Merge branch 'master' into lmm

1 files changed, 0 insertions, 150 deletions

diff --git a/wqflask/basicStatistics/updatedBasicStatisticsPage.py b/wqflask/basicStatistics/updatedBasicStatisticsPage.py
deleted file mode 100755
index 3f30619d..00000000
--- a/wqflask/basicStatistics/updatedBasicStatisticsPage.py
+++ /dev/null
@@ -1,150 +0,0 @@
-from htmlgen import HTMLgen2 as HT
-
-from base.templatePage import templatePage
-from dbFunction import webqtlDatabaseFunction
-import BasicStatisticsFunctions
-
-#Window generated from the Trait Data and Analysis page (DataEditingPage.py) with updated stats figures; takes the page's values that can bed edited by the user
-class updatedBasicStatisticsPage(templatePage):
-
-    plotMinInformative = 4
-
-    def __init__(self, fd):
-
-        templatePage.__init__(self, fd)
-
-        if not fd.genotype:
-            fd.readGenotype()
-            this_strainlist = fd.strainlist
-
-        if fd.allstrainlist:
-            this_strainlist = fd.allstrainlist
-
-        fd.readData(this_strainlist)
-
-        specialStrains = [] #This appears to be the "other/non-RISet strainlist" without parents/f1 strains; not sure what to name it
-        setStrains = []
-        for item in this_strainlist:
-            if item not in fd.strainlist and item.find('F1') < 0:
-                specialStrains.append(item)
-            else:
-                continue
-
-        specialStrains.sort()
-        if specialStrains:
-            specialStrains = fd.f1list+fd.parlist+specialStrains
-
-        self.dict['title'] = 'Basic Statistics'
-        TD_LR = HT.TD(valign="top",width="100%",bgcolor="#fafafa")
-
-        stats_row = HT.TR()
-        stats_cell = HT.TD()
-        stats_script = HT.Script(language="Javascript")
-
-        #Get strain names, values, and variances
-        strain_names = fd.formdata.getvalue('strainNames').split(',')
-        strain_vals = fd.formdata.getvalue('strainVals').split(',')
-        strain_vars = fd.formdata.getvalue('strainVars').split(',')
-
-        vals = []
-        if (len(strain_names) > 0):
-            if (len(strain_names) > 3):
-                #Need to create "vals" object
-                for i in range(len(strain_names)):
-                    try:
-                        this_strain_val = float(strain_vals[i])
-                    except:
-                        continue
-                    try:
-                        this_strain_var = float(strain_vars[i])
-                    except:
-                        this_strain_var = None
-
-                    thisValFull = [strain_names[i], this_strain_val, this_strain_var]
-                    vals.append(thisValFull)
-
-                stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-2", Class="stats_tab"),
-                                                HT.Href(text="Bar Graph (by name)", url="#statstabs-3", Class="stats_tab"), HT.Href(text="Bar Graph (by rank)", url="#statstabs-4", Class="stats_tab"),
-                                                HT.Href(text="Box Plot", url="#statstabs-5", Class="stats_tab")]
-                stats_tabs = HT.List(stats_tab_list)
-
-                stats_container = HT.Div(id="stats_tabs", Class="ui-tabs")
-                stats_container.append(stats_tabs)
-
-                stats_script_text = """$(function() { $("#stats_tabs").tabs();});""" #Javascript enabling tabs
-
-                table_div = HT.Div(id="statstabs-1", style="height:320px;width:740px;overflow:scroll;")
-                table_container = HT.Paragraph()
-
-                statsTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
-                this_trait_type = fd.formdata.getvalue('trait_type', None)
-                this_cellid = fd.formdata.getvalue('cellid', None)
-                statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=this_trait_type, cellid=this_cellid)
-                statsTable.append(HT.TR(HT.TD(statsTableCell)))
-
-                table_container.append(statsTable)
-                table_div.append(table_container)
-                stats_container.append(table_div)
-
-                normalplot_div = HT.Div(id="statstabs-2", style="height:540px;width:740px;overflow:scroll;")
-                normalplot_container = HT.Paragraph()
-                normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
-                plotTitle = fd.formdata.getvalue("normalPlotTitle","")
-                normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains)
-                normalplot.append(HT.TR(HT.TD(normalplot_img)))
-                normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \
-                normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(),
-                "More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot",
-                                target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary"))))
-                normalplot_container.append(normalplot)
-                normalplot_div.append(normalplot_container)
-                stats_container.append(normalplot_div)
-
-                barName_div = HT.Div(id="statstabs-3", style="height:540px;width:740px;overflow:scroll;")
-                barName_container = HT.Paragraph()
-                barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
-                barName_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="name")
-                barName.append(HT.TR(HT.TD(barName_img)))
-                barName_container.append(barName)
-                barName_div.append(barName_container)
-                stats_container.append(barName_div)
-
-                barRank_div = HT.Div(id="statstabs-4", style="height:540px;width:740px;overflow:scroll;")
-                barRank_container = HT.Paragraph()
-                barRank = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
-                barRank_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="rank")
-                barRank.append(HT.TR(HT.TD(barRank_img)))
-                barRank_container.append(barRank)
-                barRank_div.append(barRank_container)
-                stats_container.append(barRank_div)
-
-                boxplot_div = HT.Div(id="statstabs-5", style="height:540px;width:740px;overflow:scroll;")
-                boxplot_container = HT.Paragraph()
-                boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
-                boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals)
-                boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left")))
-                boxplot_container.append(boxplot)
-                boxplot_div.append(boxplot_container)
-                stats_container.append(boxplot_div)
-
-                stats_cell.append(stats_container)
-                stats_script.append(stats_script_text)
-
-                submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
-                stats_row.append(stats_cell)
-
-                submitTable.append(stats_row)
-                submitTable.append(stats_script)
-
-                TD_LR.append(submitTable)
-                self.dict['body'] = str(TD_LR)
-            else:
-                heading = "Basic Statistics"
-                detail = ['Fewer than %d case data were entered for %s data set. No statitical analysis has been attempted.' % (self.plotMinInformative, fd.RISet)]
-                self.error(heading=heading,detail=detail)
-                return
-        else:
-            heading = "Basic Statistics"
-            detail = ['Empty data set, please check your data.']
-            self.error(heading=heading,detail=detail)
-            return