarkerType, markerNames, ArraySize(markerNames),
cartUsualString(cart, hggMarkerType, markerNames[0]));
hPrintf("<BR>\n");
hPrintf(" column labels: ");
cgiMakeDropList(hggColumnLabels, colLabelNames, ArraySize(colLabelNames),
cartUsualString(cart, hggColumnLabels, colLabelNames[0]));
hPrintf("<BR>\n");
hPrintf("display min value: ");
cartMakeTextVar(cart, hggMinVal, "", 5);
hPrintf(" max value: ");
cartMakeTextVar(cart, hggMaxVal, "", 5);
hPrintf("<BR>\n");
hPrintf("label values: ");
cartMakeTextVar(cart, hggLabelVals, "", 32);
hPrintf("<BR>\n");
hPrintf("draw connecting lines between markers separated by up to ");
cartMakeIntVar(cart, hggMaxGapToFill, 25000000, 8);
hPrintf(" bases.<BR>");
hPrintf("<BR>\n");
hPrintf("file name: <INPUT TYPE=FILE NAME=\"%s\" VALUE=\"%s\">", hggUploadFile,
oldFileName);
hPrintf("<BR>\n");
hPrintf(" or<BR>\n");
hPrintf("Paste URLs or data:<br>");
cgiMakeTextArea(hggUploadUrl, "", 7, 73);
hPrintf("<BR>\n");
hPrintf("<BR>\n");
cgiMakeButton(hggSubmitUpload, "submit");
hPrintf("</FORM>\n");
hPrintf("<i>Note: If you are uploading more than one data set please give them ");
hPrintf("different names. Only the most recent data set of a given name is ");
hPrintf("kept. Otherwise data sets will be kept for at least 48 hours from ");
hPrintf("last use. After that time you may have to upload them again.</i>");
/* Put up section that describes file formats. */
webNewSection("Upload file formats");
hPrintf("%s",
"<P>The upload file is a table in some format. In all formats there is "
"a single line for each marker. "
"Each line starts with information on the marker, and ends with "
"the numerical values associated with that marker. The exact format "
"of the line depends on what is selected from the markers drop "
"down menu. If this is <i>chromosome base</i> then the line will "
"contain the tab or space-separated fields: chromosome, position, "
"and value(s). The first base in a chromosome is considered position 0. "
"An example <i>chromosome base</i> type line is:<PRE><TT>\n"
"chrX 100000 1.23\n"
"</TT></PRE>The lines for other marker types contain two fields: "
"marker and value(s). For dbSNP rsID's an example is:<PRE><TT>\n"
"rs10218492 0.384\n"
"</TT></PRE>"
"</P><P>"
"The file can contain multiple value fields. In this case a "
"separate graph will be available for each value column in the input "
"table. It's a "
"good idea to set the display min/max values above if you want the "
"graphs to share the same scale."
"</P>"
);
webNewSection("Using the upload page");
hPrintf(
"To upload a file in any of the supported formats, "
"locate the file on your computer using the controls next to <B>file name</B>, "
"or supply a <B>URL</B> to the data, "
"and then submit. The other controls on this form are optional, though "
"filling them out will sometimes enhance the display. In general "
"the controls that default to <i>best guess</i> can be left alone, "
"since the guess is almost always correct. The controls for display min and "
"max values and connecting lines can be set later via the configuration "
"page as well. Here is a description of each control."
"<UL>"
"<LI><B>name of data set:</B> Displayed in graph drop-down in Genome Graphs "
" and as trackname in Genome Browser. Only the first 16 characters are "
" visible in some contexts. For data sets with multiple graphs, this is the "
" first part of the name, shared with all members of the data set.</LI>"
"<LI><B>description:</B> A short sentence describing the data set. Displayed in "
"the Genome Graphs and Genome Browser configuration pages, and as the center "
"label in the Genome Browser.</LI>"
"<LI><B>file format:</B> Controls whether the upload file is a tab-separated, "
" comma-separated, or space separated table.</LI>"
"<LI><B>markers are:</B> Describes how to map the data to chromosomes. The choices "
" are either the first column of the file is an ID of some sort, or the first column "
" is a chromosome and the next a base. The IDs can be SNP rs numbers, STS marker names "
" or ID's from any of the supported genotyping platforms.</LI>"
"<LI><B>column labels:</B> Controls whether the first row of the upload file is "
" interpreted as labels rather than data. If the first row contains text in the "
" numerical fields, or if the mapping fields are empty, it is interpreted by "
" \"best guess\" as labels. This is generally correct, but you can override this "
" interpretation by explicitly setting the control. </LI>"
"<LI><B>display min value/max value:</B> Set the range of the data set that will "
" be plotted. If left blank, the range will be taken from the min/max values in the "
" data set itself. For all data sets to share the same scale usually you'll need "
" to set this.</LI>"
"<LI><B>label values:</B> A comma-separated list of numbers for the vertical axis. "
" If left blank the axis will be labeled at the 1/3 and 2/3 point. </LI>"
"<LI><B>draw connecting lines:</B> Lines connecting data points separated by "
" no more than this number of bases are drawn. </LI>"
"<LI><B>file name, or Paste URLs or data:</B> Specify the uploaded data --"
" enter either a file on your local computer; or a URL at which the data file can be"
" found; or simply paste-in the data. If entries are made in both fields, the file name will take"
" precedence. </LI>");
cartWebEnd();
}
