Support for javascript (mozilla)

.gitignore

@@ -0,0 +1,7 @@
+*.o
+*.so.1
+*.a
+*~
+*.a
+bgzip
+tabix

README.md

@@ -0,0 +1,14 @@
+Tabix
+=====
+
+How to cite:
+------------
+
+Tabix: fast retrieval of sequence features from generic TAB-delimited files
+
+Li H.
+
+Bioinformatics. 2011 Mar 1;27(5):718-9. 
+
+http://www.ncbi.nlm.nih.gov/pubmed/21208982
+

javascript/mozilla/tabix.js

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+/**
+ JAVASCRIPT BINDINGS for Tabix.
+
+ Author: Pierre Lindenbaum PhD @yokofakun http://plindenbaum.blogspot.com
+ Date: May 2013
+ Reference: http://plindenbaum.blogspot.fr/2013/05/binding-c-library-with-javascript.html
+
+ */
+
+/* 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.DLQuery = this.lib.declare("ti_query",
+				 ctypes.default_abi,
+				 ctypes.voidptr_t,
+				 ctypes.voidptr_t,
+				 ctypes.int32_t,
+				 ctypes.int32_t,
+				 ctypes.int32_t
+				 );
+
+			TabixFile.DLIterFirst = this.lib.declare("ti_iter_first",
+				 ctypes.default_abi,
+				 ctypes.voidptr_t,
+				 ctypes.voidptr_t
+				 );	
+
+			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);
+			throw 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;
+		},
+	/** 
+		returns a TABIX iterator 
+
+		if argument is a string : returns an interator to the specified region : "chr:start-end"
+		if argument.length==3 : invokes ti_query(ptr,arg[0],arg[1],arg[2])
+		if there is no argument : return an iterator to the whole tabix file.
+
+		*/
+	query : function()
+		{
+		if(this.ptr==null) return;
+		if(this.iter!=null)
+			{
+			this.log("Closing iterator");
+			this.iter.close();
+			}
+
+		var r=null;
+		switch(arguments.length)
+			{
+			case 0 : r=TabixFile.DLIterFirst(this.ptr); break;
+			case 1 : r=TabixFile.DLQueryS(this.ptr,arguments[0]); break;
+			case 3 : r=TabixFile.DLQuery(
+				this.ptr,arguments[0],
+				arguments[1],
+				arguments[2]
+				);break;
+			default : break;
+			}
+		this.log("query. "+arguments.length);
+		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.ptr=null;
+		}
+	}

javascript/mozilla/test.js

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+/*
+to run that test:
+
+ * download mozilla xulrunner-sdk : https://developer.mozilla.org/en-US/docs/XULRunner
+ * compile the tabix ldynamic ibrary using `make libtabix.so.1`
+ * run the test: 
+
+
+$ LD_LIBRARY_PATH=/path/to/xulrunner/bin:/path/to/tabix.dir \
+	/path/to/xulrunner-sdk/bin/xpcshell -f test.js
+
+*/
+
+/** query a location  */
+load("tabix.js");
+
+
+var tabix=new TabixFile("../../example.gtf.gz");
+
+print("#iteration using query(range)##################");
+
+var iter=tabix.query("chr2:32800-35441");
+while((line=iter.next())!=null)
+ {
+ print(line);
+ }
+
+
+iter=tabix.query("chr1:1873-2090");
+while((line=iter.next())!=null)
+ {
+ print(line);
+ }
+iter.close();
+
+print("#iteration using query()##################");
+ /** get the 3 first lines */
+iter=tabix.query();
+for(var i=0; i< 3 && ((line=iter.next())!=null) ; ++i)
+ {
+ print(line);
+ }
+
+tabix.close();

perl/Makefile.PL

@@ -2,7 +2,7 @@ use ExtUtils::MakeMaker;
 WriteMakefile(
 			  NAME         => 'Tabix',
 			  VERSION_FROM => 'Tabix.pm',
-			  LIBS         => ['-lz -L.. -ltabix'],
+			  LIBS         => ['-L.. -ltabix -lz'],
 			  DEFINE       => '-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE',
 			  INC          => '-I..',
 			 );