src/hg/makeDb/trackDb/trackDb.ra 1.532

Index: src/hg/makeDb/trackDb/trackDb.ra
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/trackDb.ra,v
retrieving revision 1.531
retrieving revision 1.532
diff -b -B -U 4 -r1.531 -r1.532
--- src/hg/makeDb/trackDb/trackDb.ra	17 Sep 2009 18:03:51 -0000	1.531
+++ src/hg/makeDb/trackDb/trackDb.ra	18 Sep 2009 21:57:28 -0000	1.532
@@ -2055,9 +2055,52 @@
 spectrum on
 type netAlign fr1 chainFr1
 otherDb fr1
 
+# release alpha until individual fr2 tracks are obsolete
+track chainNetFr2
+release alpha
+compositeTrack on
+shortLabel Fugu Chain/Net
+longLabel Fugu (Oct. 2004/fr2), 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 fr2
+chainMinScore 5000
+chainLinearGap loose
+spectrum on
+html chainNet
+
+    track chainFr2
+    subTrack chainNetFr2
+    subGroups view=chain
+    shortLabel $o_Organism Chain
+    longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+    type chain fr2
+
+    track netFr2
+    subTrack chainNetFr2
+    subGroups view=net
+    shortLabel $o_Organism Net
+    longLabel $o_Organism ($o_date/$o_db) Alignment Net
+    type netAlign fr2 chainFr2
+
+
+# release beta until composite chainNetFr2 track becomes the default
 track chainFr2
+release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 139.8
@@ -2069,9 +2112,11 @@
 spectrum on
 type chain fr2
 otherDb fr2
 
+# release beta until composite chainNetFr2 track becomes the default
 track netFr2
+release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 139.9
@@ -2307,9 +2352,52 @@
 spectrum on
 type netAlign petMar1 chainPetMar1
 otherDb petMar1
 
+# release alpha until individual oryLat2 tracks are obsolete
+track chainNetOryLat2
+release alpha
+compositeTrack on
+shortLabel Medaka Chain/Net
+longLabel Medaka (Oct. 2005/oryLat2), 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 165.5
+color 100,50,0
+altColor 255,240,200
+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 hg19
+chainMinScore 3000
+chainLinearGap medium
+html chainNet
+
+    track chainOryLat2
+    subTrack chainNetOryLat2
+    subGroups view=chain
+    shortLabel $o_Organism Chain 
+    longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+    type chain oryLat2
+    otherDb oryLat2
+
+    track netOryLat2
+    subTrack chainNetOryLat2
+    subGroups view=net
+    shortLabel $o_Organism Net
+    longLabel $o_Organism ($o_date/$o_db) Alignment Net
+    type netAlign oryLat2 chainOryLat2
+    otherDb oryLat2
+
+# release beta until composite oryLat2 tracks become the default
 track chainOryLat2
+release beta
 shortLabel $o_Organism Chain 
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 165.49
@@ -2321,9 +2409,11 @@
 spectrum on
 type chain oryLat2
 otherDb oryLat2
 
+# release beta until composite oryLat2 tracks become the default
 track netOryLat2
+release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 165.50
@@ -2355,9 +2445,51 @@
 spectrum on
 type netAlign oryLat1 chainOryLat1
 otherDb oryLat1
 
+# release alpha until individual gasAcu1 tracks are obsolete
+track chainNetGasAcu1
+compositeTrack on
+shortLabel Stickleback Chain/Net
+longLabel Stickleback (Feb 2006/gasAcu1), 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 181
+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 gasAcu1
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+release alpha
+
+    track chainGasAcu1
+    subTrack chainNetGasAcu1
+    subGroups view=chain
+    shortLabel $o_Organism Chain
+    longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+    type chain gasAcu1
+
+    track netGasAcu1
+    subTrack chainNetGasAcu1
+    subGroups view=net
+    shortLabel $o_Organism Net
+    longLabel $o_Organism ($o_date/$o_db) Alignment Net
+    type netAlign gasAcu1 chainGasAcu1
+
+# release beta until composite gasAcu1 tracks become the default
 track chainGasAcu1
+release beta
 shortLabel $o_Organism Chain
 longLabel $o_Organism ($o_date/$o_db) Chained Alignments
 group compGeno
 priority 165.51
@@ -2368,9 +2500,11 @@
 spectrum on
 type chain gasAcu1
 otherDb gasAcu1
 
+# release beta until composite gasAcu1 tracks become the default
 track netGasAcu1
+release beta
 shortLabel $o_Organism Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 165.52
@@ -2478,9 +2612,9 @@
 # release alpha until individual galGal3 tracks are obsolete
 track chainNetGalGal3
 compositeTrack on
 shortLabel Chicken Chain/Net
-longLabel Chicken (May. 2006/galGal3), Chain and Net Alignments
+longLabel Chicken (May 2006/galGal3), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense