Relative Accessible Surface Area

csharp/local/AntibodySequenceLiabilities.yaml

@@ -2,7 +2,7 @@ id: 01010160-093b-55c7-746b-8a3c148111b7
 name: Antibody Sequence Liabilities
 description: Create a set of boolean columns indicating the presence or absence of predefined antibody sequence liabilities.  A column illustrating the sequence and the identified liability locations is also created.
 category: Biopolymer
-version: 1.0.1
+version: 1.1.0
 serviceName: AntibodySequenceLiabilities
 serviceUri: glysade.csharp
 executorId: Glysade.CSharpDataFxn
@@ -36,12 +36,12 @@ inputFields:
     data: Annotated Liabilities
 - control:
     id: patterns
-    label: Match patterns
+    label: Sequence liabilities
     type: select
     multi: !!bool true
     options:
     - text: Asparagine Deamidation
-      value: Asparagine Deamidation,(?=(N[GSTN]))
+      value: Asparagine Deamidation,(?=(N[GSTNH]))
     - text: Aspartic Acid Fragmentation
       value: Aspartic Acid Fragmentation,DP
     - text: Aspartic Acid Isomerization
@@ -62,26 +62,51 @@ inputFields:
     id: patterns
     dataType: list(string)
     data:
-    - Asparagine Deamidation,(?=(N[GSTN]))
+    - Asparagine Deamidation,(?=(N[GSTNH]))
     - Aspartic Acid Fragmentation,DP
     - Aspartic Acid Isomerization,(?=(D[GSTDH]))
     - Cysteine,C
     - Lysine N-glycation,(?<=(K[DE]|[DE]K))
     - N-glycosylation,N[^P][TS]
     - N-terminal Glutamic Acid,^E
     - Oxidation,[MW]
+- control:
+    id: ctrlColor
+    label: Select color
+    type: color
+  request:
+    id: ctrlColor
+    dataType: string
+    data: '#ff0000'
 assembly: PublisherCore
 tags:
 - color: '#dddddd'
   text: MAB
+- color: '#AFC9E1'
+  text: annotation
 - color: '#337abc'
   text: sequence
-- color: '#f1f72d'
-  text: filter
 updateBehavior: automatic
 maximumOutputColumns: !!int 10
 maximumOutputTables: !!int 0
 chemistryFunction: !!bool false
+outputFields:
+- id: sequenceColumn
+  name: Sequence column
+  source: inputField
+  type: default
+- id: outputColumn
+  name: Annotated sequence output column
+  source: inputField
+  type: default
+- id: patterns
+  name: Selected liabilities
+  source: inputField
+  type: default
+- id: ctrlColor
+  name: Color
+  source: inputField
+  type: color
 allowedClients:
 - Analyst
 - WebPlayer

csharp/local/SequenceMotifSearch.yaml

@@ -2,7 +2,7 @@ id: 70470634-68a8-4950-9d88-348bc19e3a1d
 name: Sequence Motif Search
 description: Creates boolean columns indicating the presence or absence of an input sequence motif in a sequence column - regular expressions are also supported.  A column illustrating the sequence and the identified motif locations is also created.
 category: Biopolymer
-version: 1.0.1
+version: 1.1.0
 serviceName: SequenceMotifRegexSearch
 serviceUri: glysade.csharp
 executorId: Glysade.CSharpDataFxn
@@ -29,7 +29,7 @@ inputFields:
     type: text
     validationRules:
     - type: required
-      message: 'Enter a name for the output boolean column.'
+      message: Enter a name for the output boolean column.
   request:
     id: columnName
     dataType: string
@@ -39,7 +39,7 @@ inputFields:
     type: text
     validationRules:
     - type: required
-      message: 'Enter a name to be used in annotating the motif.'
+      message: Enter a name to be used in annotating the motif.
   request:
     id: featureName
     dataType: string
@@ -50,19 +50,48 @@ inputFields:
     rows: !!int 1
     validationRules:
     - type: required
-      message: 'A query sequence or regular expression must be entered.'
+      message: A query sequence or regular expression must be entered.
   request:
     id: expression
     dataType: string
+- control:
+    id: ctrlColor
+    label: Select color
+    type: color
+  request:
+    id: ctrlColor
+    dataType: string
+    data: '#ffa500'
 tags:
+- color: '#AFC9E1'
+  text: annotation
 - color: '#337abc'
   text: sequence
-- color: '#f1f72d'
-  text: filter
 updateBehavior: automatic
 maximumOutputColumns: !!int 2
 maximumOutputTables: !!int 0
 chemistryFunction: !!bool false
+outputFields:
+- id: sequenceColumn
+  name: Sequence column
+  source: inputField
+  type: default
+- id: columnName
+  name: Annotated sequence output column
+  source: inputField
+  type: default
+- id: featureName
+  name: Motif name
+  source: inputField
+  type: default
+- id: expression
+  name: Motif expression
+  source: inputField
+  type: default
+- id: ctrlColor
+  name: Color
+  source: inputField
+  type: color
 allowedClients:
 - Analyst
 - WebPlayer

csharp/local/SequenceRegionAnnotation.yaml

@@ -2,7 +2,7 @@ id: 1d863338-11e3-f287-a9c8-6d72792c320f
 name: Sequence Region Annotation
 description: Create GenBank region annotations for a sequence or GenBank column.
 category: Biopolymer
-version: 1.0.0
+version: 1.1.0
 serviceName: SequenceRegionAnnotationDataFunction
 serviceUri: glysade.csharp
 executorId: Glysade.CSharpDataFxn
@@ -79,6 +79,14 @@ inputFields:
   request:
     id: end
     dataType: integer
+- control:
+    id: uictrlColor
+    label: Select color
+    type: color
+  request:
+    id: uictrlColor
+    dataType: string
+    data: '#afc9e1'
 tags:
 - color: '#337abc'
   text: sequence
@@ -109,10 +117,14 @@ outputFields:
   name: Region end location
   source: inputField
   type: default
+- id: uictrlColor
+  name: Color
+  source: inputField
+  type: color
 allowedClients:
 - Analyst
 - WebPlayer
 demoUrl: 
 limitBy: none
-minimumChartsVersion: 4.4.0.0 
-confirmSubmit: 
+minimumChartsVersion: 4.4.0.0
+confirmSubmit: