Index: src/hg/makeDb/trackDb/trackDb.chainNet.ra
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/trackDb.chainNet.ra,v
retrieving revision 1.16
retrieving revision 1.17
diff -b -B -U 4 -r1.16 -r1.17
--- src/hg/makeDb/trackDb/trackDb.chainNet.ra	23 Dec 2009 19:06:33 -0000	1.16
+++ src/hg/makeDb/trackDb/trackDb.chainNet.ra	23 Dec 2009 20:09:01 -0000	1.17
@@ -41,8 +41,50 @@
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign fr2 chainFr2
 
+# release alpha until individual fr1 tracks are obsolete
+track chainNetFr1
+release alpha
+compositeTrack on
+shortLabel $o_db Chain/Net
+longLabel Fugu (Aug. 2002/fr1), 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 159
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
+matrixHeader A, C, G, T
+otherDb fr1
+chainMinScore 5000
+chainLinearGap loose
+spectrum on
+html chainNet
+
+    track chainFr1
+    release alpha
+    subTrack chainNetFr1
+    subGroups view=chain
+    shortLabel $o_Organism Chain
+    longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+    type chain fr1
+
+    track netFr1
+    release alpha
+    subTrack chainNetFr1
+    subGroups view=net
+    shortLabel $o_Organism Net
+    longLabel $o_Organism ($o_date/$o_db) Alignment Net
+    type netAlign fr1 chainFr1
+
 track chainNetTetNig2
 compositeTrack on
 shortLabel Tetraodon Chain/Net
 longLabel Tetraodon (Mar. 2007/tetNig2), Chain and Net Alignments

