#!/usr/bin/env perl

use strict;
use warnings;
use File::Basename;
use FindBin qw($Bin);
use lib "$Bin";
use HgAutomate;

sub usage() {
  printf STDERR "usage: asmHubChainNetTrackDb.pl <buildDir>\n";
  printf STDERR "expecting to find directories: buildDir/trackData/lastz.*/\n";
  printf STDERR "where each /lastz.*/ directory is one completed lastz/chainNet\n";
  printf STDERR "and basename(buildDir) is the 'target' sequence name\n";
  exit 255;
}

my $argc = scalar(@ARGV);

if ($argc != 1) {
  usage;
}

my $buildDir = shift;
my $targetDb = basename($buildDir);
my @tParts = split('_', $targetDb);
my $targetAccession = "$tParts[0]_$tParts[1]";
my @queryList;

`mkdir -p $buildDir/bbi`;
`mkdir -p $buildDir/liftOver`;

open (DL, "ls -d $buildDir/trackData/lastz.*|") or die "can not list $buildDir/trackData/lastz.*";
while (my $lastzDir = <DL>) {
  chomp $lastzDir;
  my $queryDb = basename($lastzDir);
  $queryDb =~ s/lastz.//;
  push @queryList, $queryDb;
}
close (DL);

# foreach my $queryDb (@queryList) {
#    printf STDERR "%s vs. %s\n", $queryDb, $targetDb;
# }

##### begin trackDb output ######
printf "track %sChainNet\n", $targetDb;
printf "compositeTrack on
shortLabel Chain/Net
longLabel Chain and Net alignments to target sequence: %s\n", $targetDb;
printf "subGroup1 view Views chain=Chains net=Nets\n";
printf "subGroup2 species Species";
my $N = 0;
foreach my $queryDb (@queryList) {
  printf " s%03d=%s", $N++, $queryDb;
}
printf "\n";
printf "subGroup3 clade Clade c00=human\n";
printf "dragAndDrop subTracks\n";
printf "visibility hide
group compGeno
color 0,0,0
altColor 255,255,0
type bed 3
chainLinearGap loose
chainMinScore 5000
dimensions dimensionX=clade dimensionY=species
sortOrder species=+ view=+ clade=+
configurable on\n";
printf "html html/%s.chainNet\n", $targetDb;

printf "
    track %sChainNetViewchain
    shortLabel  Chains
    view chain
    visibility pack
    subTrack %sChainNet
    spectrum on
", $targetDb, $targetDb;

$N = 0;
my $chainNetPriority = 1;
foreach my $queryDb (@queryList) {
  my $QueryDb = ucfirst($queryDb);
  my $overChain="${targetAccession}.${queryDb}.over.chain.gz";
  my $overToChain="${targetAccession}To${QueryDb}.over.chain.gz";
  my $lastzDir="lastz.$queryDb";
  `rm -f $buildDir/bbi/$targetDb.chain${QueryDb}.bb`;
  `rm -f $buildDir/bbi/$targetDb.chain${QueryDb}Link.bb`;
  `rm -f $buildDir/liftOver/${overToChain}`;
  if ( -s "$buildDir/trackData/$lastzDir/axtChain/${overChain}" ) {
     `ln -s ../trackData/$lastzDir/axtChain/${overChain} $buildDir/liftOver/${overToChain}`;
  } else {
     printf STDERR "# NOT FOUND: '%s'\n", "$buildDir/trackData/$lastzDir/axtChain/${overChain}";
  }
  `ln -s ../trackData/lastz.$queryDb/axtChain/chain${QueryDb}.bb  $buildDir/bbi/$targetDb.chain${QueryDb}.bb`;
  `ln -s ../trackData/lastz.$queryDb/axtChain/chain${QueryDb}Link.bb  $buildDir/bbi/$targetDb.chain${QueryDb}Link.bb`;
  my $queryDate = "some date";
  my $queryAsmName = "";
  if ( $queryDb !~ m/^GC/ ) {
    $queryDate = `hgsql -N -e 'select description from dbDb where name="$queryDb"' hgcentraltest | sed -e 's/ (.*//;'`;
    chomp $queryDate;
  } else {
    ($queryDate, $queryAsmName) = &HgAutomate::hubDateName($queryDb);
  }
  printf "
        track chain%s
        subTrack %sChainNetViewchain off
        subGroups view=chain species=s%03d clade=c00
        shortLabel %s Chain
        longLabel %s%s (%s) Chained Alignments
        type bigChain %s
        bigDataUrl bbi/%s.chain%s.bb
        linkDataUrl bbi/%s.chain%sLink.bb
        otherDb %s
        html html/%s.chainNet
        priority %d
", $QueryDb, $targetDb, $N, $queryDb, $queryDb, $queryAsmName, $queryDate, $queryDb, $targetDb,
     $QueryDb, $targetDb, $QueryDb, $queryDb, $targetDb, $chainNetPriority++;

  if ( -s "$buildDir/trackData/lastz.$queryDb/axtChain/chainSyn${QueryDb}.bb" ) {
    `rm -f $buildDir/bbi/$targetDb.chainSyn${QueryDb}.bb`;
    `rm -f $buildDir/bbi/$targetDb.chainSyn${QueryDb}Link.bb`;
    `ln -s ../trackData/lastz.$queryDb/axtChain/chainSyn${QueryDb}.bb  $buildDir/bbi/$targetDb.chainSyn${QueryDb}.bb`;
    `ln -s ../trackData/lastz.$queryDb/axtChain/chainSyn${QueryDb}Link.bb  $buildDir/bbi/$targetDb.chainSyn${QueryDb}Link.bb`;
  printf "
        track chainSyn%s
        subTrack %sChainNetViewchain off
        subGroups view=chain species=s%03d clade=c00
        shortLabel %s synChain
        longLabel %s%s (%s) Syntenic Chained Alignments
        type bigChain %s
        bigDataUrl bbi/%s.chainSyn%s.bb
        linkDataUrl bbi/%s.chainSyn%sLink.bb
        otherDb %s
        html html/%s.chainNet
        priority %d
", $QueryDb, $targetDb, $N, $queryDb, $queryDb, $queryAsmName, $queryDate, $queryDb, $targetDb,
     $QueryDb, $targetDb, $QueryDb, $queryDb, $targetDb, $chainNetPriority++;

  }

  if ( -s "$buildDir/trackData/lastz.$queryDb/axtChain/chainRBest${QueryDb}.bb" ) {
    `rm -f $buildDir/bbi/$targetDb.chainRBest${QueryDb}.bb`;
    `rm -f $buildDir/bbi/$targetDb.chainRBest${QueryDb}Link.bb`;
    `ln -s ../trackData/lastz.$queryDb/axtChain/chainRBest${QueryDb}.bb  $buildDir/bbi/$targetDb.chainRBest${QueryDb}.bb`;
    `ln -s ../trackData/lastz.$queryDb/axtChain/chainRBest${QueryDb}Link.bb  $buildDir/bbi/$targetDb.chainRBest${QueryDb}Link.bb`;
  printf "
        track chainRBest%s
        subTrack %sChainNetViewchain off
        subGroups view=chain species=s%03d clade=c00
        shortLabel %s rbChain
        longLabel %s%s (%s) Reciprocal Best Chained Alignments
        type bigChain %s
        bigDataUrl bbi/%s.chainRBest%s.bb
        linkDataUrl bbi/%s.chainRBest%sLink.bb
        otherDb %s
        html html/%s.chainNet
        priority %d
", $QueryDb, $targetDb, $N, $queryDb, $queryDb, $queryAsmName, $queryDate, $queryDb, $targetDb,
     $QueryDb, $targetDb, $QueryDb, $queryDb, $targetDb, $chainNetPriority++;

  }

#    ln -s ../trackData/$lastzDir/axtChain/chainLiftOver${OtherDb}.bb $buildDir/bbi/${asmId}.chainLiftOver$OtherDb.bb
#    ln -s ../trackData/$lastzDir/axtChain/chainLiftOver${OtherDb}Link.bb $buildDir/bbi/${asmId}.chainLiftOver${OtherDb}Link.bb
#    ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.liftOverNet.bb $buildDir/bbi/${asmId}.$otherDb.liftOverNet.bb
#    ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.liftOverNet.summary.bb $buildDir/bbi/${asmId}.$otherDb.liftOverNet.summary.bb

  if ( -s "$buildDir/trackData/lastz.$queryDb/axtChain/chainLiftOver${QueryDb}.bb" ) {
    `rm -f $buildDir/bbi/$targetDb.chainLiftOver${QueryDb}.bb`;
    `rm -f $buildDir/bbi/$targetDb.chainLiftOver${QueryDb}Link.bb`;
    `ln -s ../trackData/lastz.$queryDb/axtChain/chainLiftOver${QueryDb}.bb  $buildDir/bbi/$targetDb.chainLiftOver${QueryDb}.bb`;
    `ln -s ../trackData/lastz.$queryDb/axtChain/chainLiftOver${QueryDb}Link.bb  $buildDir/bbi/$targetDb.chainLiftOver${QueryDb}Link.bb`;

  printf "
        track chainLiftOver%s
        subTrack %sChainNetViewchain off
        subGroups view=chain species=s%03d clade=c00
        shortLabel %s loChain
        longLabel %s%s (%s) Lift Over Chained Alignments
        type bigChain %s
        bigDataUrl bbi/%s.chainLiftOver%s.bb
        linkDataUrl bbi/%s.chainLiftOver%sLink.bb
        otherDb %s
        html html/%s.chainNet
        priority %d
", $QueryDb, $targetDb, $N, $queryDb, $queryDb, $queryAsmName, $queryDate, $queryDb, $targetDb,
     $QueryDb, $targetDb, $QueryDb, $queryDb, $targetDb, $chainNetPriority++;

  }
  $N++;
}

printf "
    track %sMafNetViewnet
    shortLabel Nets
    view net
    visibility dense
    subTrack %sChainNet
", $targetDb, $targetDb;

$N = 0;
$chainNetPriority = 1;
foreach my $queryDb (@queryList) {
  my @targetAccession = split('_', $targetDb);
  my $targetAcc = sprintf("%s_%s", $targetAccession[0], $targetAccession[1]);
  my $QueryDb = ucfirst($queryDb);
  my $queryDate = "some date";
  my $queryAsmName = "";
  `rm -f $buildDir/bbi/$targetDb.${queryDb}.net.bb`;
  `rm -f $buildDir/bbi/$targetDb.${queryDb}.net.summary.bb`;
  if ( -s "../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.net.bb" ) {
printf STDERR "constructing net.bb links $targetDb $queryDb\n";
  `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.net.bb  $buildDir/bbi/$targetDb.${queryDb}.net.bb`;
  `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.net.summary.bb  $buildDir/bbi/$targetDb.${queryDb}.net.summary.bb`;
  if ( $queryDb !~ m/^GC/ ) {
    $queryDate = `hgsql -N -e 'select description from dbDb where name="$queryDb"' hgcentraltest | sed -e 's/ (.*//;'`;
    chomp $queryDate;
  } else {
    ($queryDate, $queryAsmName) = &HgAutomate::hubDateName($queryDb);
  }
    printf "
        track net%s
        parent %sMafNetViewnet
        subGroups view=net species=s%03d clade=c00
        shortLabel %s mafNet
        longLabel %s%s (%s) mafNet Alignment
        type bigMaf
        bigDataUrl bbi/%s.%s.net.bb
        summary bbi/%s.%s.net.summary.bb
        speciesOrder %s
        html html/%s.chainNet
        priority %d
", $QueryDb, $targetDb, $N, $queryDb, $queryDb, $queryAsmName, $queryDate, $targetDb, $queryDb, $targetDb, $queryDb, $queryDb, $targetDb, $chainNetPriority++;
  }

  `rm -f $buildDir/bbi/$targetDb.${queryDb}.synNet.bb`;
  `rm -f $buildDir/bbi/$targetDb.${queryDb}.synNet.summary.bb`;
  if ( -s "$buildDir/trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.synNet.bb" ) {
printf STDERR "constructing synNet.bb links $targetDb $queryDb\n";
  `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.synNet.bb  $buildDir/bbi/$targetDb.${queryDb}.synNet.bb`;
  `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.synNet.summary.bb  $buildDir/bbi/$targetDb.${queryDb}.synNet.summary.bb`;
    printf "
        track synNet%s
        parent %sMafNetViewnet
        subGroups view=net species=s%03d clade=c00
        shortLabel %s synNet
        longLabel %s%s (%s) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/%s.%s.synNet.bb
        summary bbi/%s.%s.synNet.summary.bb
        speciesOrder %s
        html html/%s.chainNet
        priority %d
", $QueryDb, $targetDb, $N, $queryDb, $queryDb, $queryAsmName, $queryDate, $targetDb, $queryDb, $targetDb, $queryDb, $queryDb, $targetDb, $chainNetPriority++;

  }

  `rm -f $buildDir/bbi/$targetDb.${queryDb}.rbestNet.bb`;
  `rm -f $buildDir/bbi/$targetDb.${queryDb}.rbestNet.summary.bb`;
  if ( -s "$buildDir/trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.rbestNet.bb" ) {
printf STDERR "constructing rbestNet.bb links $targetDb $queryDb\n";
  `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.rbestNet.bb  $buildDir/bbi/$targetDb.${queryDb}.rbestNet.bb`;
  `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.rbestNet.summary.bb  $buildDir/bbi/$targetDb.${queryDb}.rbestNet.summary.bb`;
    printf "
        track rbestNet%s
        parent %sMafNetViewnet
        subGroups view=net species=s%03d clade=c00
        shortLabel %s rbestNet
        longLabel %s%s (%s) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/%s.%s.rbestNet.bb
        summary bbi/%s.%s.rbestNet.summary.bb
        speciesOrder %s
        html html/%s.chainNet
        priority %d
", $QueryDb, $targetDb, $N, $queryDb, $queryDb, $queryAsmName, $queryDate, $targetDb, $queryDb, $targetDb, $queryDb, $queryDb, $targetDb, $chainNetPriority++;

  }

  `rm -f $buildDir/bbi/$targetDb.${queryDb}.liftOverNet.bb`;
  `rm -f $buildDir/bbi/$targetDb.${queryDb}.liftOverNet.summary.bb`;
  if ( -s "$buildDir/trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.liftOverNet.bb" ) {
printf STDERR "constructing liftOverNet links $targetDb $queryDb\n";
  `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.liftOverNet.bb  $buildDir/bbi/$targetDb.${queryDb}.liftOverNet.bb`;
  `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.liftOverNet.summary.bb  $buildDir/bbi/$targetDb.${queryDb}.liftOverNet.summary.bb`;
    printf "
        track liftOverNet%s
        parent %sMafNetViewnet
        subGroups view=net species=s%03d clade=c00
        shortLabel %s liftOverNet
        longLabel %s%s (%s) Lift Over Net Alignment
        type bigMaf
        bigDataUrl bbi/%s.%s.liftOverNet.bb
        summary bbi/%s.%s.liftOverNet.summary.bb
        speciesOrder %s
        html html/%s.chainNet
        priority %d
", $QueryDb, $targetDb, $N, $queryDb, $queryDb, $queryAsmName, $queryDate, $targetDb, $queryDb, $targetDb, $queryDb, $queryDb, $targetDb, $chainNetPriority++;

  }
  $N++;
}

printf "\n" if ($N > 0);