--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/proteomics.py	Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,181 @@
+"""
+Proteomics format classes
+"""
+import logging
+import re
+from galaxy.datatypes.data import *
+from galaxy.datatypes.xml import *
+from galaxy.datatypes.sniff import *
+from galaxy.datatypes.binary import *
+
+log = logging.getLogger(__name__)
+
+
+class Xls( Binary ):
+    """Class describing a binary excel spreadsheet file"""
+    file_ext = "xls"
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        if not dataset.dataset.purged:
+            dataset.peek  = "Excel Spreadsheet file"
+            dataset.blurb = data.nice_size( dataset.get_size() )
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+    def display_peek( self, dataset ):
+        try:
+            return dataset.peek
+        except:
+            return "Binary xls file (%s)" % ( data.nice_size( dataset.get_size() ) )
+
+class PepXml(GenericXml):
+    """pepXML data"""
+    file_ext = "pepxml"
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+            dataset.blurb = 'pepXML data'
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+    def sniff( self, filename ):
+        """
+        Determines whether the file is pepXML
+        """
+        #TODO - Use a context manager on Python 2.5+ to close handle
+        handle = open(filename)
+        xmlns_re = re.compile(".*pepXML\"")
+        for i in range(3):
+            line = handle.readline()
+            if xmlns_re.match(line.strip()):
+                handle.close()
+                return True
+
+        handle.close()
+        return False
+
+class MzML( GenericXml ):
+    """mzML data"""
+    file_ext = "mzml"
+    
+    def set_peek( self, dataset, is_multi_byte=False ):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+            dataset.blurb = 'mzML Mass Spectrometry data'
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def sniff( self, filename ):
+        handle = open(filename)
+        xmlns_re = re.compile("^<mzML")
+        for i in range(3):
+            line = handle.readline()
+            if xmlns_re.match(line.strip()):
+                handle.close()
+                return True
+
+        handle.close()
+        return False
+
+
+class ProtXML( Text ):
+    """protXML data"""
+    file_ext = "protxml"
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+            dataset.blurb = 'prot XML Search Results'
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+    def sniff( self, filename ):
+        protxml_header = [ '<?xml version="1.0" encoding="ISO-8859-1"?>',
+        'xmlns="http://regis-web.systemsbiology.net/protXML"' ]
+
+        for i, line in enumerate( file( filename ) ):
+            if i >= len( pepxml_header ):
+                return True
+            line = line.rstrip( '\n\r' )
+            if protxml_header[ i ] not in line:
+                return False
+
+
+
+class MzXML( Text ):
+    """mzXML data"""
+    file_ext = "mzXML"
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+            dataset.blurb = 'mzXML Mass Spectrometry data'
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+    def sniff( self, filename ):
+        mzxml_header = [ '<?xml version="1.0" encoding="ISO-8859-1"?>',
+        '<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_2.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_2.1 http://sashimi.sourceforge.net/schema_revision/mzXML_2.1/mzXML_idx_2.1.xsd">' ]
+        for i, line in enumerate( file( filename ) ):
+            if i >= len( mzxml_header ):
+                return True
+            line = line.rstrip( '\n\r' )
+            if line != mzxml_header[ i ]:
+                return False        
+ 
+class Mgf( Text ):
+    """Mascot Generic Format data"""
+    file_ext = "mgf"
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+            dataset.blurb = 'mgf Mascot Generic Format'
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+
+    def sniff( self, filename ):
+        mgf_begin_ions = "BEGIN IONS"
+        max_lines=100
+
+        for i, line in enumerate( file( filename ) ):
+            line = line.rstrip( '\n\r' )
+            if line==mgf_begin_ions:
+                return True
+            if i>max_lines:
+                return False
+            
+                
+class MascotDat( Text ):
+    """Mascot search results """
+    file_ext = "mascotdat"
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+            dataset.blurb = 'mascotdat Mascot Search Results'
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+
+    def sniff( self, filename ):
+        mime_version = "MIME-Version: 1.0 (Generated by Mascot version 1.0)"
+        max_lines=10
+
+        for i, line in enumerate( file( filename ) ):
+            line = line.rstrip( '\n\r' )
+            if line==mime_version:
+                return True
+            if i>max_lines:
+                return False