src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.7

Index: src/hg/makeDb/trackDb/trackDb.chainNet.ra
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/trackDb.chainNet.ra,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 4 -r1.6 -r1.7
--- src/hg/makeDb/trackDb/trackDb.chainNet.ra	11 Dec 2009 22:22:43 -0000	1.6
+++ src/hg/makeDb/trackDb/trackDb.chainNet.ra	11 Dec 2009 23:51:26 -0000	1.7
@@ -162,8 +162,9 @@
     otherDb oryLat2
 
 # release alpha until individual gasAcu1 tracks are obsolete
 track chainNetGasAcu1
+release alpha
 compositeTrack on
 shortLabel Stickleback Chain/Net
 longLabel Stickleback (Feb 2006/gasAcu1), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
@@ -184,9 +185,8 @@
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
-release alpha
 
     track chainGasAcu1
     release alpha
     subTrack chainNetGasAcu1
@@ -204,8 +204,9 @@
     type netAlign gasAcu1 chainGasAcu1
 
 # release alpha until individual galGal3 tracks are obsolete
 track chainNetGalGal3
+release alpha
 compositeTrack on
 shortLabel Chicken Chain/Net
 longLabel Chicken (May 2006/galGal3), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
@@ -226,9 +227,8 @@
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
-release alpha
 
     track chainGalGal3
     release alpha
     subTrack chainNetGalGal3
@@ -246,8 +246,9 @@
     type netAlign galGal3 chainGalGal3
 
 # release alpha until ornAna1 individual chain/net tracks phased out
 track chainNetOrnAna1
+release alpha
 compositeTrack on
 shortLabel Platypus Chain/Net
 longLabel Platypus (Mar. 2007/ornAna1), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
@@ -268,9 +269,8 @@
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
-release alpha
 
     track chainOrnAna1
     release alpha
     subTrack chainNetOrnAna1
@@ -367,8 +367,9 @@
     type netAlign monDom5 chainMonDom5
 
 # release alpha until mm9 individual chain/net tracks phased out
 track chainNetMm9
+release alpha
 compositeTrack on
 shortLabel Mouse Chain/Net
 longLabel Mouse (Jul. 2007/mm9), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
@@ -389,9 +390,8 @@
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
-release alpha
 
     track chainMm9
     release alpha
     subTrack chainNetMm9
@@ -489,8 +489,9 @@
     type netAlign equCab2 chainEquCab2
 
 # release alpha until bosTau4 individual tracks phased out
 track chainNetBosTau4
+release alpha
 compositeTrack on
 shortLabel Cow Chain/Net
 longLabel Cow (Oct. 2007/bosTau4), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
@@ -511,9 +512,8 @@
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
-release alpha
 
     track chainBosTau4
     release alpha
     subTrack chainNetBosTau4
@@ -531,8 +531,9 @@
     type netAlign bosTau4 chainBosTau4
 
 # release alpha until bosTau3 individual tracks phased out
 track chainNetBosTau3
+release alpha
 compositeTrack on
 shortLabel Cow Chain/Net
 longLabel Cow (Aug. 2006/bosTau3), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
@@ -553,9 +554,8 @@
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
-release alpha
 
     track chainBosTau3
     release alpha
     subTrack chainNetBosTau3
@@ -573,8 +573,9 @@
     type netAlign bosTau3 chainBosTau3
 
 # release alpha until bosTau2 individual tracks phased out
 track chainNetBosTau2
+release alpha
 compositeTrack on
 shortLabel Cow Chain/Net
 longLabel Cow (Mar. 2005/bosTau2), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
@@ -595,9 +596,8 @@
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
-release alpha
 
     track chainBosTau2
     release alpha
     subTrack chainNetBosTau2
@@ -615,8 +615,9 @@
     type netAlign bosTau2 chainBosTau2
 
 # release alpha until canFam2 individual tracks phased out
 track chainNetCanFam2
+release alpha
 compositeTrack on
 shortLabel Dog Chain/Net
 longLabel Dog (May 2005/canFam2), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
@@ -637,9 +638,8 @@
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
-release alpha
 
     track chainCanFam2
     release alpha
     subTrack chainNetCanFam2
@@ -655,8 +655,50 @@
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign canFam2 chainCanFam2
 
+# release alpha until felCat3 individual tracks phased out
+track chainNetFelCat3
+release alpha
+compositeTrack on
+shortLabel Cat Chain/Net
+longLabel Cat (Mar. 2006/felCat3), 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 240
+color 0,0,0
+altColor 255,255,0
+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 felCat3
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+
+    track chainFelCat3
+    release alpha
+    subTrack chainNetFelCat3
+    subGroups view=chain
+    shortLabel $o_Organism Chain
+    longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+    type chain felCat3
+
+    track netFelCat3
+    release alpha
+    subTrack chainNetFelCat3
+    subGroups view=net
+    shortLabel $o_Organism Net
+    longLabel $o_Organism ($o_date/$o_db) Alignment Net
+    type netAlign felCat3 chainFelCat3
+
 track chainNetVenter
 compositeTrack on
 shortLabel Venter Chain/Net
 longLabel J. Craig Venter Chain and Net Alignments