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Create LICENSE #2

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eb49308
Create LICENSE
FJEagle May 25, 2021
32d3996
fix obvious typo and error
FJEagle May 25, 2021
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fix obvious typo and error
@FJEagle
FJEagle committed May 25, 2021
commit 32d3996bdfefe718b41c21fdbf34509e2ef8d2e4
118 changes: 59 additions & 59 deletions index.js
View file
Original file line number Diff line number Diff line change
@@ -16,13 +16,13 @@ var ABIF_TYPES = {
19: 'cString'
};

module.exports = function(buf){
module.exports = function (buf) {
return new Reader(buf);
};

module.exports.Reader = Reader;

function Reader(buf){
function Reader (buf) {
this.buf = buf;
this.pos = 0;
this.type = this.readNextString(4);
@@ -32,45 +32,45 @@ function Reader(buf){
this.seek(dir.dataoffset);

this.entries = [];
for(var i =0; i<= dir.numelements -1; i++){
for (var i = 0; i <= dir.numelements - 1; i++) {
var e = new DirEntry(this);
this.entries.push(e);
}
}
Reader.prototype.showEntries = function(){
this.entries.map(function(entry){
Reader.prototype.showEntries = function () {
this.entries.map(function (entry) {
console.log(entry.name);
});
};

Reader.prototype.getData = function(name, num){
if(num === undefined){
Reader.prototype.getData = function (name, num) {
if (num === undefined) {
num = 1;
}
var entry = this.getEntry(name, num);
if(!entry){
if (!entry) {
// throw new Error('Entry ' + name + ' (' +num + ') not found.');
return undefined;
}
this.seek(entry.mydataoffset);
data = this.readData(entry.elementtype, entry.numelements);
var data = this.readData(entry.elementtype, entry.numelements);
return data.length === 1 ? data[0] : data;
};


Reader.prototype.getEntry = function(name, num){
Reader.prototype.getEntry = function (name, num) {
var entry;

this.entries.some(function(e){
if(e.name === name && e.number === num){
this.entries.some(function (e) {
if (e.name === name && e.number === num) {
entry = e;
return true;
}
});
return entry;
};

Reader.prototype.readData = function(type, num){
Reader.prototype.readData = function (type, num) {
var m = {
1: 'Byte',
3: 'UnsignedInt',
@@ -84,98 +84,98 @@ Reader.prototype.readData = function(type, num){
13: 'Bool'
};

if(m[type]){
if (m[type]) {
return this._loop(m[type], num);
}
else if(type === 2){
else if (type === 2) {
return this.readNextString(num);
}
else if(type === 18){
else if (type === 18) {
return this.readNextpString(num);
}
else if(type === 19){
else if (type === 19) {
return this.readNextcString(num);
}
return this[m[type]](num);
};

Reader.prototype._loop = function(type, num){
Reader.prototype._loop = function (type, num) {
var buf = [],
method = 'readNext' + type;

for(var i=0; i < num; i++){
for (var i = 0; i < num; i++) {
buf.push(this[method]());
}
return buf;
};

Reader.prototype.readNextShort = function(){
Reader.prototype.readNextShort = function () {
var v = this.buf.readInt16BE(this.pos);
this.pos += 2;
return v;
};
Reader.prototype.readNextInt = function(){
Reader.prototype.readNextInt = function () {
var v = this.buf.readInt32BE(this.pos);
this.pos += 4;
return v;
};

Reader.prototype.readNextChar = function(){
var v = this.buf.toString('ascii', this.pos, this.pos+1);
Reader.prototype.readNextChar = function () {
var v = this.buf.toString('ascii', this.pos, this.pos + 1);
this.pos += 1;
return v;
};

Reader.prototype.readNextByte = function(){
Reader.prototype.readNextByte = function () {
var v = this.buf.readUInt8(this.pos);
this.pos += 1;
return v;
};

Reader.prototype.readNextUnsignedInt = function(){
Reader.prototype.readNextUnsignedInt = function () {
var v = this.buf.readUInt32BE(this.pos);
this.pos += 4;
return v;
};

Reader.prototype.readNextLong = function(){
Reader.prototype.readNextLong = function () {
var v = this.buf.readInt32BE(this.pos);
this.pos += 4;
return v;
};

Reader.prototype.readNextFloat = function(){
Reader.prototype.readNextFloat = function () {
var v = this.buf.readFloatBE(this.pos);
this.pos += 4;
return v;
};


Reader.prototype.readNextDouble = function(){
Reader.prototype.readNextDouble = function () {
var v = this.buf.readDoubleBE(this.pos);
this.pos += 8;
return v;
};

Reader.prototype.readNextBool = function(){
Reader.prototype.readNextBool = function () {
return this.readNextByte() === 1;
};

Reader.prototype.readNextDate = function(){
Reader.prototype.readNextDate = function () {
var d = new Date();
var y = this.readNextShort();
var m = this.readNextByte();
var day = this.readNextByte();

console.log(y. m, day);
console.log(y.m, day);
d.setYear(y);
d.setMonth(m);
d.setDate(day);
return d;
};


Reader.prototype.readNextTime = function(){
Reader.prototype.readNextTime = function () {
var d = new Date();
d.setHours(this.readNextByte());
d.setMinutes(this.readNextByte());
@@ -184,7 +184,7 @@ Reader.prototype.readNextTime = function(){
return d;
};

Reader.prototype.readNextThumb = function(){
Reader.prototype.readNextThumb = function () {
return [
this.readNextLong(),
this.readNextLong(),
@@ -193,24 +193,24 @@ Reader.prototype.readNextThumb = function(){
];
};

Reader.prototype.readNextString = function(size){
Reader.prototype.readNextString = function (size) {
var chars = [];
for(var i = 0; i <= size -1; i++){
for (var i = 0; i <= size - 1; i++) {
chars.push(this.readNextChar());
}
return chars.join('');
};

Reader.prototype.readNextpString = function(){
Reader.prototype.readNextpString = function () {
return this.readNextString(this.readNextByte());
};

Reader.prototype.readNextcString = function(){
Reader.prototype.readNextcString = function () {
var chars = [],
c;
while(true){
while (true) {
c = this.readNextChar();
if(c.charAt(0) === 0){
if (c.charAt(0) === 0) {
return chars.join('');
}
else {
@@ -219,15 +219,15 @@ Reader.prototype.readNextcString = function(){
}
};

Reader.prototype.tell = function(){
Reader.prototype.tell = function () {
return this.pos;
};

Reader.prototype.seek = function(pos){
Reader.prototype.seek = function (pos) {
this.pos = pos;
};

function DirEntry(buf){
function DirEntry (buf) {
this.name = buf.readNextString(4);
this.number = buf.readNextInt();

@@ -245,35 +245,35 @@ function DirEntry(buf){

// http://cpansearch.perl.org/src/VITA/Bio-Trace-ABIF-1.05/lib/Bio/Trace/ABIF.pm

Read.prototype.getAnalyzedDataForChannel = function(channel){
if(channel === 5){
Reader.prototype.getAnalyzedDataForChannel = function (channel) {
if (channel === 5) {
channel = 205;
}
else {
channel += 8;
}
if (channel < 9 || (channel > 12 && channel!= 205)) {
if (channel < 9 || (channel > 12 && channel != 205)) {
return null;
}
return this.getEntry('DATA', channel);
};

Read.protoype.getBaseOrder = function(){
Reader.prototype.getBaseOrder = function () {
return this.getData('FWO_').split('');
};

Read.prototype.getChannel = function(base){
Reader.prototype.getChannel = function (base) {
base = base.toUpperCase();
var order = this.getBaseOrder();
for(var i = 0; i <= order.length; i++){
if(order[i] === base){
for (var i = 0; i <= order.length; i++) {
if (order[i] === base) {
return i + 1;
}
}
return undefined;
};

Reader.prototype.getPeaks = function(){
Reader.prototype.getPeaks = function () {
// sub peaks {
// my ($self, $n) = @_;
// my $k = '_PEAK' . $n;
@@ -308,7 +308,7 @@ Reader.prototype.getPeaks = function(){
// }
};

Reader.prototype.getRawDataForChannel = function(channel){
Reader.prototype.getRawDataForChannel = function (channel) {
// sub raw_data_for_channel {
// my ($self, $channel_number) = @_;
// if ($channel_number == 5) {
@@ -329,7 +329,7 @@ Reader.prototype.getRawDataForChannel = function(channel){
// }
};

Reader.prototype.getRawTrace = function(base){
Reader.prototype.getRawTrace = function (base) {
// sub raw_trace {
// my ($self, $base) = @_;
// my %ob = ();
@@ -340,7 +340,7 @@ Reader.prototype.getRawTrace = function(base){
// }
};

Reader.prototype.getTrace = function(base){
Reader.prototype.getTrace = function (base) {
// sub trace {
// my ($self, $base) = @_;
// my %ob = ();
@@ -482,19 +482,19 @@ var accessors = {
'well_id': 'TUBE'
};

Object.keys(accessors).map(function(accessor){
var r = /[-_]([a-z])/g;
var name = accessor.replace(regexp, function(match, c){
Object.keys(accessors).map(function (accessor) {
var regexp = /[-_]([a-z])/g;
var name = accessor.replace(regexp, function (match, c) {
return c.toUpperCase();
});
name = method.charAt(0).toUpperCase() + method.substring(1);
name = name.charAt(0).toUpperCase() + name.substring(1);

var args = accessors[accessor];
if(!Array.isArray(args)){
if (!Array.isArray(args)) {
args = [args];
}

Reader.prototype['get' + name] = function(){
Reader.prototype['get' + name] = function () {
return this.getData.apply(this, args);
};