diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index 30c8fd0786c..b0d3481001f 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -9,12 +9,7 @@
-
-
+
@@ -25,7 +20,7 @@
-
+
@@ -51,7 +46,7 @@
-
+
@@ -93,7 +88,7 @@
-
+
@@ -103,7 +98,7 @@
-
+
@@ -115,7 +110,7 @@
-
+
@@ -156,7 +151,7 @@
-
+
@@ -172,7 +167,7 @@
-
+
@@ -190,7 +185,7 @@
-
+
@@ -203,7 +198,6 @@
-
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 5cbe223c81e..2a478d7f6df 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -103,7 +103,7 @@ class Bam( Binary ):
"""Class describing a BAM binary file"""
file_ext = "bam"
track_type = "ReadTrack"
- data_sources = { "data": "bai", "index": [ "bigwig", "summary_tree" ] }
+ data_sources = { "data": "bai", "index": "bigwig" }
MetadataElement( name="bam_index", desc="BAM Index File", param=metadata.FileParameter, file_ext="bai", readonly=True, no_value=None, visible=False, optional=True )
diff --git a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
index 739cca3d268..35f7b224083 100644
--- a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
@@ -1,7 +1,14 @@
- bedtools genomecov -bg -split -ibam $input -g $chromInfo | wigToBigWig stdin $chromInfo $output
+ bedtools genomecov -bg -split -ibam $input -g $chromInfo
+
+ ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this
+ ## should only be used on systems with large RAM.
+ ## | wigToBigWig stdin $chromInfo $output
+
+ ## This can be used anywhere.
+ > temp.bg ; bedGraphToBigWig temp.bg $chromInfo $output
diff --git a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml b/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml
deleted file mode 100644
index 5c05f020f56..00000000000
--- a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-
-
-
- sam_or_bam_to_summary_tree_converter.py --bam $input1 $input1.metadata.bam_index $output1
-
-
-
-
-
-
-
-
-
-
diff --git a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
new file mode 100644
index 00000000000..c0648f61481
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
@@ -0,0 +1,25 @@
+
+
+
+ ## Remove comments and sort by chromosome.
+ grep -v '^#' $input | sort -k1,1 |
+
+ ## Generate coverage bedgraph.
+ bedtools genomecov -bg -split -i stdin -g $chromInfo
+
+ ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this
+ ## should only be used on systems with large RAM.
+ ## | wigToBigWig stdin $chromInfo $output
+
+ ## This can be used anywhere.
+ > temp.bg ; bedGraphToBigWig temp.bg $chromInfo $output
+
+
+
+
+
+
+
+
+
+
diff --git a/lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.xml b/lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.xml
deleted file mode 100644
index b9067648f80..00000000000
--- a/lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-
-
- interval_to_summary_tree_converter.py $input1 $output1
-
-
-
-
-
-
-
-
-
-
-
diff --git a/lib/galaxy/datatypes/converters/encodepeak_to_summary_tree_converter.xml b/lib/galaxy/datatypes/converters/encodepeak_to_summary_tree_converter.xml
deleted file mode 100644
index fc5db2e4bde..00000000000
--- a/lib/galaxy/datatypes/converters/encodepeak_to_summary_tree_converter.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-
-
- interval_to_summary_tree_converter.py
- -c ${input1.metadata.chromCol}
- -s ${input1.metadata.startCol}
- -e ${input1.metadata.endCol}
- $input1 $output1
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/lib/galaxy/datatypes/converters/gff_to_summary_tree_converter.xml b/lib/galaxy/datatypes/converters/gff_to_summary_tree_converter.xml
deleted file mode 100644
index f61cdb6d90d..00000000000
--- a/lib/galaxy/datatypes/converters/gff_to_summary_tree_converter.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-
-
- interval_to_summary_tree_converter.py $input1 $output1 --gff
-
-
-
-
-
-
-
-
-
-
-
diff --git a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py b/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py
deleted file mode 100644
index e61429f3eb5..00000000000
--- a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py
+++ /dev/null
@@ -1,63 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Convert from interval file to summary tree file. Default input file format is BED (0-based, half-open intervals).
-
-usage: %prog in_file out_file
- -c, --chr-col: chromosome column, default=1
- -s, --start-col: start column, default=2
- -e, --end-col: end column, default=3
- -t, --strand-col: strand column, default=6
- -G, --gff: input is GFF format, meaning start and end coordinates are 1-based, closed interval
-"""
-from __future__ import division
-
-import sys, fileinput, optparse
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
-from galaxy.visualization.tracks.summary import *
-from bx.intervals.io import *
-from galaxy.datatypes.util.gff_util import *
-
-def main():
- # Read options, args.
- parser = optparse.OptionParser()
- parser.add_option( '-c', '--chr-col', type='int', dest='chrom_col', default=1 )
- parser.add_option( '-s', '--start-col', type='int', dest='start_col', default=2 )
- parser.add_option( '-e', '--end-col', type='int', dest='end_col', default=3 )
- parser.add_option( '-t', '--strand-col', type='int', dest='strand_col', default=6 )
- parser.add_option( '-G', '--gff', dest="gff_format", action="store_true" )
- (options, args) = parser.parse_args()
- input_fname, output_fname = args
-
- # Convert column indices to 0-based.
- options.chrom_col -= 1
- options.start_col -= 1
- options.end_col -= 1
- options.strand_col -= 1
-
- # Do conversion.
- if options.gff_format:
- reader_wrapper_class = GFFReaderWrapper
- chr_col, start_col, end_col, strand_col = ( 0, 3, 4, 6 )
- else:
- reader_wrapper_class = NiceReaderWrapper
- chr_col, start_col, end_col, strand_col = ( options.chrom_col, options.start_col, options.end_col, options.strand_col )
- reader_wrapper = reader_wrapper_class( fileinput.FileInput( input_fname ),
- chrom_col=chr_col,
- start_col=start_col,
- end_col=end_col,
- strand_col=strand_col,
- fix_strand=True )
- st = SummaryTree()
- for feature in list( reader_wrapper ):
- if isinstance( feature, GenomicInterval ):
- # Tree expects BED coordinates.
- if type( feature ) is GFFFeature:
- convert_gff_coords_to_bed( feature )
- st.insert_range( feature.chrom, long( feature.start ), long( feature.end ) )
-
- st.write( output_fname )
-
-if __name__ == "__main__":
- main()
diff --git a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.xml b/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.xml
deleted file mode 100644
index 103c7fa4d16..00000000000
--- a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-
-
- interval_to_summary_tree_converter.py
- -c ${input1.metadata.chromCol}
- -s ${input1.metadata.startCol}
- -e ${input1.metadata.endCol}
- $input1 $output1
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py b/lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py
deleted file mode 100644
index 951fac7f88b..00000000000
--- a/lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import division
-
-import sys, os, optparse
-sys.stderr = open(os.devnull, 'w') # suppress stderr as cython produces warning on some systems:
- # csamtools.so:6: RuntimeWarning: __builtin__.file size changed
-
-from galaxy import eggs
-import pkg_resources
-
-if sys.version_info[:2] == (2, 4):
- pkg_resources.require( "ctypes" )
-pkg_resources.require( "pysam" )
-
-from pysam import csamtools
-from galaxy.visualization.tracks.summary import *
-
-def main():
- parser = optparse.OptionParser()
- parser.add_option( '-S', '--sam', action="store_true", dest="is_sam" )
- parser.add_option( '-B', '--bam', action="store_true", dest="is_bam" )
- options, args = parser.parse_args()
-
- if options.is_bam:
- input_fname = args[0]
- index_fname = args[1]
- out_fname = args[2]
- samfile = csamtools.Samfile( filename=input_fname, mode='rb', index_filename=index_fname )
- elif options.is_sam:
- input_fname = args[0]
- out_fname = args[1]
- samfile = csamtools.Samfile( filename=input_fname, mode='r' )
-
- st = SummaryTree()
- for read in samfile.fetch():
- st.insert_range( samfile.getrname( read.rname ), read.pos, read.pos + read.rlen )
-
- st.write(out_fname)
-
-if __name__ == "__main__":
- main()
diff --git a/lib/galaxy/datatypes/converters/sam_to_summary_tree_converter.xml b/lib/galaxy/datatypes/converters/sam_to_summary_tree_converter.xml
deleted file mode 100644
index 6dd1c50ac05..00000000000
--- a/lib/galaxy/datatypes/converters/sam_to_summary_tree_converter.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-
-
- sam_or_bam_to_summary_tree_converter.py --sam $input1 $output1
-
-
-
-
-
-
-
-
-
-
-
diff --git a/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.py b/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.py
deleted file mode 100644
index e46ddf7ca76..00000000000
--- a/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.py
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Convert from VCF file to summary tree file.
-
-usage: %prog in_file out_file
-"""
-from __future__ import division
-
-import optparse
-import galaxy_utils.sequence.vcf
-from galaxy.visualization.tracks.summary import SummaryTree
-
-def main():
- # Read options, args.
- parser = optparse.OptionParser()
- (options, args) = parser.parse_args()
- in_file, out_file = args
-
- # Do conversion.
- st = SummaryTree()
- for line in list( galaxy_utils.sequence.vcf.Reader( open( in_file ) ) ):
- # VCF format provides a chrom and 1-based position for each variant.
- # SummaryTree expects 0-based coordinates.
- st.insert_range( line.chrom, long( line.pos-1 ), long( line.pos ) )
-
- st.write(out_file)
-
-if __name__ == "__main__":
- main()
\ No newline at end of file
diff --git a/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.xml
deleted file mode 100644
index 1217b8afffb..00000000000
--- a/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-
-
- vcf_to_summary_tree_converter.py $input1 $output1
-
-
-
-
-
-
-
-
-
-
-
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index f564e2e041c..f6e14e31fd3 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -47,7 +47,7 @@ class Interval( Tabular ):
file_ext = "interval"
line_class = "region"
track_type = "FeatureTrack"
- data_sources = { "data": "tabix", "index": "summary_tree" }
+ data_sources = { "data": "tabix", "index": "bigwig" }
"""Add metadata elements"""
MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter )
@@ -354,7 +354,7 @@ class BedGraph( Interval ):
class Bed( Interval ):
"""Tab delimited data in BED format"""
file_ext = "bed"
- data_sources = { "data": "tabix", "index": "summary_tree", "feature_search": "fli" }
+ data_sources = { "data": "tabix", "index": "bigwig", "feature_search": "fli" }
track_type = Interval.track_type
"""Add metadata elements"""
@@ -569,7 +569,7 @@ class Gff( Tabular, _RemoteCallMixin ):
"""Tab delimited data in Gff format"""
file_ext = "gff"
column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ]
- data_sources = { "data": "interval_index", "index": "summary_tree", "feature_search": "fli" }
+ data_sources = { "data": "interval_index", "index": "bigwig", "feature_search": "fli" }
track_type = Interval.track_type
"""Add metadata elements"""
@@ -1288,7 +1288,7 @@ class ENCODEPeak( Interval ):
file_ext = "encodepeak"
column_names = [ 'Chrom', 'Start', 'End', 'Name', 'Score', 'Strand', 'SignalValue', 'pValue', 'qValue', 'Peak' ]
- data_sources = { "data": "tabix", "index": "summary_tree" }
+ data_sources = { "data": "tabix", "index": "bigwig" }
"""Add metadata elements"""
MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter )
@@ -1307,7 +1307,7 @@ class ChromatinInteractions( Interval ):
file_ext = "chrint"
track_type = "DiagonalHeatmapTrack"
- data_sources = { "data": "tabix", "index": "summary_tree" }
+ data_sources = { "data": "tabix", "index": "bigwig" }
column_names = [ 'Chrom1', 'Start1', 'End1', 'Chrom2', 'Start2', 'End2', 'Value' ]
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index 8d0559a1526..c8858c61472 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -359,7 +359,7 @@ class Taxonomy( Tabular ):
class Sam( Tabular ):
file_ext = 'sam'
track_type = "ReadTrack"
- data_sources = { "data": "bam", "index": "summary_tree" }
+ data_sources = { "data": "bam", "index": "bigwig" }
def __init__(self, **kwd):
"""Initialize taxonomy datatype"""
@@ -537,7 +537,7 @@ class ElandMulti( Tabular ):
class Vcf( Tabular ):
""" Variant Call Format for describing SNPs and other simple genome variations. """
track_type = "VariantTrack"
- data_sources = { "data": "tabix", "index": "summary_tree" }
+ data_sources = { "data": "tabix", "index": "bigwig" }
file_ext = 'vcf'
column_names = [ 'Chrom', 'Pos', 'ID', 'Ref', 'Alt', 'Qual', 'Filter', 'Info', 'Format', 'data' ]
diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py
index b3e073dcf21..6a54633c8d6 100644
--- a/lib/galaxy/visualization/data_providers/genome.py
+++ b/lib/galaxy/visualization/data_providers/genome.py
@@ -14,7 +14,6 @@ from galaxy.util.json import from_json_string
from bx.interval_index_file import Indexes
from bx.bbi.bigwig_file import BigWigFile
from galaxy.util.lrucache import LRUCache
-from galaxy.visualization.tracks.summary import summary_tree_from_file
from galaxy.visualization.data_providers.basic import BaseDataProvider
from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and_cigar
from galaxy.datatypes.interval import Bed, Gff, Gtf
@@ -800,79 +799,6 @@ class RawVcfDataProvider( VcfDataProvider ):
return line_filter_iter()
-class SummaryTreeDataProvider( GenomeDataProvider ):
- """
- Summary tree data provider for the Galaxy track browser.
- """
-
- dataset_type = 'summary_tree'
-
- CACHE = LRUCache( 20 ) # Store 20 recently accessed indices for performance
-
- def valid_chroms( self ):
- st = summary_tree_from_file( self.converted_dataset.file_name )
- return st.chrom_blocks.keys()
-
- def get_data( self, chrom, start, end, level=None, resolution=None, detail_cutoff=None, draw_cutoff=None, **kwargs ):
- """
- Returns summary tree data for a given genomic region.
- """
- filename = self.converted_dataset.file_name
- st = self.CACHE[filename]
- if st is None:
- st = summary_tree_from_file( self.converted_dataset.file_name )
- self.CACHE[filename] = st
-
- # Look for chrom in tree using both naming conventions.
- if chrom not in st.chrom_blocks:
- chrom = _convert_between_ucsc_and_ensemble_naming( chrom )
- if chrom not in st.chrom_blocks:
- return None
-
- # Get or compute level.
- if level:
- level = int( level )
- elif resolution:
- resolution = max( 1, ceil( float( resolution ) ) )
- level = ceil( log( resolution, st.block_size ) ) - 1
- level = int( max( level, 0 ) )
- else:
- # Either level or resolution is required.
- return None
-
- if level <= 1:
- return "detail"
-
- # Use level to get results.
- stats = st.chrom_stats[ chrom ]
- results = st.query( chrom, int(start), int(end), level, detail_cutoff=detail_cutoff, draw_cutoff=draw_cutoff )
- if results == "detail" or results == "draw":
- return results
- else:
- return {
- 'dataset_type': self.dataset_type,
- 'data': results,
- 'max': stats[ level ][ "max" ],
- 'avg': stats[ level ][ "avg" ],
- 'delta': stats[ level ][ "delta" ],
- 'level': level
- }
-
- def has_data( self, chrom ):
- """
- Returns true if dataset has data for this chrom
- """
-
- # Get summary tree.
- filename = self.converted_dataset.file_name
- st = self.CACHE[filename]
- if st is None:
- st = summary_tree_from_file( self.converted_dataset.file_name )
- self.CACHE[filename] = st
-
- # Check for data.
- return st.chrom_blocks.get(chrom, None) or st.chrom_blocks.get(_convert_between_ucsc_and_ensemble_naming(chrom), None)
-
class BamDataProvider( GenomeDataProvider, FilterableMixin ):
"""
Provides access to intervals from a sorted indexed BAM file. Coordinate
diff --git a/lib/galaxy/visualization/data_providers/registry.py b/lib/galaxy/visualization/data_providers/registry.py
index 797b3f4a57c..a86cd73a2cd 100644
--- a/lib/galaxy/visualization/data_providers/registry.py
+++ b/lib/galaxy/visualization/data_providers/registry.py
@@ -29,7 +29,6 @@ class DataProviderRegistry( object ):
"interval_index": genome.IntervalIndexDataProvider,
"bai": genome.BamDataProvider,
"bam": genome.SamDataProvider,
- "summary_tree": genome.SummaryTreeDataProvider,
"bigwig": genome.BigWigDataProvider,
"bigbed": genome.BigBedDataProvider
}
diff --git a/lib/galaxy/visualization/tracks/summary.py b/lib/galaxy/visualization/tracks/summary.py
deleted file mode 100644
index 801fb37ed87..00000000000
--- a/lib/galaxy/visualization/tracks/summary.py
+++ /dev/null
@@ -1,117 +0,0 @@
-'''
-This module cannot be moved due to the use of pickling.
-'''
-
-import sys, os
-import cPickle
-
-# TODO: What are the performance implications of setting min level to 1? Data
-# structure size and/or query speed? It would be nice to have level 1 data
-# so that client does not have to compute it.
-MIN_LEVEL = 2
-
-class SummaryTree:
- '''
- Summary tree data structure for feature aggregation across large genomic regions.
- '''
- def __init__( self, block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30 ):
- self.chrom_blocks = {}
- self.levels = levels
- self.draw_cutoff = draw_cutoff
- self.detail_cutoff = detail_cutoff
- self.block_size = block_size
- self.chrom_stats = {}
-
- def find_block( self, num, level ):
- """ Returns block that num is in for level. """
- return ( num / self.block_size ** level )
-
- def insert_range( self, chrom, start, end ):
- """ Inserts a feature at chrom:start-end into the tree. """
-
- # Get or set up chrom blocks.
- if chrom in self.chrom_blocks:
- blocks = self.chrom_blocks[ chrom ]
- else:
- blocks = self.chrom_blocks[ chrom ] = {}
- self.chrom_stats[ chrom ] = {}
- for level in range( MIN_LEVEL, self.levels + 1 ):
- blocks[ level ] = {}
-
- # Insert feature into all matching blocks at all levels.
- for level in range( MIN_LEVEL, self.levels + 1 ):
- block_level = blocks[ level ]
- starting_block = self.find_block( start, level )
- ending_block = self.find_block( end, level )
- for block in range( starting_block, ending_block + 1 ):
- if block in block_level:
- block_level[ block ] += 1
- else:
- block_level[ block ] = 1
-
- def finish( self ):
- """ Compute stats for levels. """
-
- for chrom, blocks in self.chrom_blocks.iteritems():
- for level in range( self.levels, MIN_LEVEL - 1, -1 ):
- # Set level's stats.
- max_val = max( blocks[ level ].values() )
- self.chrom_stats[ chrom ][ level ] = {}
- self.chrom_stats[ chrom ][ level ][ "delta" ] = self.block_size ** level
- self.chrom_stats[ chrom ][ level ][ "max" ] = max_val
- self.chrom_stats[ chrom ][ level ][ "avg" ] = float( max_val ) / len( blocks[ level ] )
-
- self.chrom_blocks[ chrom ] = dict( [ ( key, value ) for key, value in blocks.iteritems() ] )
-
- def query( self, chrom, start, end, level, draw_cutoff=None, detail_cutoff=None ):
- """ Queries tree for data. """
-
- # Set cutoffs to self's attributes if not defined.
- if draw_cutoff != 0:
- draw_cutoff = self.draw_cutoff
- if detail_cutoff != 0:
- detail_cutoff = self.detail_cutoff
-
- # Get data.
- if chrom in self.chrom_blocks:
- stats = self.chrom_stats[ chrom ]
-
- # For backwards compatibility:
- if "detail_level" in stats and level <= stats[ "detail_level" ]:
- return "detail"
- elif "draw_level" in stats and level <= stats[ "draw_level" ]:
- return "draw"
-
- # If below draw, detail level, return string to denote this.
- max = stats[ level ][ "max" ]
- if max < detail_cutoff:
- return "detail"
- if max < draw_cutoff:
- return "draw"
-
- # Return block data.
- blocks = self.chrom_blocks[ chrom ]
- results = []
- multiplier = self.block_size ** level
- starting_block = self.find_block( start, level )
- ending_block = self.find_block( end, level )
- for block in range( starting_block, ending_block + 1 ):
- val = 0
- if block in blocks[ level ]:
- val = blocks[ level ][ block ]
- results.append( ( block * multiplier, val ) )
- return results
-
- return None
-
- def write( self, filename ):
- """ Writes tree to file. """
- self.finish()
- cPickle.dump( self, open( filename, 'wb' ), 2 )
-
-def summary_tree_from_file( filename ):
- st_file = open( filename, "rb" )
- st = cPickle.load( st_file )
- st_file.close()
- return st
-
diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py
index 6d66328c198..8e38f85fce8 100644
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -145,32 +145,41 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin, UsesHistory
extra_info = None
mode = kwargs.get( "mode", "Auto" )
- # Handle histogram mode uniquely for now:
data_provider_registry = trans.app.data_provider_registry
+
+ # Coverage mode uses index data.
if mode == "Coverage":
# Get summary using minimal cutoffs.
indexer = data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' )
- summary = indexer.get_data( chrom, low, high, detail_cutoff=0, draw_cutoff=0, **kwargs )
- if summary == "detail":
- # Use maximum level of detail--2--to get summary data no matter the resolution.
- summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ],
- level=2, detail_cutoff=0, draw_cutoff=0 )
- return summary
+ return indexer.get_data( chrom, low, high, **kwargs )
- if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and mode == "Auto":
- # Only check for summary_tree if it's Auto mode (which is the default)
- #
- # Have to choose between indexer and data provider
+ # TODO:
+ # (1) add logic back in for no_detail
+ # (2) handle scenario where mode is Squish/Pack but data requested is large, so reduced data needed to be returned.
+
+ # If mode is Auto, need to determine what type of data to return.
+ if mode == "Auto":
+ # Get stats from indexer.
indexer = data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' )
- summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ] )
- if summary is None:
- return { 'dataset_type': indexer.dataset_type, 'data': None }
-
- if summary == "draw":
- kwargs["no_detail"] = True # meh
- extra_info = "no_detail"
- elif summary != "detail":
- return summary
+ stats = indexer.get_data( chrom, low, high, stats=True )
+
+ # If stats were requested, return them.
+ if 'stats' in kwargs:
+ if stats[ 'data' ][ 'max' ] == 0:
+ return { 'dataset_type': indexer.dataset_type, 'data': None }
+ else:
+ return stats
+
+ # Use heuristic based on max depth and region size to determine whether to
+ # return coverage data. When zoomed out and region is large, max depth
+ # is determining factor. However, when sufficiently zoomed in and region is
+ # small, coverage data is no longer provided.
+ if int( high ) - int( low ) > 50000 and stats[ 'data' ][ 'max' ] > 1000:
+ return indexer.get_data( chrom, low, high )
+
+ #
+ # Provide individual data points.
+ #
# Get data provider.
data_provider = data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='data' )
diff --git a/static/scripts/utils/config.js b/static/scripts/utils/config.js
index a35ddd7ce47..7a79a412dc8 100644
--- a/static/scripts/utils/config.js
+++ b/static/scripts/utils/config.js
@@ -58,7 +58,6 @@ var ConfigSetting = Backbone.Model.extend({
{ key: 'mode', type: 'string', default_value: this.mode, hidden: true },
{ key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: null },
{ key: 'show_differences', label: 'Show differences only', type: 'bool', default_value: true },
- { key: 'histogram_max', label: 'Histogram maximum', type: 'float', default_value: null, help: 'Clear value to set automatically' },
{ key: 'mode', type: 'string', default_value: this.mode, hidden: true }
]
});
diff --git a/static/scripts/viz/trackster/painters.js b/static/scripts/viz/trackster/painters.js
index d7608e51bdf..69a0783e0f2 100644
--- a/static/scripts/viz/trackster/painters.js
+++ b/static/scripts/viz/trackster/painters.js
@@ -133,49 +133,6 @@ Painter.prototype.default_prefs = {};
*/
Painter.prototype.draw = function(ctx, width, height, w_scale) {};
-/**
- * SummaryTreePainter, a histogram showing number of intervals in a region
- */
-var SummaryTreePainter = function(data, view_start, view_end, prefs, mode) {
- Painter.call(this, data, view_start, view_end, prefs, mode);
-};
-
-SummaryTreePainter.prototype.default_prefs = { show_counts: false };
-
-SummaryTreePainter.prototype.draw = function(ctx, width, height, w_scale) {
- var view_start = this.view_start,
- points = this.data.data,
- max = (this.prefs.histogram_max ? this.prefs.histogram_max : this.data.max),
- // Set base Y so that max label and data do not overlap. Base Y is where rectangle bases
- // start. However, height of each rectangle is relative to required_height; hence, the
- // max rectangle is required_height.
- base_y = height,
- delta_x_px = Math.ceil(this.data.delta * w_scale);
- ctx.save();
-
- for (var i = 0, len = points.length; i < len; i++) {
- var x = Math.floor( (points[i][0] - view_start) * w_scale );
- var y = points[i][1];
-
- if (!y) { continue; }
- var y_px = y / max * height;
- if (y !== 0 && y_px < 1) { y_px = 1; }
-
- ctx.fillStyle = this.prefs.block_color;
- ctx.fillRect( x, base_y - y_px, delta_x_px, y_px );
-
- // Draw number count if it can fit the number with some padding, otherwise things clump up
- var text_padding_req_x = 4;
- if (this.prefs.show_counts && (ctx.measureText(y).width + text_padding_req_x) < delta_x_px) {
- ctx.fillStyle = this.prefs.label_color;
- ctx.textAlign = "center";
- ctx.fillText(y, x + (delta_x_px/2), 10);
- }
- }
-
- ctx.restore();
-};
-
var LinePainter = function(data, view_start, view_end, prefs, mode) {
Painter.call( this, data, view_start, view_end, prefs, mode );
var i, len;
@@ -1692,7 +1649,6 @@ extend(VariantPainter.prototype, Painter.prototype, {
return {
Scaler: Scaler,
- SummaryTreePainter: SummaryTreePainter,
LinePainter: LinePainter,
LinkedFeaturePainter: LinkedFeaturePainter,
ReadPainter: ReadPainter,
diff --git a/static/scripts/viz/trackster/tracks.js b/static/scripts/viz/trackster/tracks.js
index 05bece4d0d5..79f6f33121f 100644
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -2076,11 +2076,10 @@ var Tile = function(track, region, resolution, canvas, data) {
*/
Tile.prototype.predisplay_actions = function() {};
-var SummaryTreeTile = function(track, region, resolution, canvas, data, max_val) {
+var LineTrackTile = function(track, region, resolution, canvas, data) {
Tile.call(this, track, region, resolution, canvas, data);
- this.max_val = max_val;
};
-extend(SummaryTreeTile.prototype, Tile.prototype);
+LineTrackTile.prototype.predisplay_actions = function() {};
var FeatureTrackTile = function(track, region, resolution, canvas, data, w_scale, mode, message, all_slotted, feature_mapper) {
// Attribute init.
@@ -2601,7 +2600,7 @@ extend(Track.prototype, Drawable.prototype, {
track.enabled = false;
track.tile_cache.clear();
track.data_manager.clear();
- track.content_div.css("height", "auto");
+ track.tiles_div.css("height", "auto");
/*
if (!track.content_div.text()) {
track.content_div.text(DATA_LOADING);
@@ -2669,7 +2668,7 @@ extend(Track.prototype, Drawable.prototype, {
track.tiles_div.css( "height", track.visible_height_px + "px" );
track.enabled = true;
// predraw_init may be asynchronous, wait for it and then draw
- $.when(track.predraw_init()).done(function() {
+ $.when.apply($, track.predraw_init()).done(function() {
init_deferred.resolve();
track.container_div.removeClass("nodata error pending");
track.request_draw();
@@ -2688,7 +2687,29 @@ extend(Track.prototype, Drawable.prototype, {
/**
* Additional initialization required before drawing track for the first time.
*/
- predraw_init: function() {},
+ predraw_init: function() {
+ var track = this;
+ return $.getJSON( track.dataset.url(),
+ { data_type: 'data', stats: true, chrom: track.view.chrom, low: 0,
+ high: track.view.max_high, hda_ldda: track.dataset.get('hda_ldda') }, function(result) {
+ track.container_div.addClass( "line-track" );
+ var data = result.data;
+
+ // Tracks may not have stat data either because there is no data or data is not yet ready.
+ if (data && data.min && data.max) {
+ // Compute default minimum and maximum values
+ var min_value = data.min,
+ max_value = data.max;
+ // If mean and sd are present, use them to compute a ~95% window
+ // but only if it would shrink the range on one side
+ min_value = Math.floor( Math.min( 0, Math.max( min_value, data.mean - 2 * data.sd ) ) );
+ max_value = Math.ceil( Math.max( 0, Math.min( max_value, data.mean + 2 * data.sd ) ) );
+ // Update the prefs
+ track.prefs.min_value = min_value;
+ track.prefs.max_value = max_value;
+ }
+ });
+ },
/**
* Returns all drawables in this drawable.
@@ -2800,6 +2821,32 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
};
},
+ /**
+ * Set track bounds for current chromosome.
+ */
+ set_min_max: function() {
+ var track = this;
+
+ return $.getJSON( track.dataset.url(),
+ { data_type: 'data', stats: true, chrom: track.view.chrom, low: 0,
+ high: track.view.max_high, hda_ldda: track.dataset.get('hda_ldda') },
+ function(result) {
+ var data = result.data;
+ if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) {
+ // Compute default minimum and maximum values
+ var min_value = data.min,
+ max_value = data.max;
+ // If mean and sd are present, use them to compute a ~95% window
+ // but only if it would shrink the range on one side
+ min_value = Math.floor( Math.min( 0, Math.max( min_value, data.mean - 2 * data.sd ) ) );
+ max_value = Math.ceil( Math.max( 0, Math.min( max_value, data.mean + 2 * data.sd ) ) );
+ // Update the prefs
+ track.prefs.min_value = min_value;
+ track.prefs.max_value = max_value;
+ }
+ });
+ },
+
/**
* Change track's mode.
*/
@@ -2808,6 +2855,10 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
// TODO: is it necessary to store the mode in two places (.mode and track_config)?
track.mode = new_mode;
track.config.values['mode'] = new_mode;
+ // FIXME: find a better way to get Auto data w/o clearing cache; using mode in the
+ // data manager would work if Auto data were checked for compatibility when a specific
+ // mode is chosen.
+ if (new_mode === 'Auto') { this.data_manager.clear(); }
track.request_draw(true);
this.action_icons.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")");
return track;
@@ -2954,10 +3005,11 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
/**
* Add a maximum/minimum label to track.
*/
- _add_yaxis_label: function(type, val, pref_name, on_change) {
+ _add_yaxis_label: function(type, on_change) {
var track = this,
css_class = (type === 'max' ? 'top' : 'bottom'),
text = (type === 'max' ? 'max' : 'min'),
+ pref_name = (type === 'max' ? 'max_value' : 'min_value'),
// Default action for on_change is to redraw track.
on_change = on_change || function() {
track.request_draw(true);
@@ -2966,11 +3018,11 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
if (label.length !== 0) {
// Label already exists, so update value.
- label.text(val);
+ label.text(track.prefs[pref_name]);
}
else {
// Add label.
- label = $("").text(val).make_text_editable({
+ label = $("").text(track.prefs[pref_name]).make_text_editable({
num_cols: 12,
on_finish: function(new_val) {
$(".bs-tooltip").remove();
@@ -2989,6 +3041,29 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
* drawn/fetched and shown.
*/
postdraw_actions: function(tiles, width, w_scale, clear_after) {
+ //
+ // If some tiles have line track tiles (which denote coverage data), redraw all tiles using coverage data.
+ //
+ var non_line_track_tiles = _.filter(tiles, function(tile) {
+ return !(tile instanceof LineTrackTile);
+ });
+
+ if (tiles.length !== non_line_track_tiles.length) {
+ // Clear because this is set when drawing.
+ this.max_height_px = 0;
+ var track = this;
+ _.each(non_line_track_tiles, function(tile) {
+ tile.html_elt.remove();
+ track.draw_helper(true, tile.region, tile.resolution, track.tiles_div, w_scale, { mode: 'Coverage' });
+ });
+
+ track._add_yaxis_label('max');
+ }
+ else {
+ // Remove Y-axis labels because there are no line track tiles.
+ this.container_div.find('.yaxislabel').remove();
+ }
+
//
// If some tiles have icons, set padding of tiles without icons so features and rows align.
//
@@ -3004,16 +3079,6 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
}
});
}
-
- //
- // If using SummaryTree tiles, show max.
- //
- var track = this,
- first_tile = tiles[0];
- if (first_tile instanceof SummaryTreeTile) {
- var max_val = (this.prefs.histogram_max ? this.prefs.histogram_max : first_tile.max_val);
- this._add_yaxis_label('max', max_val, 'histogram_max');
- }
},
/**
@@ -3021,12 +3086,13 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
* jQuery.Deferred object that is fulfilled when tile can be drawn again.
*/
draw_helper: function(force, region, resolution, parent_element, w_scale, kwargs) {
- var track = this,
- key = this._gen_tile_cache_key(w_scale, region),
- is_tile = function(o) { return (o && 'track' in o); };
-
// Init kwargs if necessary to avoid having to check if kwargs defined.
if (!kwargs) { kwargs = {}; }
+
+ var track = this,
+ key = this._gen_tile_cache_key(w_scale, region),
+ is_tile = function(o) { return (o && 'track' in o); },
+ mode = kwargs.mode || track.mode;
// Check tile cache, if found show existing tile in correct position
var tile = (force ? undefined : track.tile_cache.get_elt(key));
@@ -3041,7 +3107,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
var can_draw_now = true;
// Get the track data, maybe a deferred
- var tile_data = track.data_manager.get_data(region, track.mode, resolution, track.data_url_extra_params);
+ var tile_data = track.data_manager.get_data(region, mode, resolution, track.data_url_extra_params);
if ( is_deferred( tile_data ) ) {
can_draw_now = false;
}
@@ -3049,7 +3115,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
// Get reference data if needed, maybe a deferred
var seq_data;
if ( view.reference_track ) {
- seq_data = view.reference_track.data_manager.get_data(region, track.mode, resolution, view.reference_track.data_url_extra_params);
+ seq_data = view.reference_track.data_manager.get_data(region, mode, resolution, view.reference_track.data_url_extra_params);
if ( is_deferred( seq_data ) ) {
can_draw_now = false;
}
@@ -3066,7 +3132,6 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
// HACK: this is FeatureTrack-specific.
// If track mode is Auto, determine mode and update.
- var mode = track.mode;
if (mode === "Auto" && track.get_mode) {
mode = track.get_mode(tile_data);
track.update_auto_mode(mode);
@@ -3079,7 +3144,6 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
tile_high = region.get('end'),
width = Math.ceil( (tile_high - tile_low) * w_scale ) + track.left_offset,
height = track.get_canvas_height(tile_data, mode, w_scale, width);
-
canvas.width = width;
canvas.height = height;
var ctx = canvas.getContext('2d');
@@ -3115,12 +3179,14 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
},
/**
- * Draw a track tile for summary tree data.
+ * Draw line (bigwig) data onto tile.
*/
- _draw_summary_tree_tile: function(result, ctx, region, resolution, w_scale) {
- var painter = new painters.SummaryTreePainter(result, region.get('start'), region.get('end'), this.prefs);
- painter.draw(ctx, ctx.canvas.width, ctx.canvas.height, w_scale);
- return new SummaryTreeTile(this, region, resolution, ctx.canvas, result.data, result.max);
+ _draw_line_track_tile: function(result, ctx, mode, resolution, region, w_scale) {
+ var canvas = ctx.canvas,
+ painter = new painters.LinePainter(result.data, region.get('start'), region.get('end'), this.prefs, mode);
+ painter.draw(ctx, canvas.width, canvas.height, w_scale);
+
+ return new LineTrackTile(this, region, resolution, canvas, result.data);
},
/**
@@ -3277,10 +3343,17 @@ var LabelTrack = function (view, container) {
};
extend(LabelTrack.prototype, Track.prototype, {
build_header_div: function() {},
+
init: function() {
// Enable by default because there should always be data when drawing track.
this.enabled = true;
},
+
+ /**
+ * Additional initialization required before drawing track for the first time.
+ */
+ predraw_init: function() {},
+
_draw: function() {
var view = this.view,
range = view.high - view.low,
@@ -3623,8 +3696,8 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
t = function() { track.update_all_min_max(); };
// Add min, max labels.
- this._add_yaxis_label('min', this.drawables[0].prefs.min_value, 'min_value', t);
- this._add_yaxis_label('max', this.drawables[0].prefs.max_value, 'max_value', t);
+ this._add_yaxis_label('min', t);
+ this._add_yaxis_label('max', t);
}
});
@@ -3655,6 +3728,11 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
this.enabled = true;
},
+ /**
+ * Additional initialization required before drawing track for the first time.
+ */
+ predraw_init: function() {},
+
can_draw: Drawable.prototype.can_draw,
/**
@@ -3716,42 +3794,15 @@ var LineTrack = function (view, container, obj_dict) {
saved_values: obj_dict.prefs,
onchange: function() {
track.set_name(track.prefs.name);
- track.vertical_range = track.prefs.max_value - track.prefs.min_value;
track.request_redraw(true);
}
});
this.prefs = this.config.values;
this.visible_height_px = this.config.values.height;
- this.vertical_range = this.config.values.max_value - this.config.values.min_value;
};
extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
- predraw_init: function() {
- var track = this;
- track.vertical_range = undefined;
- return $.getJSON( track.dataset.url(),
- { data_type: 'data', stats: true, chrom: track.view.chrom, low: 0,
- high: track.view.max_high, hda_ldda: track.dataset.get('hda_ldda') }, function(result) {
- track.container_div.addClass( "line-track" );
- var data = result.data;
- if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) {
- // Compute default minimum and maximum values
- var min_value = data.min,
- max_value = data.max;
- // If mean and sd are present, use them to compute a ~95% window
- // but only if it would shrink the range on one side
- min_value = Math.floor( Math.min( 0, Math.max( min_value, data.mean - 2 * data.sd ) ) );
- max_value = Math.ceil( Math.max( 0, Math.min( max_value, data.mean + 2 * data.sd ) ) );
- // Update the prefs
- track.prefs.min_value = min_value;
- track.prefs.max_value = max_value;
- }
- track.vertical_range = track.prefs.max_value - track.prefs.min_value;
- track.total_frequency = data.total_frequency;
- });
- },
-
/**
* Actions to be taken before drawing.
*/
@@ -3759,18 +3810,10 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
before_draw: function() {},
/**
- * Draw LineTrack tile.
+ * Draw track tile.
*/
draw_tile: function(result, ctx, mode, resolution, region, w_scale) {
- // Paint onto canvas.
- var
- canvas = ctx.canvas,
- tile_low = region.get('start'),
- tile_high = region.get('end'),
- painter = new painters.LinePainter(result.data, tile_low, tile_high, this.prefs, mode);
- painter.draw(ctx, canvas.width, canvas.height, w_scale);
-
- return new Tile(this, region, resolution, canvas, result.data);
+ return this._draw_line_track_tile(result, ctx, mode, resolution, region, w_scale);
},
/**
@@ -3811,14 +3854,12 @@ var DiagonalHeatmapTrack = function (view, container, obj_dict) {
saved_values: obj_dict.prefs,
onchange: function() {
track.set_name(track.prefs.name);
- track.vertical_range = track.prefs.max_value - track.prefs.min_value;
this.request_redraw(true);
}
});
this.prefs = this.config.values;
this.visible_height_px = this.config.values.height;
- this.vertical_range = this.config.values.max_value - this.config.values.min_value;
};
extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
/**
@@ -3863,7 +3904,8 @@ var FeatureTrack = function(view, container, obj_dict) {
{ key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
{ key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true,
help: 'Show the number of items in each bin when drawing summary histogram' },
- { key: 'histogram_max', label: 'Histogram maximum', type: 'float', default_value: null, help: 'clear value to set automatically' },
+ { key: 'min_value', label: 'Histogram minimum', type: 'float', default_value: null, help: 'clear value to set automatically' },
+ { key: 'max_value', label: 'Histogram maximum', type: 'float', default_value: null, help: 'clear value to set automatically' },
{ key: 'connector_style', label: 'Connector style', type: 'select', default_value: 'fishbones',
options: [ { label: 'Line with arrows', value: 'fishbone' }, { label: 'Arcs', value: 'arcs' } ] },
{ key: 'mode', type: 'string', default_value: this.mode, hidden: true },
@@ -3905,12 +3947,14 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
* drawn/fetched and shown.
*/
postdraw_actions: function(tiles, width, w_scale, clear_after) {
- TiledTrack.prototype.postdraw_actions.call(this, tiles, clear_after);
+ TiledTrack.prototype.postdraw_actions.call(this, tiles, width, w_scale, clear_after);
var track = this,
i;
// If mode is Coverage and tiles do not share max, redraw tiles as necessary using new max.
+ /*
+ This code isn't used right now because Coverage mode uses predefined max in preferences.
if (track.mode === "Coverage") {
// Get global max.
var global_max = -1;
@@ -3928,7 +3972,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
track.draw_helper(true, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, { more_tile_data: { max: global_max } } );
}
}
- }
+ }
+ */
//
// Update filter attributes, UI.
@@ -3992,17 +4037,17 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
this.action_icons.show_more_rows_icon.hide();
}
},
+
update_auto_mode: function( mode ) {
var mode;
if ( this.mode === "Auto" ) {
if ( mode === "no_detail" ) {
mode = "feature spans";
- } else if ( mode === "summary_tree" ) {
- mode = "coverage histogram";
}
this.action_icons.mode_icon.attr("title", "Set display mode (now: Auto/" + mode + ")");
}
},
+
/**
* Place features in slots for drawing (i.e. pack features).
* this.slotters[level] is created in this method. this.slotters[level]
@@ -4022,15 +4067,13 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
return slotter.slot_features( features );
},
+
/**
* Returns appropriate display mode based on data.
*/
get_mode: function(data) {
- if (data.dataset_type === "summary_tree") {
- mode = "summary_tree";
- }
// HACK: use no_detail mode track is in overview to prevent overview from being too large.
- else if (data.extra_info === "no_detail" || this.is_overview) {
+ if (data.extra_info === "no_detail" || this.is_overview) {
mode = "no_detail";
}
else {
@@ -4054,12 +4097,13 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
}
return mode;
},
+
/**
* Returns canvas height needed to display data; return value is an integer that denotes the
* number of pixels required.
*/
get_canvas_height: function(result, mode, w_scale, canvas_width) {
- if (mode === "summary_tree" || mode === "Coverage") {
+ if (mode === "Coverage" || result.dataset_type === 'bigwig') {
return this.summary_draw_height;
}
else {
@@ -4071,6 +4115,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
return Math.max(MIN_TRACK_HEIGHT, dummy_painter.get_required_height(rows_required, canvas_width) );
}
},
+
/**
* Draw FeatureTrack tile.
* @param result result from server
@@ -4087,10 +4132,10 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
tile_low = region.get('start'),
tile_high = region.get('end'),
left_offset = this.left_offset;
-
- // Drawing the summary tree.
- if (mode === "summary_tree" || mode === "Coverage") {
- return this._draw_summary_tree_tile(result, ctx, region, resolution, w_scale);
+
+ // If data is line track data, draw line track tile.
+ if (result.dataset_type === 'bigwig') {
+ return this._draw_line_track_tile(result, ctx, 'Histogram', resolution, region, w_scale);
}
// Handle row-by-row tracks
@@ -4147,6 +4192,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
return new FeatureTrackTile(track, region, resolution, canvas, result.data, w_scale, mode, result.message, all_slotted, feature_mapper);
},
+
/**
* Returns true if data is compatible with a given mode.
*/
@@ -4155,24 +4201,25 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
if (mode === "Auto") {
return true;
}
- // Histogram mode requires summary_tree data.
+ // Histogram mode requires bigwig data.
else if (mode === "Coverage") {
- return data.dataset_type === "summary_tree";
+ return data.dataset_type === "bigwig";
}
// All other modes--Dense, Squish, Pack--require data + details.
- else if (data.extra_info === "no_detail" || data.dataset_type === "summary_tree") {
+ else if (data.extra_info === "no_detail") {
return false;
}
else {
return true;
}
},
+
/**
* Returns true if data can be subsetted.
*/
can_subset: function(data) {
- // Do not subset summary tree data, entries with a message, or data with no detail.
- if (data.dataset_type === "summary_tree" || data.message || data.extra_info === "no_detail") {
+ // Do not subset entries with a message or data with no detail.
+ if (data.dataset_type === 'bigwig' || data.message || data.extra_info === "no_detail") {
return false;
}
@@ -4217,9 +4264,9 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
* Draw tile.
*/
draw_tile: function(result, ctx, mode, resolution, region, w_scale) {
- // Data could be summary tree data or variant data.
- if (result.dataset_type === 'summary_tree') {
- return this._draw_summary_tree_tile(result, ctx, region, resolution, w_scale);
+ // Data could be coverage data or variant data.
+ if (result.dataset_type === 'bigwig') {
+ return this._draw_line_track_tile(result, ctx, "Histogram", region, resolution, w_scale);
}
else { // result.dataset_type === 'variant'
var view = this.view,
@@ -4235,7 +4282,7 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
* number of pixels required.
*/
get_canvas_height: function(result, mode, w_scale, canvas_width) {
- if (result.dataset_type === 'summary_tree') {
+ if (result.dataset_type === 'bigwig') {
return this.summary_draw_height;
}
else {
@@ -4264,9 +4311,11 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
* Additional initialization required before drawing track for the first time.
*/
predraw_init: function() {
+ var deferreds = [ Track.prototype.predraw_init.call(this) ];
if (!this.dataset.get_metadata('sample_names')) {
- return this.dataset.fetch();
+ deferreds.push(this.dataset.fetch());
}
+ return deferreds;
},
/**
@@ -4277,7 +4326,7 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
TiledTrack.prototype.postdraw_actions.call(this, tiles, width, w_scale, clear_after);
// Add summary/sample labels if needed and not already included.
- if ( !(tiles[0] instanceof SummaryTreeTile) && this.prefs.show_labels) {
+ if ( !(tiles[0] instanceof LineTrackTile) && this.prefs.show_labels) {
var font_size;
// Add and/or style labels.
@@ -4343,7 +4392,6 @@ var ReadTrack = function (view, container, obj_dict) {
{ key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false },
{ key: 'show_differences', label: 'Show differences only', type: 'bool', default_value: true },
{ key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true },
- { key: 'histogram_max', label: 'Histogram maximum', type: 'float', default_value: null, help: 'Clear value to set automatically' },
{ key: 'mode', type: 'string', default_value: this.mode, hidden: true }
],
saved_values: obj_dict.prefs,
diff --git a/static/scripts/viz/visualization.js b/static/scripts/viz/visualization.js
index c80ccc68e85..ada037dcf75 100644
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -505,9 +505,6 @@ var GenomeDataManager = Cache.extend({
// FIXME: constant should go somewhere.
extra_params.num_samples = 1000 * detail_multiplier;
}
- else if (cur_data.dataset_type === 'summary_tree') {
- extra_params.level = Math.min(cur_data.level - 1, 2);
- }
return this.load_data(region, mode, resolution, extra_params);
},
@@ -579,7 +576,7 @@ var GenomeDataManager = Cache.extend({
data_point[0] <= subregion.get('end');
});
},
- 'refseq': function(data, subregion) {
+ refseq: function(data, subregion) {
var seq_start = subregion.get('start') - entry.region.get('start'),
seq_end = entry.data.length - ( entry.region.get('end') - subregion.get('end') );
return entry.data.slice(seq_start, seq_end);