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GUI fixes #343

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merged 3 commits into from
Sep 11, 2024
Merged

GUI fixes #343

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3e0b742
Update GUI for release
GeorgWa Sep 10, 2024
e934654
fix #234
GeorgWa Sep 10, 2024
25dfebb
fix bug
GeorgWa Sep 10, 2024
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8 changes: 4 additions & 4 deletions alphadia/constants/default.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -89,9 +89,9 @@ search:

target_num_candidates: 2
# target ms1 tolerance in ppm
target_ms1_tolerance: 15
target_ms1_tolerance: 5
# target ms2 tolerance in ppm
target_ms2_tolerance: 15
target_ms2_tolerance: 10
# target ion mobility tolerance in 1/K_0
target_mobility_tolerance: 0.0 # default is to optimize automatically
# target retention time tolerance in seconds if > 1, or a proportion of the total gradient length if < 1
Expand Down Expand Up @@ -143,10 +143,10 @@ search_initial:
initial_ms2_tolerance: 30

# initial ion mobility tolerance in 1/K_0
initial_mobility_tolerance: 0.08
initial_mobility_tolerance: 0.1

# initial retention time tolerance in seconds if > 1, or a proportion of the total gradient length if < 1
initial_rt_tolerance: 240
initial_rt_tolerance: 0.5

selection_config:
peak_len_rt: 10.
Expand Down
4 changes: 2 additions & 2 deletions alphadia/libtransform.py
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Expand Up @@ -324,11 +324,11 @@ def forward(self, input: SpecLibBase) -> SpecLibBase:
model_mgr = ModelManager(device=device)

# will load other model than default generic
if self.peptdeep_model_type is not None:
if self.peptdeep_model_type:
logging.info(f"Loading PeptDeep models of type {self.peptdeep_model_type}")
model_mgr.load_installed_models(self.peptdeep_model_type)

if self.peptdeep_model_path is not None:
if self.peptdeep_model_path and self.peptdeep_model_path != "":
if not os.path.exists(self.peptdeep_model_path):
raise ValueError(
f"PeptDeep model checkpoint folder {self.peptdeep_model_path} does not exist"
Expand Down
4 changes: 2 additions & 2 deletions gui/src/main/modules/engine.js
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Expand Up @@ -263,7 +263,7 @@ class CMDExecutionEngine extends BaseExecutionEngine {
"--no-capture-output",
"alphadia",
"--config",
path.join(workflow.output_directory.path, "config.yaml")
`"${path.join(workflow.output_directory.path, "config.yaml")}"`
] , { env:{...process.env, PATH}, shell: true});
run.pid = run.process.pid

Expand Down Expand Up @@ -423,7 +423,7 @@ class BundledExecutionEngine extends BaseExecutionEngine {
// use binary location as cwd and binary name as command
run.process = spawn(prefix + binaryName,
["--config",
path.join(workflow.output_directory.path, "config.yaml")
`"${path.join(workflow.output_directory.path, "config.yaml")}"`
],
{
env:{...process.env, PATH},
Expand Down
3 changes: 1 addition & 2 deletions gui/src/renderer/components/ParameterInput.js
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Expand Up @@ -16,8 +16,7 @@ const SingleFolderSelection = ({parameter, onChange = () => {}}) => {
console.log(err);
})
}

const folderName = parameter.replace(/^.*[\\\/]/, '')
const folderName = parameter ? parameter.replace(/^.*[\\\/]/, '') : ''

return (
<>
Expand Down
85 changes: 36 additions & 49 deletions gui/workflows/PeptideCentric.v1.json
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Original file line number Diff line number Diff line change
Expand Up @@ -35,13 +35,6 @@
"description": "Number of threads to use for parallel processing.",
"type": "integer"
},
{
"id": "reuse_calibration",
"name": "Reuse Calibration",
"value": false,
"description": "AlphaDIA will save the calibration parameters in the project file. If this option is enabled, the calibration parameters will be reused for subsequent searches of the same file.",
"type": "boolean"
},
{
"id": "reuse_quant",
"name": "Reuse Ion Quantities",
Expand Down Expand Up @@ -153,7 +146,7 @@
{
"id": "max_var_mod_num",
"name": "Maximum variable modifications",
"value": 1,
"value": 2,
"description": "Variable modifications for in-silico digest. At the moment localisation is not supported. Semicolon separated list \n Example: Oxidation@M;Acetyl@ProteinN-term",
"type": "integer"
},
Expand Down Expand Up @@ -241,7 +234,7 @@
{
"id": "peptdeep_model_path",
"name": "PeptDeep Model Path",
"value": "",
"value": null,
"description": "Select a custom PeptDeep model for library prediction. This can be a DDA or DIA trained model. Please make sure that you use the same instrument type and NCE for prediction as the model was trained on.",
"type": "singleFolderSelection"
},
Expand All @@ -265,6 +258,34 @@
"name": "Search",
"hidden": false,
"parameters": [
{
"id": "target_ms1_tolerance",
"name": "MS1 Tolerance",
"value": 5,
"description": "MS1 tolerance in ppm. Search windows are optimized and calibrated during processing. The window is reduced until this tolerance is reached.",
"type": "float"
},
{
"id": "target_ms2_tolerance",
"name": "MS2 Tolerance",
"value": 10,
"description": "MS2 tolerance in ppm. Search windows are optimized and calibrated during processing. The window is reduced until this tolerance is reached.",
"type": "float"
},
{
"id": "target_mobility_tolerance",
"name": "Mobility Tolerance",
"value": 0.0,
"description": "Mobility tolerance in 1/K_0. Search windows are optimized and calibrated during processing. The window is reduced until this tolerance is reached. Set to enable automatic optimization.",
"type": "float"
},
{
"id": "target_rt_tolerance",
"name": "RT Tolerance",
"value": 0.0,
"description": "Retention time tolerance in seconds if greater than 1 or as a proportion of the gradient length if less than 1. Search windows are optimized and calibrated during processing. The window is reduced until this tolerance is reached. Automatic optimization is enabled if set to 0.",
"type": "float"
},
{
"id": "channel_filter",
"name": "Channel Filter",
Expand Down Expand Up @@ -293,34 +314,7 @@
"description": "For every precursor in the library a number of top scoring candidates will be extracted. This number is the maximum number of candidates that will be extracted per precursor.",
"type": "integer"
},
{
"id": "target_ms1_tolerance",
"name": "MS1 Tolerance",
"value": 5,
"description": "MS1 tolerance in ppm. Search windows are optimized and calibrated during processing. The window is reduced until this tolerance is reached.",
"type": "float"
},
{
"id": "target_ms2_tolerance",
"name": "MS2 Tolerance",
"value": 10,
"description": "MS2 tolerance in ppm. Search windows are optimized and calibrated during processing. The window is reduced until this tolerance is reached.",
"type": "float"
},
{
"id": "target_mobility_tolerance",
"name": "Mobility Tolerance",
"value": 0.04,
"description": "Mobility tolerance in 1/K_0. Search windows are optimized and calibrated during processing. The window is reduced until this tolerance is reached.",
"type": "float"
},
{
"id": "target_rt_tolerance",
"name": "RT Tolerance",
"value": 100,
"description": "Retention time tolerance in seconds if greater than 1 or as a proportion of the gradient length if less than 1. Search windows are optimized and calibrated during processing. The window is reduced until this tolerance is reached.",
"type": "float"
},

{
"id": "quant_window",
"name": "Quant window",
Expand All @@ -332,7 +326,7 @@
{
"id": "quant_all",
"name": "Use all MS2 observations",
"value": false,
"value": true,
"description": "Use all MS2 observations for quantification. If disabled only the best scoring observation is used for quantification. Recommended for synchro-PASEF data.",
"type": "boolean"

Expand Down Expand Up @@ -374,13 +368,6 @@
"heuristic"
]
},
{
"id": "competetive_scoring",
"name": "Competetive Scoring",
"value": true,
"description": "If enabled, only the best scoring candidate per target decoy pair is retained.",
"type": "boolean"
},
{
"id": "channel_wise_fdr",
"name": "Channel wise FDR",
Expand All @@ -405,7 +392,7 @@
{
"id": "initial_num_candidates",
"name": "Number of Candidates",
"value": 2,
"value": 1,
"description": "Initial number of candidates to extract per precursor.",
"type": "integer"
},
Expand All @@ -426,14 +413,14 @@
{
"id": "initial_mobility_tolerance",
"name": "Mobility Tolerance",
"value": 0.08,
"value": 0.1,
"description": "Initial mobility tolerance in 1/K_0.",
"type": "float"
},
{
"id": "initial_rt_tolerance",
"name": "RT Tolerance",
"value": 240,
"value": 0.5,
"description": "Initial retention time tolerance in seconds if greater than 1 or as a proportion of the gradient length if less than 1.",
"type": "float"
}
Expand All @@ -445,7 +432,7 @@
"hidden": true,
"parameters": [
{
"id": "multiplexed_quant",
"id": "enabled",
"name": "Enable Multiplexing",
"value": false,
"description": "Quantify and score identification across non-isobaric labled channels.",
Expand Down
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