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logviewapp.go
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logviewapp.go
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package main
import (
"fmt"
"github.com/lxn/walk"
. "github.com/lxn/walk/declarative"
"log"
"strconv"
"strings"
)
//Declare global variables
var flagClickA = true
var flagClickB = true
var flagParm = true
var inputSeq string
var inputSeq2 string
var modeRun = "mode-1 for plan1-2-3"
var defaultInputSeq = "ctgatgaccaaactcggcctgtccgggaccacccgcggcaaagcccgcaggaccacgatcgctgatccggccAcagcccgtcccgccgatctcgtccagcgccgcttcggaccaccagcacctaaccggctgtgggtagcagacctcacctatgtgtcgacctgggcagggttcgcctacgtggcctttgtcaccgacgcctacgtcgcaggatcctgggctggcgggtcgcttccacgatggcca"
var defaultInputSeq2 = "GCGATATCTGGTGGTCTGCACGGCGTCGGCGTGTCGGTGGTTAACGCGCTATCCACCCGGCTCGAAGTCGAGATCAAGCGCGACGGGTACGAGTGGTCTCAGGTTTATGAGAAGTCGGAACCCCTGGGCCTCAAGCAAGGGGCGCCGACCAAGAAGACGGGGTCAACGGTGCGGTTCTGGGCCGACCCCGCTGTTTTCGAAACCACGG"
//var defaultInputSeq = "GCGATATCTGGTGGTCTGCACGGCGTCGGCGTGTCGGTGGTTAACGCGCTATCCACCCGGCTCGAAGTCGAGATCAAGCGCGACGGGTACGAGTGGTCTCAGGTTTATGAGAAGTCGGAACCCCTGGGCCTCAAGCAAGGGGCGCCGACCAAGAAGACGGGGTCAACGGTGCGGTTCTGGGCCGACCCCGCTGTTTTCGAAACCACGG"
// wg is used to monitor go routines
var seq1, seq2, lenUS, selfPaired, numGCUS, circleThresh, circleThreshPlan3, maxOutput, showProcess, batchInput, threshold *walk.LineEdit
var modeRuns *walk.ComboBox
//var proBar *walk.ProgressBar
var (
//Corresponding input variable
seq1Name string
batchUS int64 = 11
threshGC float64 = 0.7
maxOutSeqNum int64 = 10
lengthUS int64 = 22
lengthS4 = 8
lowGCUS int64 = 13
highGCUS int64 = 15
lowCircleThresh int64 = 6
highCircleThresh int64 = 8
lowCircleThreshPlan3 int64 = 0
highCircleThreshPlan3 int64 = 0
selfPairedNum int64 = 5
//progressBar = 0
)
func initText() {
//Initialize the input variable
seq1Name = seq1.Text()
if seq1Name != "" {
inputSeq = seq1Name
} else {
inputSeq = defaultInputSeq
}
if seq2.Text() != "" {
seq2Name := seq2.Text()
inputSeq2 = seq2Name
} else {
inputSeq2 = defaultInputSeq2
}
if threshold.Text() != "" {
thresh := threshold.Text()
threshGC, _ = strconv.ParseFloat(thresh, 64)
}
if maxOutput.Text() != "" {
maxNum := maxOutput.Text()
maxOutSeqNum, _ = strconv.ParseInt(maxNum, 10, 64)
}
if lenUS.Text() != "" {
lensUS := lenUS.Text()
lengthUS, _ = strconv.ParseInt(lensUS, 10, 64)
}
if selfPaired.Text() != "" {
selfPaireds := selfPaired.Text()
selfPairedNum, _ = strconv.ParseInt(selfPaireds, 10, 64)
}
//if lenS4.Text() != "" {
// lensS4 := lenS4.Text()
// lengthS4s, _ := strconv.ParseInt(lensS4, 10, 64)
// strInt64 := strconv.FormatInt(lengthS4s, 10)
// lengthS4, _ = strconv.Atoi(strInt64)
//}
if batchInput.Text() != "" {
maxNum := batchInput.Text()
batchUS, _ = strconv.ParseInt(maxNum, 10, 64)
}
if numGCUS.Text() != "" {
threshGCUS := numGCUS.Text()
lowGCUS, _ = strconv.ParseInt(strings.Split(threshGCUS, ",")[0], 10, 64)
highGCUS, _ = strconv.ParseInt(strings.Split(threshGCUS, ",")[1], 10, 64)
}
if modeRuns.Text() != "" {
threshGCUS := modeRuns.Text()
modeRun = threshGCUS
}
if circleThresh.Text() != "" {
circleThreshs := circleThresh.Text()
lowCircleThresh, _ = strconv.ParseInt(strings.Split(circleThreshs, ",")[0], 10, 64)
highCircleThresh, _ = strconv.ParseInt(strings.Split(circleThreshs, ",")[1], 10, 64)
}
if circleThreshPlan3.Text() != "" {
circleThreshs := circleThreshPlan3.Text()
lowCircleThreshPlan3, _ = strconv.ParseInt(strings.Split(circleThreshs, ",")[0], 10, 64)
highCircleThreshPlan3, _ = strconv.ParseInt(strings.Split(circleThreshs, ",")[1], 10, 64)
}
if lowGCUS < 0 || highGCUS > lengthUS || highGCUS < lowGCUS {
log.Println("Error, please check your GC number of US and restart program!")
flagParm = false
}
if lowCircleThresh < 0 || highCircleThresh > lengthUS || highCircleThresh < lowCircleThresh {
log.Println("Error, please check your loop gap and restart program!")
flagParm = false
}
if batchUS < 0 || batchUS > int64(numberBatchs) {
log.Println("Error, please check your batchUS and restart program! (0 <= batchUS <= 2000)")
flagParm = false
}
if threshGC < 0 || threshGC > 1 {
log.Println("Error, please check your threshold and restart program!")
flagParm = false
}
if maxOutSeqNum <= 0 {
log.Println("Error, please check your maxSqeNum and restart program!")
flagParm = false
}
if selfPairedNum <= 0 {
log.Println("Error, please check your selfPairedNum and restart program!")
flagParm = false
}
if lengthUS <= 0 || lengthS4 < 0 {
log.Println(lengthS4)
log.Println(lengthS4 <= 0)
log.Println("Error, please check your length of US or 4S and restart program!")
flagParm = false
}
//if threshGC > 0 && threshGC < 1 && maxOutSeqNum > 0 && lengthS4 >= 0 && lengthUS > 0 && lowGCUS > 0 && highGCUS < lengthUS && highGCUS > lowGCUS && lowCircleThresh > 0 && highCircleThresh < lengthUS && highCircleThresh > lowCircleThresh {
// flagParm = true
//}
inputSeq = transa2A(inputSeq)
inputSeq2 = transa2A(inputSeq2)
seq1.SetText(inputSeq)
seq2.SetText(inputSeq2)
}
func main() {
var mw *walk.MainWindow
if err := (MainWindow{
AssignTo: &mw,
//Icon: "sjtu2.ico",
Title: "Primer Designing by SJTU Biomedical Imaging Informatics Lab",
MinSize: Size{850, 600},
Layout: VBox{},
Children: []Widget{
//VSplitter{
Composite{
Layout: Grid{Columns: 2},
Children: []Widget{
Label{MaxSize: Size{150, 50},
Text: "The 1st sequence",
},
LineEdit{AssignTo: &seq1, Text: defaultInputSeq},
Label{MaxSize: Size{150, 50},
Text: "The 2nd sequence",
},
LineEdit{AssignTo: &seq2, Text: defaultInputSeq2},
Label{MaxSize: Size{150, 50},
Text: "Progress display",
},
LineEdit{AssignTo: &showProcess, Text: "0", ReadOnly: true},
},
},
//ProgressBar{
// AssignTo: &proBar,
// MaxValue: 10000,
// MinValue: 0,
// Value: progressBar,
//},
Composite{
Layout: Grid{Columns: 6},
Children: []Widget{
Label{MaxSize: Size{150, 50},
Text: "The value of the GC threshold",
},
LineEdit{AssignTo: &threshold, Text: fmt.Sprintf("%.2f", threshGC)},
Label{MaxSize: Size{150, 50},
Text: "The length of US",
},
LineEdit{AssignTo: &lenUS, Text: fmt.Sprintf("%d", lengthUS)},
Label{MaxSize: Size{150, 50},
Text: "The GC number section of US",
},
LineEdit{AssignTo: &numGCUS, Text: fmt.Sprintf("%d,%d", lowGCUS, highGCUS)},
Label{MaxSize: Size{150, 50},
Text: "The gap of loop in plan1-2",
},
LineEdit{AssignTo: &circleThresh, Text: fmt.Sprintf("%d,%d", lowCircleThresh, highCircleThresh)},
Label{MaxSize: Size{150, 50},
Text: "The gap of loop in plan3",
},
LineEdit{AssignTo: &circleThreshPlan3, Text: fmt.Sprintf("%d,%d", lowCircleThreshPlan3, highCircleThreshPlan3)},
Label{MaxSize: Size{150, 50},
Text: "The max number of the output",
},
LineEdit{AssignTo: &maxOutput, Text: fmt.Sprintf("%d", maxOutSeqNum)},
Label{MaxSize: Size{150, 50},
Text: "The batches of US (0-100)",
},
LineEdit{AssignTo: &batchInput, Text: fmt.Sprintf("%d", batchUS)},
Label{MaxSize: Size{150, 50},
Text: "The serial num of self-paired",
},
LineEdit{AssignTo: &selfPaired, Text: fmt.Sprintf("%d", selfPairedNum)},
Label{
Text: "The running mode for different plan",
},
ComboBox{
Editable: true,
AssignTo: &modeRuns,
Model: []string{"mode-1 for plan1-2-3", "mode-2 for plan4"},
},
},
},
PushButton{
Text: "Analysis input sequence",
OnClicked: func() {
if flagClickA {
log.Println("############################################################################################")
log.Println("The program start...")
initText()
log.Println("The run mode:")
log.Println(modeRun)
log.Println("The input 1st sequence:")
log.Println(inputSeq)
log.Println("The input 2nd sequence:")
log.Println(inputSeq2)
log.Println("The input GC threshold:")
log.Println(threshGC)
log.Println("The input length of US:")
log.Println(lengthUS)
log.Println("The lowest and highest GC number of US:")
log.Println(lowGCUS, highGCUS)
log.Println("The lowest and highest gap of loop in plan1-2:")
log.Println(lowCircleThresh, highCircleThresh)
log.Println("The lowest and highest gap of loop in plan3:")
log.Println(lowCircleThreshPlan3, highCircleThreshPlan3)
log.Println("The input max number of the output sequence:")
log.Println(maxOutSeqNum)
log.Println("The batches of US:")
log.Println(batchUS)
log.Println("############################################################################################")
if flagParm {
flagClickA = false
log.Println("############################################################################################")
log.Println("Strat to analysis the input sequence:")
if modeRun == "mode-1 for plan1-2-3" {
//go func() {
analysisInput(inputSeq)
//}()
log.Println("Find paired sequence between 1S and 2A in plan1-2:", len(input1S))
log.Println("Find paired sequence between 1S, 2A, 3S and 4S in plan3:", len(input3S1))
log.Println("############################################################################################")
} else {
analysisInputPlan4(inputSeq, inputSeq2)
log.Println("Find paired sequence between 1S and 2A in plan4:", len(input4S1))
log.Println("Find paired sequence between 3S and 4A in plan4:", len(input4S3))
log.Println("############################################################################################")
}
} else {
log.Println("The program detects parameter exceptions. Please check the input and restart the program!")
}
} else {
log.Println("Please do not click while the program is running. If want to restart, please restart the program.", "\r")
}
},
},
PushButton{
Text: "Run for making primers",
OnClicked: func() {
if flagClickB {
if flagParm {
flagClickB = false
if flagClickA == true {
log.Println("############################################################################################")
log.Println("The program start...")
initText()
log.Println("The run mode:")
log.Println(modeRun)
log.Println("The input 1st sequence:")
log.Println(inputSeq)
log.Println("The input 2nd sequence:")
log.Println(inputSeq2)
log.Println("The input GC threshold:")
log.Println(threshGC)
log.Println("The input length of US:")
log.Println(lengthUS)
log.Println("The lowest and highest GC number of US:")
log.Println(lowGCUS, highGCUS)
log.Println("The lowest and highest gap of loop in plan1-2:")
log.Println(lowCircleThresh, highCircleThresh)
log.Println("The lowest and highest gap of loop in plan3:")
log.Println(lowCircleThreshPlan3, highCircleThreshPlan3)
log.Println("The input max number of the output sequence:")
log.Println(maxOutSeqNum)
log.Println("The batches of US:")
log.Println(batchUS)
log.Println("############################################################################################")
}
if modeRun == "mode-1 for plan1-2-3" {
if flagClickA == true {
analysisInput(inputSeq)
log.Println("Find paired sequence between 1S and 2A in plan1-2:", len(input1S))
log.Println("Find paired sequence between 1S, 2A, 3S and 4S in plan3:", len(input3S1))
log.Println("############################################################################################")
}
getOutOfPlan3()
go func() {
makeUSOdd()
}()
} else {
if flagClickA == true {
analysisInputPlan4(inputSeq, inputSeq2)
log.Println("Find paired sequence between 1S and 2A in plan4:", len(input4S1))
log.Println("Find paired sequence between 3S and 4A in plan4:", len(input4S3))
log.Println("############################################################################################")
}
go func() {
getOutOfPlan4()
}()
}
log.Println("############################################################################################")
} else {
log.Println("The program detects parameter exceptions. Please check the input and restart the program!")
}
} else {
log.Println("Please do not click while the program is running. If want to restart, please restart the program.", "\r")
}
//flagClickA = true
//flagClickB = true
},
},
},
}.Create()); err != nil {
log.Fatal(err)
}
lv, err := NewLogView(mw)
if err != nil {
log.Fatal(err)
}
// //Let the interface take over the log output
log.SetOutput(lv)
lv.PostAppendText("All components have been loaded, please set the parameters before click RUN to start the program.")
mw.Run()
}