added a bunch of stuff, miRBase integration, .fasta file integration

output.fa

@@ -1,4 +1,2 @@
 >Toehold Switch 
-GAUCGAUCGAUCGAAAAAAGUCGAUCGAUCGAUGGAUUUGCAAAAAAAAGAGGAGAGUAAAAUGAUCGAUCGAUCGACUUUUAACCUGGCGGCAGCGCAAAAG 
->And gate between 2 (CUAGCUAGCUAGCUAGCUAC)  and 1 (AUCGAUGCAGCUAGCUAGCUA)  
-GUAGCUAUUUUUUCAUCGAU 
+UGACGUCGAAAUACGCUAAUCGUUGGAUUUGCAAAAAAAAGAGGAGAGUAAAAUGAACGAUUAGCGUAUUUCGAACCUGGCGGCAGCGCAAAAG 

thsGen.py

@@ -554,7 +554,7 @@ def start():
         print("miRNA: ", miRNA)
         print(ths)
         thsStrand = Strand(ths, name="ths")
-        miRNAStrand = Strand(miRNA, name="miRNA")
+        miRNAStrand = Strand(reverse(miRNA), name="miRNA")
 
         tube = Tube(strands = {thsStrand:1e-5}, complexes=SetSpec(max_size = 1), name="thsTube")
         tubeResult = tube_analysis(tubes = [tube], compute = ["pairs", "mfe"], model=thsModel)

thsGenerator.kv

@@ -38,6 +38,7 @@
 
         GridLayout:
             cols: 3
+            spacing: 25
 
             Button:
                 text: "Add miRNA"
@@ -47,40 +48,73 @@
                 text: "Remove miRNA"
                 on_press: root.removeMiRNA()
 
-            Button:
-                text: "Get miRNA from miRBase"
-                on_press: root.getMirBase()
+            BoxLayout:
+                orientation: "vertical"
+
+                Label:
+                    text: "Import miRNA..."
+                    size_hint_y: 0.1
+
+                BoxLayout:
+                    orientation: "horizontal"
+                    size_hint_y: 0.9
+
+                    Button:
+                        text: "...From miRBase"
+                        on_press: root.getMirBase()
+
+                    Button:
+                        text: "...From fasta file"
+                        on_press: root.browseFasta()
 
         BoxLayout:
             orientation: "horizontal"
+            size_hint_y: 0.05
 
             Label:
-                text: "MiRNA name"
+                text: "miRNA name"
+                size_hint_x: 0.3
 
             Label:
-                text: "MiRNA sequence"
+                text: "miRNA sequence"
+                size_hint_x: 0.5
 
             Label:
                 text: "Reversed"
+                size_hint_x: 0.2
 
         GridLayout:
             cols: 3
             id: inputGrid
+            padding: 5
+            spacing: 5
 
             TextInput:
+                height: 45
+                size_hint_y: None
+                size_hint_x: 0.3
+                height: 50
                 multiline: False
                 font_size: 18
 
             TextInput:
+                height: 45
+                size_hint_y: None
+                size_hint_x: 0.5
+                height: 50
                 multiline: False
                 font_size: 18
 
             CheckBox:
+                size_hint_x: 0.2
+                height: 45
+                size_hint_y: None
                 # on_active: root.reverse(self, self.active)
 
 
         GridLayout:
             cols: 3
+            spacing: 25
 
             Button:
                 id: submitButton
@@ -111,6 +145,7 @@
             text: "Toehold Switch"
             size_hint: 1, None
             size: self.texture_size
+            font_size: 25
 
         BoxLayout:
             orientation: "horizontal"
@@ -139,6 +174,7 @@
             text: "Trigger Complex"
             size_hint: 1, None
             size: self.texture_size
+            font_size: 25
 
         BoxLayout:
             orientation: "horizontal"
@@ -172,6 +208,7 @@
             text: "Activated Toehold Switch"
             size_hint: 1, None
             size: self.texture_size
+            font_size: 25
 
         BoxLayout:
             orientation: "horizontal"
@@ -317,4 +354,72 @@
                 text: "to activated toehold switch results"
                 size_hint: 1, 0.9
                 on_press: root.manager.current = "fourth"
-
+
+<fileManager>
+
+    name: "fileManager"
+
+    BoxLayout:
+        spacing: 25
+        padding: 30
+        orientation: "vertical"
+
+        BoxLayout:
+            orientation: "horizontal"
+
+            FileChooserIconView:
+                id: fileChooser
+                on_selection: root.selected(fileChooser.selection)
+
+            ScrollView:
+                do_scroll_x: False
+                size_hint: 1, 0.75
+                size: root.width, root.height * 0.75
+                GridLayout:
+                    cols: 3
+                    size_hint: 1, None
+                    height: self.minimum_height
+                    id: fastaSearchGrid
+                    padding: 25
+                    spacing: 25
+
+        BoxLayout:
+            size_hint: 1, 0.3
+            orientation: "horizontal"
+
+
+            Button:
+                text: "back"
+                size_hint: 1, 1
+                on_press: root.manager.current = "first"
+
+            BoxLayout:
+                orientation: "vertical"
+                size_hint: 1.3, 1
+
+                Label:
+                    text: "miRNA selected:"
+                    size_hint: 1, 0.03
+                    id: fastaSelectText
+
+                BoxLayout:
+                    padding: 30
+                    orientation: "vertical"
+
+                    GridLayout:
+                        cols: 3
+                        spacing: 15
+                        id: fastaSelectBox
+
+            Button:
+                id: fastaSubmitButton
+                text: "submit"
+                size_hint: 1, 1
+                on_press: root.submitFromFasta()
+
+            Button: 
+                id: nextButton3
+                text: "next"
+                size_hint: 1, 1
+                disabled: True
+                on_press: root.manager.current = "second"