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May 29, 2013 13:54
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javascript bindings for tabix.
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/** | |
JAVASCRIPT BINDINGS for Tabix. | |
Author: Pierre Lindenbaum PhD @yokofakun http://plindenbaum.blogspot.com | |
Date: 2013 | |
*/ | |
/* import js-ctypes */ | |
Components.utils.import("resource://gre/modules/ctypes.jsm") | |
/** iterator constructor */ | |
function TabixIterator(owner,ptr) | |
{ | |
this.owner=owner; | |
this.ptr=ptr; | |
} | |
/* tabix file constructor */ | |
function TabixFile(filename) | |
{ | |
this.init(); | |
this.log("Opening "+filename); | |
this.ptr=TabixFile.DLOpen(filename,0); | |
this.iter=null; | |
if(this.ptr.isNull()) throw "I/O ERROR: Cannot open \""+filename+"\""; | |
}; | |
/* TabixFile prototype methods below */ | |
TabixFile.prototype.LOADED=false; | |
TabixFile.prototype= { | |
LOADED : false, | |
DEBUG : false, | |
log: function(msg) | |
{ | |
if(!this.DEBUG) return; | |
print("FileReader: " + msg); | |
}, | |
/* release the dynamic libraries */ | |
dispose: function() | |
{ | |
if(!this.LOADED) return; | |
this.lib.close(); | |
this.LOADED=false; | |
}, | |
/* initialize the dynamic libraries */ | |
init : function() | |
{ | |
if(this.LOADED) return; | |
try | |
{ | |
this.lib = ctypes.open("libtabix.so.1"); | |
this.log("OK loaded"); | |
/* https://developer.mozilla.org/en-US/docs/Mozilla/js-ctypes/js-ctypes_reference/Library#declare%28%29 */ | |
TabixFile.DLOpen= this.lib.declare("ti_open", | |
ctypes.default_abi, | |
ctypes.voidptr_t, | |
ctypes.char.ptr, | |
ctypes.int32_t | |
); | |
TabixFile.DLClose= this.lib.declare("ti_close", | |
ctypes.default_abi, | |
ctypes.void_t, | |
ctypes.voidptr_t | |
); | |
TabixFile.DLQueryS = this.lib.declare("ti_querys", | |
ctypes.default_abi, | |
ctypes.voidptr_t, | |
ctypes.voidptr_t, | |
ctypes.char.ptr | |
); | |
TabixFile.DLIterDestroy = this.lib.declare("ti_iter_destroy", | |
ctypes.default_abi, | |
ctypes.void_t, | |
ctypes.voidptr_t | |
); | |
TabixFile.DLIterRead = this.lib.declare("ti_read", | |
ctypes.default_abi, | |
ctypes.char.ptr, | |
ctypes.voidptr_t, | |
ctypes.voidptr_t, | |
ctypes.int32_t.ptr | |
); | |
this.LOADED=true; | |
} | |
catch(e) | |
{ | |
this.log(e); | |
} | |
}, | |
/** close this TabixFile */ | |
close: function() | |
{ | |
this.log("closing"); | |
if(this.iter!=null) this.iter.close(); | |
if(this.ptr==null) return; | |
TabixFile.DLClose(this.ptr); | |
this.ptr=null; | |
}, | |
/** return a TABIX iterator to the specified region "chr:start-end" */ | |
query : function(region) | |
{ | |
if(this.ptr==null) return; | |
if(this.iter!=null) this.iter.close(); | |
var r=TabixFile.DLQueryS(this.ptr,region); | |
this.iter=new TabixIterator(this,r); | |
return this.iter; | |
} | |
}; | |
/** Iterator protorype */ | |
TabixIterator.prototype={ | |
/** returns the next line or NULL */ | |
next: function() | |
{ | |
if(this.ptr==null || this.owner.iter !== this) return null; | |
/* https://developer.mozilla.org/en-US/docs/Mozilla/js-ctypes/Using_js-ctypes/Declaring_types */ | |
var len=ctypes.int32_t(0); | |
var line=TabixFile.DLIterRead(this.owner.ptr,this.ptr,len.address()); | |
if(line.isNull()) | |
{ | |
this.close(); | |
return; | |
} | |
return line.readString(); | |
}, | |
/** release that iterator */ | |
close : function() | |
{ | |
if(this.ptr!=null) TabixFile.DLIterDestroy(this.ptr); | |
this.owner.iter=null; | |
this.ptr=null; | |
} | |
} |
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