GDBgui.pm from eXtensible Genome Data Broker at Krugle

Show GDBgui.pm syntax highlighted

#!/usr/bin/perl
package GDBgui;

do 'SITEDEF.pl';

use CGI ":all";

sub new{
  my $class = shift;
  my ($argHR) = @_;
  my $self = {};
  bless $self, ref($class) || $class;
  return $self;
}

sub printXGDB_page{
  my ($self,$cpHR) = @_;

  $self->printXGDB_Head($cpHR);
  $self->printXGDB_StartHtml($cpHR);
  print $cpHR->{preHeader};
  $self->print_SiteHeader($cpHR);
  print "<div align=\"center\">" . $cpHR->{main} . "</div>\n";
  print $cpHR->{preFooter};
  $self->print_SiteFooter($cpHR);
  $self->printXGDB_EndHtml($cpHR);

  return 1;
}

sub printXGDB_Head{
  my ($self,$cpHR) = @_;

  ## set default HTML <head> properties ($cpHR->{headHR})
  
  print header(%{$cpHR->{headHR}}) . "\n";;

  return 1;
}

sub printXGDB_StartHtml{
  my ($self,$cpHR) = @_;

  ## set default HTML <html> properties ($cpHR->{htmlHR})
  $cpHR->{htmlHR}->{-title} =(exists($cpHR->{htmlHR}->{-title})) ? $cpHR->{htmlHR}->{-title} : $SITENAME;
  $cpHR->{htmlHR}->{-bgcolor} = "#FFFFFF" if(!exists($cpHR->{htmlHR}->{-bgcolor}));
  $cpHR->{htmlHR}->{-style} = {-src=>$defaultStyleSheet} if(!exists($cpHR->{htmlHR}->{-style}));

  if(exists($cpHR->{htmlHR}->{-onLoad})){
    $cpHR->{htmlHR}->{-onLoad} .= 'reloadTracks();';
#    $cpHR->{htmlHR}->{-onLoad} .= 'reloadTracks();mmLoadMenus();';
  }elsif($cpHR->{htmlHR}->{-onLoad} !~ /reloadTracks\(/){
    $cpHR->{htmlHR}->{-onLoad} = 'reloadTracks();';
#    $cpHR->{htmlHR}->{-onLoad} = 'reloadTracks();mmLoadMenus();';
  }

  if(exists($cpHR->{htmlHR}->{-script})){
    push(@{$cpHR->{htmlHR}->{-script}},({-src=>"${JSPATH}XGDBheader.js"},{-src=>"${JSPATH}tracks.js"},{-src=>"${JSPATH}gdbmenus.js"},{-src=>"${JSPATH}mm_menu.js"}));
  }else{
    $cpHR->{htmlHR}->{-script}  =  [{-src=>"${JSPATH}XGDBheader.js"},{-src=>"${JSPATH}tracks.js"},{-src=>"${JSPATH}gdbmenus.js"},{-src=>"${JSPATH}mm_menu.js"}];
  }

  print start_html(%{$cpHR->{htmlHR}}) . "\n";

  return 1;
}

sub printXGDB_EndHtml{
  my ($self,$cpHR) = @_;

  print end_html();

  return 1;
}

sub print_SiteHeader{
  my ($self,$cpHR) = @_;
  my $fontstyle  = "'font-family: Verdana,Arial,sans-serif;font-size: 12px;'";
  my $fontstyle2 = "'font-family: Verdana,Arial,sans-serif;font-size: 16px;'";
  my $link_color = (exists($cpHR->{gseg_gi}))?'#0000FF':'#FFFFFF';
 

  ## Print header javascript
  my $CHRLIST = join(',',@{$DBver[$cpHR->{dbid}]->{chrSIZE}});
  print <<END_OF_PRINT;
<SCRIPT LANGUAGE="JavaScript">
var ChrLen   = new Array(${CHRLIST});
var GSQwebpath = "${GSQwebpath}";
var UCAwebpath = "${ucaPATH}AnnotationTool.pl";
var CGIPATH  = "${CGIPATH}";
var HAS_TRACK_CONTROL = 0;
var xgdb_state = "${SITENAMEshort}_state";
</SCRIPT>

END_OF_PRINT


  ## Print form tag and default inputs
  print <<END_OF_PRINT;
<form METHOD="POST"  ENCTYPE="multipart/form-data" NAME="guiFORM">
<input type="text" name="wsize" value="$cpHR->{wsize}" class='debug'>
<input type="text" name="resid" value="$cpHR->{resid}" class='debug'>
<input type="text" name="curDBID" value="$cpHR->{dbid}" class='debug'>
<input type="text" name="userid" value="$cpHR->{USERid}" class='debug'>
<input type="text" name="trackORDER" value="$cpHR->{trackORDER}" class='debug'>
<input type="text" name="trackVISIBLE" value="$cpHR->{trackVISIBLE}" class='debug'>
<input type="text" name="trackDATA" value="$cpHR->{trackDATA}" class='debug'>
<input type="text" name="customORDER" value="$cpHR->{customORDER}" class='debug'>
<input type="text" name="customVISIBLE" value="$cpHR->{customVISIBLE}" class='debug'>

END_OF_PRINT


  ## Print logo and title ( header top )
  print <<END_OF_PRINT;
<MAP name="ftuLOGO">
<AREA shape="RECT" coords="0,0,136,18" href="${GDBDIR}site_map.php">
<AREA shape="RECT" coords="0,18,136,35" href="$WEBMASTER">
</MAP>
<div id='HeaderLogos'>
<a href="${GDBhome}"><img id='topLeftLogo' src="${TOP_LEFT_LOGO}"></a>
<img id='topCenterLogo' src="${TOP_CENTER_LOGO}">
<img id='topRightLogo' src="${TOP_RIGHT_LOGO}" usemap="#ftuLOGO">
</div>

END_OF_PRINT


  ## Print site nav row ( header row 1 )
  print <<END_OF_PRINT;
<div id='HeaderRow1'>
<table id='navTable'>
<td><a href="${GDBhome}">Home</a></td>
<td><a href="${CGIPATH}search.pl">Search</a></td>
<td><a href="${CGIPATH}blastGDB.pl" onmousemove="window.status='Run BLAST';" onmouseout="window.status='';">BLAST @ ${SITENAMEshort}</a></td>
<td><a href="javascript:RunGeneSeqer();" onmousemove="window.status='Use GeneSeqer';" onmouseout="window.status='';">GeneSeqer @ ${SITENAMEshort}</a></td>
<td><a href="javascript:doAnnotation('$cpHR->{altCONTEXT}','$cpHR->{blastDB}');" onmousemove="window.status='Contribute an annotation';" onmouseout="window.status='';">Annotation @ ${SITENAMEshort}</a></td>
<td><a href="${GDBDIR}site_map.php">Site Map</a></td>
<td><a href="${GDBDIR}tutorial/">Tutorial</a></td>
</table>
</div>

END_OF_PRINT


  ## Print query search row ( header row 2 )
  my $LOGGEDin   = ((exists($cpHR->{USERid}))&&($cpHR->{USERid}))?
    "<A CLASS='userID' HREF=\"javascript:goHome('${CGIPATH}UserHome.pl');\">$cpHR->{USERid} @ ${SITENAMEshort}</A>":
    "Anonymous";
  print <<END_OF_PRINT;
<div id='HeaderRow2'>
<P id='userIDleft'>$LOGGEDin</P>
<P id='userIDright'>$LOGGEDin</P>
<P id='searchCONTROL'>
<input class='searchINPUT' name="searchSTR" type="text" size=35 value="" onfocus="this.value=''" onKeyPress="check2KEY(event,'${CGIPATH}findRegion.pl','${CGIPATH}findRecord.pl')">
Search:
<INPUT class='searchINPUT' name="Genome" TYPE="button" VALUE="Genome" ONCLICK="submitTo('${CGIPATH}findRegion.pl');">
<INPUT class='searchINPUT' name="Records" TYPE="button" VALUE="Records" ONCLICK="submitTo('${CGIPATH}findRecord.pl');">
<A id="searchHELP" href="${DOCDIR}searchDOC.html"><IMG id='searchHELP' src="${IMAGEDIR}helpINFO.gif"></A>
</P>
</div>

END_OF_PRINT

  
  ## Print genome navigation row ( header row 3 )
  my $chrDROPDOWN  = '';
  for($x=1;$x<=scalar(@{$DBver[$cpHR->{dbid}]->{chrSIZE}});$x++){
    $chrDROPDOWN .= ($x == $cpHR->{chr})?"      <OPTION VALUE=\"$x\" SELECTED>$x</OPTION>\n":"      <OPTION VALUE=\"$x\">$x</OPTION>\n";
  }
  my $dbidDROPDOWN = '';
  for($x=0;$x<=$#DBver;$x++){
    $dbidDROPDOWN .= ($x == $cpHR->{dbid})?"      <OPTION VALUE=\"$x\" SELECTED>$DBver[$x]->{DBtag}</OPTION>\n":"      <OPTION VALUE=\"$x\">$DBver[$x]->{DBtag}</OPTION>\n";
  }
  my $loginMenu = ((exists($cpHR->{USERid}))&&($cpHR->{USERid}))?
    "<A HREF=\"${PlantGDBadminPATH}logout.php\">Logout</A>":
    "<A HREF=\"javascript:doLogin('${PlantGDBadminPATH}login.php?lastPage=$ENV{REQUEST_URI}');\">Login</A> / <A HREF=\"javascript:doRegister('${PlantGDBadminPATH}createAccount.php');\">Register</A>"
#"<A HREF=\"${PlantGDBadminPATH}login.php?lastPage=".$ENV{REQUEST_URI}."\" target=\"_blank\">Login</A> / <A HREF=\"javascript:doRegister('${PlantGDBadminPATH}createAccount.php');\">Register</A>"

;
  
  my $ACname = '';

## print SITEDEF defined alternativecontexts
if(defined($altCONTEXT)){
  foreach $ACname (keys %$altCONTEXT){
    print <<END_OF_PRINT;
<div id='HeaderRow3_${ACname}'>
<p id='loginMenu'>$loginMenu</p>
<p id='annotationLink'><A HREF="javascript:doAnnotation('$cpHR->{altCONTEXT}','$cpHR->{blastDB}');">Provide Expert<BR>Annotation</A></p>

$altCONTEXT->{$ACname}
</div>

END_OF_PRINT
  }
}
  


## print standard alternative context ( BAC )
  if(!exists($altCONTEXT->{BAC})){
    print <<END_OF_PRINT;
<div id='HeaderRow3_BAC'>
<p id='loginMenu'>$loginMenu</p>
<p id='annotationLink'><A HREF="javascript:doAnnotation('$cpHR->{altCONTEXT}','$cpHR->{blastDB}');">Provide Expert<BR>Annotation</A></p>

<p class='navCONTROL' id='bacNav'>
BAC / Clone gi-<INPUT NAME="gseg_gi" class='navINPUT' TYPE="text" VALUE="$cpHR->{gseg_gi}" SIZE=12><BR> 
Start:<INPUT NAME="bac_lpos" class='navINPUT' TYPE="text" VALUE="$cpHR->{l_pos}" SIZE=12 onKeyPress="checkEnter(event,'')">
End:<INPUT NAME="bac_rpos" class='navINPUT' TYPE="text" VALUE="$cpHR->{r_pos}" SIZE=12 onKeyPress="checkEnter(event,'')">
<INPUT NAME="bac_GoButton" class='navINPUT' TYPE="button" VALUE="Go" ONCLICK="getRegion('${CGIPATH}getGSEG_Region.pl');">
</p>
</div>

END_OF_PRINT
}

## print default context ( pseudo-chromosome )
  print <<END_OF_PRINT;
<div id='HeaderRow3_pCHR'>
<p id='loginMenu'>$loginMenu</p>
<p id='annotationLink'><A HREF="javascript:doAnnotation('$cpHR->{altCONTEXT}','$cpHR->{blastDB}');">Provide Expert<BR>Annotation</A></p>

<p class='navCONTROL' id='pseudochromosomeNav'>
${COMMONORGN} Genome Assembly<SELECT ID="dbid" NAME="dbid" class='navINPUT'>${dbidDROPDOWN}</SELECT><BR>
Chromosome:<SELECT ID="chr" NAME="chr" class='navINPUT'>${chrDROPDOWN}</SELECT>
Start:<INPUT NAME="l_pos" class='navINPUT' TYPE="text" VALUE="$cpHR->{l_pos}" SIZE=12 onKeyPress="checkEnter(event,'')">
End:<INPUT NAME="r_pos" class='navINPUT' TYPE="text" VALUE="$cpHR->{r_pos}" SIZE=12 onKeyPress="checkEnter(event,'')">
<INPUT NAME="GoButton" class='navINPUT' TYPE="button" VALUE="Go" ONCLICK="getRegion('${CGIPATH}getRegion.pl');">
</p>
</div>

END_OF_PRINT

#####################################################
#print "<HR><P>" . join(':',@INC) . "</P><HR>";

  return 1;
}

sub print_LeftSidebar{
  my($self) = @_;

  do 'xgdbSidebarLEFT.pl'; ## define @sidebarLinks

  my @links = (); my $linkAR = '';
  foreach $linkAR (@sidebarLinks){
    push(@links,a($linkAR->[0],$linkAR->[1]));
  }
  my $link_list = ul({-type=>'none',-id=>'LinkList'},li({-class=>'LinkList'},\@links));

  print <<END_OF_PRINT;
<div id='LeftSidebar'>
<h3 class='GroupID'>Links</h3>
$link_list
<h3 class='GroupID'>&nbsp;</h3>
END_OF_PRINT

  my $menu = "";
  my $NavLinkGroup = "";
  @sidebarNavMenuORDER = sort {return $a cmp $b;} keys %sidebarNavMenu if(! scalar(@sidebarNavMenuORDER));
  foreach $menu (@sidebarNavMenuORDER){
    if(exists($sidebarNavMenu{$menu})){
      @links = ();
      $linkAR = shift(@{$sidebarNavMenu{$menu}});
      $NavLinkGroup = a($linkAR->[0],$menu);
      print stderr ">> $#$linkAR << \n";
      if(scalar(@{$sidebarNavMenu{$menu}})){
	my $NLGheader = a({-class=>'NLGheader',%{$linkAR->[0]}},$linkAR->[1]) if($#$linkAR);
	foreach $linkAR (@{$sidebarNavMenu{$menu}}){
	  $linkAR->[0]{-class} = 'NavLink';
	  push(@links,a($linkAR->[0],$linkAR->[1]));
	}
	print "<div class='NavMenu' onmouseover='IEsucksAtCSS(this,\"NavMenu_hover\");' onmouseout='IEsucksAtCSS(this,\"NavMenu\");'>\n";
	print ul({-id=>"${menu}NLG",-class=>'NavLinkGroup'},li({-class=>'NLGheader'},[$NLGheader]) . li({-class=>"${menu}NLG"},\@links));
	print "\n${NavLinkGroup}\n<img id='arrow' src='${IMAGEDIR}GDBmenuArrow2.png'><img id='mo_arrow' src='${IMAGEDIR}GDBmenuArrow.png'></div>\n";
      }else{
	print "<div class='NavMenu'>${NavLinkGroup}</div>\n";
      }
    }
  }

  print <<END_OF_PRINT;
<div class='NavMenu'><a href="${GDBDIR}resource.php">Data & Methods</a></div>
<div class='NavMenu'><a href="${GDBDIR}download.php">Downloads</a></div>
</div>
END_OF_PRINT

  return 1;
}

sub print_RightSidebar{
  my ($self) = @_;

  do 'xgdbSidebarRIGHT.pl'; ## define @sidebarNoteworthy

  my @links = (); my $linkAR = '';
  foreach $linkAR (@sidebarNoteworthy){
    push(@links,a($linkAR->[0],$linkAR->[1]));
  }
  my $noteworthy_list = ul({-type=>'none',-id=>'NoteworthyList'},li({-class=>'NoteworthyList'},\@links));

  print <<END_OF_PRINT;
<div id="RightSidebar">
<h3 class='GroupID'>Noteworthy</h3>
$noteworthy_list
</div>

END_OF_PRINT

  return 1;
}

sub print_SiteFooter{
  my ($self) = @_;

  print <<END_OF_PRINT;
<HR id='footer'>

<table border=0 width="100%" !cellspacing="30" cellpadding="2" align="center">

<td align="center" valign="bottom"><a href="http://www.plantgdb.org/AtGDB/" style="text-decoration:none;">
<img src="${IMAGEDIR}AtGDB_logo.png" width=100 border=0>
<br><font style="font-size:10pt; font-family:Arial; text-decoration:underline;">AtGDB</font></a></font></td>

<td align="center" valign="bottom"><a href="http://www.plantgdb.org/" style="text-decoration:none;">
<img src="${IMAGEDIR}PlantGDB.gif" width=75 border=0>
<br><font style="font-size:10pt; font-family:Arial; text-decoration:underline;">PlantGDB</a></font></td>

<td align="center" valign="bottom"><a href="http://www.maizegdb.org/" style="text-decoration:none;">
<img src="${IMAGEDIR}maizeGDB.gif" width=125 border=0>
<br><font style="font-size:10pt; font-family:Arial; text-decoration:underline;">MaizeGDB</font></a></td>

<td align="center" valign="bottom"><a href="http://www.nsf.gov/bio/dbi/dbi_pgr.htm" style="text-decoration:none;">
<img src="${IMAGEDIR}nsfgray.gif" border=0 height=50>
<br><font style="font-size:10pt; font-family:Arial; text-decoration:underline;">NSF Plant Genome Research</font></a></td>

<td align="center" valign="bottom"><a href="http://gremlin1.gdcb.iastate.edu/~volker/" style="text-decoration:none;">
<img src="${IMAGEDIR}BGlogo.jpg" width=60 border=0>
<br><font style="font-size:10pt; font-family:Arial; text-decoration:underline;">Brendel Group</font></a></td>

<td align="center" valign="bottom"><a href="http://www.plantsciences.iastate.edu/" style="text-decoration:none;">
<img src="${IMAGEDIR}PSI.gif" width=60 border=0>
<br><font style="font-size:10pt; font-family:Arial; text-decoration:underline;">Plant Sciences Institute</font></a></td>

<td align="center" valign="bottom"><a href="http://www.iastate.edu/" style="text-decoration:none;">
<img src="${IMAGEDIR}isu.gif" border=0 width=100>
<br><font style="font-size:10pt; font-family:Arial; text-decoration:underline;">Iowa State University</font></a></td>

</table>



</form>

END_OF_PRINT

  return 1;
}
See more files for this project here