cd9e9bc3bea3e5438c2da40e57ffcb69c8fa2672
max
  Fri May 19 13:35:52 2017 -0700
adding all.joiner for the interactions track, refs #13634

diff --git src/hg/hgGeneGraph/hgGeneGraph src/hg/hgGeneGraph/hgGeneGraph
index 6164183..f8cb051 100755
--- src/hg/hgGeneGraph/hgGeneGraph
+++ src/hg/hgGeneGraph/hgGeneGraph
@@ -343,38 +343,38 @@
                                   )
     # store the preformatted text as htmlText
     htmlText = htmlGenerator.data()
     return htmlText
 
 def reqMinSupp(links, minArtSupp, maxResCount, targetGene):
     """ remove all 'text mining only' links with less than minArtSupp supporting documents
         The only exception is targetGene which we always want to stay connected
 
         Also remove links that are PPI-only and have a high minResCount.
     """
     newLinks = defaultdict(set)
     genes = set()
     targetConns = {}
     for genePair, linkData in links.iteritems():
-        docCount, dbCount, tagSet, minResCount = linkData[:4]
+        docCount, dbCount, tagSet, pairMinResCount = linkData[:4]
         if targetGene in genePair:
             targetConns[genePair] = linkData
         # remove text-mining links with only one article
         if "text" in tagSet and docCount < minArtSupp:
             continue
         # remove noisy PPI links 
-        if len(tagSet)==1 and "ppi" in tagSet and minResCount > maxResCount:
+        if len(tagSet)==1 and "ppi" in tagSet and pairMinResCount > maxResCount: 
             continue
         genes.update(genePair)
         newLinks[genePair] = linkData
 
     # is the target gene still connected to something? If not add it back and
     # accept that these links are less than minSupp
     if targetGene not in genes:
         for genePair, linkData in targetConns.iteritems():
             newLinks[genePair] = linkData
     return newLinks
 
 def scorePair(docCount, tagSet):
     " return the score for a gene pair "
     # pairs that have no text mining results get assigned artifical
     # article counts, based on this query:
@@ -453,31 +453,31 @@
     highLinksFiltered = defaultdict(set)
     for pair, linkData in graphLinks.iteritems():
         g1, g2 = pair
         if pair in highPairs or g1==targetGene or g2==targetGene:
             #print "high", pair
             highLinksFiltered[pair] = linkData
         else:
             #print "low"
             lowLinks[pair] = linkData
     return highLinksFiltered, lowLinks
         
 
 def splitHighLowLinks(links, gene, minSupp, lowLinks, geneCount):
     """ split into two sets of links: high = best geneCount genes and best 2*geneCount links
     between them, low = all the others"""
-    links = reqMinSupp(links, minSupp, LTCUTOFF, gene)
+    links = reqMinSupp(links, minSupp, 999999999, gene)
 
     highLinks, lowLinks = limitGenes(links, geneCount, gene, lowLinks)
     #print "lowLinks", lowLinks, "<p>"
     #print "highLinks", highLinks, "<p>"
 
     highLinks, lowLinks = limitLinks(highLinks, lowLinks, 2*geneCount, gene)
     #print "bestLinks", highLinks, "<p>"
 
     return highLinks, lowLinks
 
 def queryLinks(conn, gene=None, genes=None):
     """ query the mysql table ggLink for either all links to gene
     or all links between all pairs of genes
     Return result as a dict (gene1, gene2) ->
     (docCount, tagSet, snippet)
@@ -1957,31 +1957,31 @@
 
     page = getCgiVar("page")
     if page=="stats":
         showStats()
         exit(0)
 
     showGraphBrowser()
 
 def main():
     cgiSetup()
 
     format = getCgiVar("format")
     if format in ["pdf", "svg", "sif", "json"]:
         conn = sqlConnect(GGDB)
         gene, alg, addNeighbors, sortByCount, geneCount = parseGraphArgs()
-        graphLinks, lowLinks = buildGraph(conn, gene, geneCount, 2, addNeighbors)
+        graphLinks, lowLinks = buildGraph(conn, gene, geneCount, MINSUPP, addNeighbors)
         weightedLinks, minAbsCount = flattenLink(graphLinks)
         printGraph(conn, weightedLinks, alg, addNeighbors, gene, format)
         sys.exit(0)
 
 
     printContentType()
 
     if cgiString("debug") is not None:
         global DEBUG
         DEBUG = True
 
     htmlHeader()
     printInlineAndStyles()
     htmlMiddle()
     htmlPageEnd()