src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.3

Index: src/hg/makeDb/trackDb/trackDb.chainNet.ra
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/trackDb.chainNet.ra,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 4 -r1.2 -r1.3
--- src/hg/makeDb/trackDb/trackDb.chainNet.ra	8 Dec 2009 23:44:45 -0000	1.2
+++ src/hg/makeDb/trackDb/trackDb.chainNet.ra	9 Dec 2009 00:26:33 -0000	1.3
@@ -137,9 +137,9 @@
 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
+otherDb oryLat2
 chainMinScore 3000
 chainLinearGap medium
 html chainNet
 
@@ -286,8 +286,49 @@
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign ornAna1 chainOrnAna1
 
+track chainNetMonDom4
+release alpha
+compositeTrack on
+shortLabel Opossum Chain/Net
+longLabel Opossum (Jan. 2006/monDom4), 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 191
+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 monDom4
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+
+    track chainMonDom4
+    release alpha
+    subTrack chainNetMonDom4
+    subGroups view=chain
+    shortLabel $o_Organism Chain
+    longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+    type chain monDom4
+
+    track netMonDom4
+    release alpha
+    subTrack chainNetMonDom4
+    subGroups view=net
+    shortLabel $o_Organism Net
+    longLabel $o_Organism ($o_date/$o_db) Alignment Net
+    type netAlign monDom4 chainMonDom4
+
 track chainNetMonDom5
 compositeTrack on
 shortLabel Opossum Chain/Net
 longLabel Opossum (Oct. 2006/monDom5), Chain and Net Alignments
@@ -602,8 +643,128 @@
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment net
     type netAlign hg19 chainHg19
 
+track chainNetPanTro2
+release alpha
+compositeTrack on
+shortLabel Chimp Chain/Net
+longLabel Chimp (Mar. 2006/panTro2), 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 100,50,0
+altColor 255,240,200
+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 panTro2
+chainMinScore 3000
+chainLinearGap medium
+html chainNet
+
+    track chainPanTro2
+    release alpha
+    subTrack chainNetPanTro2
+    subGroups view=chain
+    shortLabel $o_Organism Chain
+    longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+    type chain panTro2
+
+    track netPanTro2
+    release alpha
+    subTrack chainNetPanTro2
+    subGroups view=net
+    shortLabel $o_Organism Net
+    longLabel $o_Organism ($o_date/$o_db) Alignment net
+    type netAlign panTro2 chainPanTro2
+
+track chainNetPonAbe2
+release alpha
+compositeTrack on
+shortLabel Orangutan Chain/Net
+longLabel Orangutan (Jul. 2007/ponAbe2), 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 100,50,0
+altColor 255,240,200
+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 ponAbe2
+chainMinScore 3000
+chainLinearGap medium
+html chainNet
+
+    track chainPonAbe2
+    release alpha
+    subTrack chainNetPonAbe2
+    subGroups view=chain
+    shortLabel $o_Organism Chain
+    longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+    type chain ponAbe2
+
+    track netPonAbe2
+    release alpha
+    subTrack chainNetPonAbe2
+    subGroups view=net
+    shortLabel $o_Organism Net
+    longLabel $o_Organism ($o_date/$o_db) Alignment net
+    type netAlign ponAbe2 chainPonAbe2
+
+track chainNetRheMac2
+release alpha
+compositeTrack on
+shortLabel Rhesus Chain/Net
+longLabel Rhesus (Jan. 2006/rheMac2), 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 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 rheMac2
+chainMinScore 3000
+chainLinearGap medium
+html chainNet
+
+    track chainRheMac2
+    release alpha
+    subTrack chainNetRheMac2
+    subGroups view=chain
+    shortLabel $o_Organism Chain
+    longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+    type chain rheMac2
+
+    track netRheMac2
+    release alpha
+    subTrack chainNetRheMac2
+    subGroups view=net
+    shortLabel $o_Organism Net
+    longLabel $o_Organism ($o_date/$o_db) Alignment net
+    type netAlign rheMac2 chainRheMac2
+
 track chainNetPoodle
 compositeTrack on
 shortLabel Poodle Chain/Net
 longLabel Poodle Chain and Net Alignments