diff hmmer/hmmer.py @ 0:914f50b4c8c1 default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hmmer/hmmer.py	Tue Jun 07 16:41:43 2011 -0400
@@ -0,0 +1,55 @@
+"""
+Hmmer classes
+"""
+
+import data
+import logging
+import re
+import string
+from cgi import escape
+from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes import metadata
+import galaxy.model
+from galaxy import util
+from sniff import *
+
+log = logging.getLogger(__name__)
+
+class Hmm( data.Text ):
+    """Class for hmmer database files"""
+
+    file_ext = 'hmm'
+
+    def init_meta( self, dataset, copy_from=None ):
+        data.Text.init_meta( self, dataset, copy_from=copy_from )
+
+class HmmPressed( Hmm ):
+    """Class describing a hmmer database produced by hmmpress"""
+
+    file_ext = 'hmmPressed'
+    composite_type='basic'
+
+    MetadataElement( readonly=True, optional=True, visible=False, no_value=0 )
+
+    def __init__(self,**kwd):
+        data.Data.__init__(self, **kwd)
+        self.add_composite_file('hmm')
+        self.add_composite_file('hmm.h3m')
+        self.add_composite_file('hmm.h3i')
+        self.add_composite_file('hmm.h3f')
+        self.add_composite_file('hmm.h3p')
+    def set_peek( self, dataset, is_multi_byte=False ):
+        if not dataset.dataset.purged:
+            dataset.peek  = "Folder of multiple files"
+            dataset.blurb = "Folder of multiple files"
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+    def display_peek( self, dataset ):
+        try:
+            return dataset.peek
+        except:
+            return "Folder of multiple files"
+    def get_mime(self):
+        """Returns the mime type of the datatype"""
+        return 'text/plain'