src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.2

Index: src/hg/makeDb/trackDb/trackDb.chainNet.ra
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/trackDb.chainNet.ra,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/makeDb/trackDb/trackDb.chainNet.ra	7 Dec 2009 22:00:51 -0000	1.1
+++ src/hg/makeDb/trackDb/trackDb.chainNet.ra	8 Dec 2009 23:44:45 -0000	1.2
@@ -366,8 +366,50 @@
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign mm9 chainMm9
 
+# release alpha until rn4 individual chain/net tracks phased out
+track chainNetRn4
+release alpha
+compositeTrack on
+shortLabel Rat Chain/Net
+longLabel Rat (Nov. 2004/rn4), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 209
+color 100,50,0
+altColor 255,240,200
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb rn4
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+
+    track chainRn4
+    release alpha
+    subTrack chainNetRn4
+    subGroups view=chain
+    shortLabel $o_Organism Chain
+    longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+    type chain rn4
+
+    track netRn4
+    release alpha
+    subTrack chainNetRn4
+    subGroups view=net
+    shortLabel $o_Organism Net
+    longLabel $o_Organism ($o_date/$o_db) Alignment Net
+    type netAlign rn4 chainRn4
+
 track chainNetEquCab2
 compositeTrack on
 shortLabel Horse Chain/Net
 longLabel Horse (Sep. 2007/equCab2), Chain and Net Alignments
@@ -483,8 +525,48 @@
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign venter1 chainVenter1
     otherDb venter1
 
+track chainNetHg18
+release alpha
+compositeTrack on
+shortLabel Human Chain/Net
+longLabel Human (Mar. 2006/hg18), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 498
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90
+matrixHeader A, C, G, T
+otherDb hg18
+chainMinScore 3000
+chainLinearGap medium
+html chainNet
+
+    track chainHg18
+    release alpha
+    subTrack chainNetHg18
+    subGroups view=chain
+    shortLabel $o_Organism Chain
+    longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+    type chain hg18
+
+    track netHg18
+    release alpha
+    subTrack chainNetHg18
+    subGroups view=net
+    shortLabel $o_Organism Net
+    longLabel $o_Organism ($o_date/$o_db) Alignment net
+    type netAlign hg18 chainHg18
+
 track chainNetHg19
 compositeTrack on
 shortLabel Human Chain/Net
 longLabel Human (Feb. 2009/hg19), Chain and Net Alignments