Fixed issue that caused removed strains to still appear in the haplotype analyst track

4 files changed, 44 insertions, 40 deletions

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 1ce0e725..f4d5ca66 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -235,7 +235,7 @@ class DisplayMappingResults(object):
 
         self.selectedChr = int(start_vars['selected_chr'])
 
-        self.strainlist = self.dataset.group.samplelist
+        self.strainlist = start_vars['samples']
         self.genotype = self.dataset.group.read_genotype_file()
         if self.mapping_method == "reaper" and self.manhattan_plot != True:
             self.genotype = self.genotype.addinterval()
@@ -343,20 +343,19 @@ class DisplayMappingResults(object):
 ## BEGIN HaplotypeAnalyst
 ## count the amount of individuals to be plotted, and increase self.graphHeight
         if self.haplotypeAnalystChecked and self.selectedChr > -1:
-           #thisTrait = self.traitList[0]
-           thisTrait = self.this_trait
-           _strains, _vals, _vars, _aliases = thisTrait.export_informative()
-           smd=[]
-           for ii, _val in enumerate(_vals):
-               temp = GeneralObject(name=_strains[ii], value=_val)
-               smd.append(temp)
-           samplelist = list(self.genotype.prgy)
-           for j,_geno in enumerate (self.genotype[0][1].genotype):
-               for item in smd:
-                   if item.name == samplelist[j]:
-                       self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1
+            thisTrait = self.this_trait
+            _strains, _vals, _vars, _aliases = thisTrait.export_informative()
+            smd=[]
+            for ii, _val in enumerate(_vals):
+                temp = GeneralObject(name=_strains[ii], value=_val)
+                smd.append(temp)
+            samplelist = list(self.genotype.prgy)
+            for j,_geno in enumerate (self.genotype[0][1].genotype):
+                for item in smd:
+                    if item.name == samplelist[j]:
+                        self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1
 # default:
-           self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS+10) * self.EACH_GENE_HEIGHT
+            self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS+10) * self.EACH_GENE_HEIGHT
 ## END HaplotypeAnalyst
 
         ################################################################
@@ -1159,13 +1158,8 @@ class DisplayMappingResults(object):
         if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol:
             return
 
-        clickableRegionLabelFont=pid.Font(ttf="verdana", size=9, bold=0)
-
         xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
         plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-        plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-        yZero = canvas.size[1] - yBottomOffset
-        fontZoom = zoom
 
         yPaddingTop = yTopOffset
 
@@ -1174,7 +1168,7 @@ class DisplayMappingResults(object):
 
         smd=[]
         for ii, _val in enumerate(_vals):
-            if _strains[ii] in self.dataset.group.samplelist:
+            if _strains[ii] in self.samples:
                 temp = GeneralObject(name=_strains[ii], value=_val)
                 smd.append(temp)
 
@@ -1188,11 +1182,11 @@ class DisplayMappingResults(object):
         plotRight = xRightOffset
 
 #### find out PlotRight
-        for i, _chr in enumerate(self.genotype):
+        for _chr in self.genotype:
             if _chr.name == self.ChrList[self.selectedChr][0]:
-                for j, _locus in enumerate(_chr):
-                    txStart = _chr[j].Mb
-                    txEnd   = _chr[j].Mb
+                for i, _locus in enumerate(_chr):
+                    txStart = _chr[i].Mb
+                    txEnd   = _chr[i].Mb
 
                     geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb)  - 0
                     geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) - 0
@@ -1204,7 +1198,7 @@ class DisplayMappingResults(object):
                         drawit = 0;
 
                     if drawit == 1:
-                        if _chr[j].name != " - " :
+                        if _chr[i].name != " - " :
                             plotRight = geneEndPix + 4
 
 #### end find out PlotRight
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index a0466c0f..4770b14b 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -56,27 +56,35 @@ class RunMapping(object):
         self.json_data = {}
         self.json_data['lodnames'] = ['lod.hk']
 
-        self.samples = [] # Want only ones with values
-        self.vals = []
-
         all_samples_ordered = self.dataset.group.all_samples_ordered()
         primary_sample_names = list(all_samples_ordered)
 
-        for sample in self.dataset.group.samplelist:
-            # sample is actually the name of an individual
-            in_trait_data = False
-            for item in self.this_trait.data:
-                if self.this_trait.data[item].name == sample:
-                    value = start_vars['value:' + self.this_trait.data[item].name]
-                    self.samples.append(self.this_trait.data[item].name)
-                    self.vals.append(value)
-                    in_trait_data = True
-                    break
-            if not in_trait_data:
+        self.vals = []
+        if 'samples' in start_vars:
+            self.samples = start_vars['samples'].split(",")
+            for sample in self.samples:
                 value = start_vars.get('value:' + sample)
                 if value:
-                    self.samples.append(sample)
                     self.vals.append(value)
+        else:
+            self.samples = []
+
+            for sample in self.dataset.group.samplelist:
+                # sample is actually the name of an individual
+                in_trait_data = False
+                for item in self.this_trait.data:
+                    if self.this_trait.data[item].name == sample:
+                        value = start_vars['value:' + self.this_trait.data[item].name]
+                        if value != "x":
+                            self.samples.append(self.this_trait.data[item].name)
+                            self.vals.append(value)
+                        in_trait_data = True
+                        break
+                if not in_trait_data:
+                    value = start_vars.get('value:' + sample)
+                    if value:
+                        self.samples.append(sample)
+                        self.vals.append(value)
 
         #ZS: Check if genotypes exist in the DB in order to create links for markers
         if "geno_db_exists" in start_vars:
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index f31c5fe5..ba4d4d7c 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -22,6 +22,7 @@
         {% endif %}
         <input type="hidden" name="results_path" value="{{ mapping_results_path }}">
         <input type="hidden" name="method" value="{{ mapping_method }}">
+        <input type="hidden" name="samples" value="{{ samples|join(",") }}">
         {% for sample in samples %}
         <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
         {% endfor %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index d0c75a5b..109e30cc 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -585,6 +585,7 @@ def mapping_results_page():
         'dataset',
         'group',
         'species',
+        'samples',
         'vals',
         'first_run',
         'gwa_filename',