synview.module

<?php

/**
 * @file
 * The main file for the tripal go module.
 */

// Application Programmers Interface
require_once 'api/synview.api.inc';

// insert/delete synteny blocks according to synteny file 
require_once 'includes/synview.syn_parser.inc';

// synteny Node functionality
require_once 'includes/synview.node.inc';

// Functions specific to themeing (ie: preprocess)
require_once 'theme/synview.theme.inc';

// Administration for furture
//require_once 'includes/synview.admin.inc';

/**
 * Implements hook_menu().
 */
function synview_menu() {
  // search syntenic block form
  $items['synview/search'] = array(
    'title' => 'Search Syntenic Blocks',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('synview_search_form'),
    'access arguments' => array('access content'),
    'file' => 'includes/synview_search_form.inc',
    'type' => MENU_NORMAL_ITEM,
  );

  // display search result
  $items['synview/search/result/%'] = array(
    'title' => 'Search Result for Syntenic Blocks',
    'page callback' => 'synview_search_result',
    'page arguments' => array(3),
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK,
  );

  // synteny (MCScanX) dataset Node 
  $items['node__syn'] = array(
    'template' => 'node--syn',
    'render element' => 'node',
    'base hook' => 'node',
    'path' => 'themesyn',
  );

  // Display Syntenic Block
  $items['synview/block/%'] = array(
    'title' => 'Display Syntenic Blocks',
    'page callback' => 'display_block',
    'page arguments' => array(2),
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK,
  );

  // help
  $items['admin/tripal/extension/tripal_synview'] = array(
    'title' => 'Tripal Synview',
    'description' => 'Tripal Synview Configuration',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_synview_admin_settings'),
    'access arguments' => array('administer tripal'),
    'type' => MENU_NORMAL_ITEM,
  );
  
  // help
  $items['admin/tripal/extension/tripal_synview/help'] = array(
    'title' => 'Help',
    'page callback' => 'theme',
    'page arguments' => array('synview_help'),
    'access arguments' => array('administer tripal'),
    'type' => MENU_LOCAL_TASK,
  );

  return $items;
}

function tripal_synview_admin_settings () {
  $form = array();
  $form['feature_type1'] = array(
    '#type' => 'select',
    '#title' => 'Feature Type 1',
    '#description' => t('For Genome1, synteny analysis was performed using this feaure type.'),
    '#options' => array('gene' => 'gene', 'mRNA' => 'mRNA', 'CDS' => 'CDS'),
    '#default_value' => variable_get('tripal_synview_feature_type1', 'mRNA'),
  );
  $form['feature_type2'] = array(
    '#type' => 'select',
    '#title' => 'Feature Type 2',
    '#description' => t('For Genome2, synteny analysis was performed using this feaure type.'),
    '#options' => array('gene' => 'gene', 'mRNA' => 'mRNA', 'CDS' => 'CDS'),
    '#default_value' => variable_get('tripal_synview_feature_type2', 'mRNA'),
  );
  $form['block_examples'] = array(
      '#type' => 'textfield',
      '#title' => 'Block Examples',
      '#description' => 'Block example to show on the Synview Search form',
      '#default_value' => variable_get('tripal_synview_block_examples', t("'hjhnB1908' or 'abrjB0957'"))
  );
  $form['genomes'] = array(
      '#type' => 'fieldset',
      '#title' => 'Genome Grouping',
      '#description' => 'Categorize genomes into groups so synteny comparison will be made only within each group. 
                                       For example, you can have prokaryote and eukaryote groups so that the genomes in one group 
                                       won\'t be compared to the ones in the other group. Please note that if you enable the grouping, 
                                       genomes that do not belong to any group will not be shown. Clearing all group names will reset
                                       Synteny Viewer to no grouping.',
      '#collapsible' => TRUE,
      '#collapsed' => FALSE
  );
  $gtitle = variable_get('tripal_synview_grouping_title', 'Genome Category');
  $form['genomes']['grouping_title'] = array(
    '#type' => 'textfield',
    '#title' => 'Title (Display Only)',
    '#description' => 'Title to show on the search form for genome grouping',
    '#default_value' => $gtitle,
  );
  $genomes = tripal_synview_get_genomes(TRUE);
  asort($genomes);
  $genome_groups = variable_get('tripal_synview_genome_groups', array());
  $gval = array();
  foreach ($genome_groups AS $k => $vals) {
    foreach ($vals AS $id => $v) {
      $gval[$id] = $k;
    }
  }
  foreach ($genomes AS $analysis_id => $genome) {
      $form['genomes']['genome_' . $analysis_id] = array(
          '#type' => textfield,
          '#title' => 'Group for ' . $genome,
          '#default_value' => isset($gval[$analysis_id]) ? $gval[$analysis_id] : '',
      );
  }
  $disabled_genomes = variable_get('tripal_synview_disabled_genomes', array());
  $form['disabled_genomes'] = array(
    '#type' => 'checkboxes',
    '#options' => $genomes,
    '#title' => 'Disable the following genome(s) from the Synview search form',
    '#description' => "Check boxes for the unpublished genomes that you want to hide from the users.",
    '#default_value' => $disabled_genomes
  );
  return system_settings_form($form);
}

function tripal_synview_admin_settings_validate($form, &$form_state) {
  // featyre types
  $ftype1= $form_state['values']['feature_type1'];
  $ftype2= $form_state['values']['feature_type2'];
  variable_set('tripal_synview_feature_type1', $ftype1);
  variable_set('tripal_synview_feature_type2', $ftype2);
  
  //block examples
  $block_examples = $form_state['values']['block_examples'];
  variable_set('tripal_synview_block_examples', $block_examples);
  
  // genome grouping
  $genomes = tripal_synview_get_genomes(TRUE);
  $genome_groups = array();
  $has_group = FALSE;
  foreach ($genomes AS $analysis_id => $genome) {
    $grp = trim($form_state['values']['genome_' . $analysis_id]);
    if ($grp) {
      $has_group = TRUE;
      if (array_key_exists($grp, $genome_groups)) {
        $genome_groups[$grp][$analysis_id] = $genome;
      }
      else {
        $genome_groups[$grp] = array($analysis_id => $genome);
      }
    }
  }
  $gtitle = $form_state['values']['grouping_title'];
  variable_set('tripal_synview_grouping_title', $gtitle);
  if ($has_group) {
    variable_set('tripal_synview_genome_groups', $genome_groups);
  }
  else {
    variable_del('tripal_synview_genome_groups');
  }
  
  // hide genomes
  $disabled_genomes = $form_state['values']['disabled_genomes'];
  variable_set('tripal_synview_disabled_genomes', $disabled_genomes);
}
/**
 * Implements hook_theme().
 */
function synview_theme() {

  $items = array();
  $path = drupal_get_path('module', 'synview');

  // explain the detail
  // this hook create a array of theme through array item
  // the key in array is like show_goenrich_report
  // the value tell drupal where to find template page 
  //   template: template name, and file must has suffix .tpl.php 
  //   path: where to find template file 
  // use theme('key') to call the them

  // search result
  $items['synview_search_result'] = array(
    'template' => 'synview_search_result',
    'path' => "$path/theme",
  );


  // Displays the pwy enrich results for each job
  $items['display_block'] = array(
    'template' => 'display_block',
    'path' => "$path/theme",
  );

  // Module Help
  $items['synview_help'] = array(
    'template' => 'synview_help',
    'path' => "$path/theme",
  );

  $items['tripal_feature_synteny'] = array(
    'variables' => array('node' => NULL),
    'template' => 'tripal_feature_synteny',  //template file name without .tpl.php
    'path' =>  $path . '/tripal_feature', // the path of tpl file
  );
  return $items;
}

/**
 * Implements hook_help().
 */
function synview_help($path, $arg) {
  if ($path == 'admin/help#synview') {
    return theme('synview_help');
  }
}

/**
 * Dispaly single block 
 *
 * @param $block_id
 *
 * @return $result
 *  Return HTML output of the block to be displayed to the user
 *
 */
function display_block($block_id) {
  return theme('display_block', array('block_id' => $block_id));
}

/**
 * retrieve blocks from drupal database according to location
 * 
 * @param org_id chr start end array_of_ref_org_id
 * 
 * @return $block
 *         array of searched blocks
 */
function synview_search_result($action) {

  if (!array_key_exists('tripal_synview_search', $_SESSION)) {
    drupal_goto('synview/search');
  }

  $analysis_id  = $_SESSION['tripal_synview_search']['SELECT_GENOME'];
  $chr     = $_SESSION['tripal_synview_search']['SELECT_CHR'];
  //$start   = $_SESSION['tripal_synview_search']['START'];
  //$end     = $_SESSION['tripal_synview_search']['END'];
  $ref_genome = $_SESSION['tripal_synview_search']['refGenome'];
  //dpm('SELECTED GENOME: ' . $analysis_id);
  //dpm(array('REF GENOMES' => $ref_genome));
  //$end_pos = $_SESSION['tripal_synview_search']['RLEN'][$org_id][$chr];

  //dpm($_SESSION['tripal_synview_search']);

/*   if ($action) {
    if ($action == 'left') {
      if ($start > 100000) { 
        $start = $start - 1000000; 
      } else {
        $start = 1;
      }
      if ($end > 1000000) {
        $end = $end - 1000000;
      }
    }
    elseif ($action == 'right') {
      if ($end < $end_pos - 1000000) {
        $end = $end + 1000000;
      } else {
        $end = $end_pos;
      }
      
      if ($start < $end - 1000000) {
        $start = $start + 1000000;
      }
    }
    else {

    }
  } */

  //$_SESSION['tripal_synview_search']['START'] = $start;
  //$_SESSION['tripal_synview_search']['END'] = $end;

  $genome_opts = tripal_synview_get_genomes();
  get_reference($genome_opts);

  // search block on one organism of select chrosome
  // find block between start and end, also cover start and end, 
  $args = array( 
    ':type_name' => 'syntenic_region',
    ':analysis_id' => $analysis_id, 
    ':chr' => $chr
  );

  $where_location = '';//"AND 
  //  ((FL.fmin < :start AND FL.fmax > :start) OR 
  //   (FL.fmin < :end AND FL.fmax > :end) OR 
  //   (FL.fmin > :start AND FL.fmax < :end)
  //  )";
  //$args[':start'] = $start;
  //$args[':end'] = $end;

  $sql = "SELECT F.feature_id, F.name, FL.srcfeature_id, FL.fmin, FL.fmax, FL.strand 
     FROM chado.feature F
     LEFT JOIN chado.cvterm CVT ON F.type_id = CVT.cvterm_id 
     LEFT JOIN chado.featureloc FL ON F.feature_id = FL.feature_id 
     INNER JOIN chado.analysisfeature AF ON AF.feature_id = FL.srcfeature_id
     WHERE
       CVT.name = :type_name AND AF.analysis_id = :analysis_id AND FL.srcfeature_id = :chr
       $where_location
     ORDER BY FL.fmin
     ";
  $results = chado_query($sql, $args);
  
  // get all the feature_id of selected synteny_region 
  // then retrieve all corresponding synteny_regions in other organisms of these selected synteny_region 
  $search_feature_id = array();
  $search_results = array();

  foreach ($results as $r) {
    $search_feature_id[] = $r->feature_id;
    $search_results[$r->feature_id] = $r;
  }

  $sql = "SELECT S.blockid, S.b1, S.b2, S.score, S.evalue FROM synblock S
     WHERE S.b1 IN (:bid) OR S.b2 IN (:bid)";
  $res = chado_query($sql, array(':bid' => $search_feature_id));

  // filter the result by $ref_genome
  // only the blocks in match ref_org will be exported
  $blocks = array();
  // the array syn_region used for store region information
  $syn_region = array(); 

  // jdata: array for json data
  $jdata = array();

  $sql_loc = "
    SELECT 
      FL.srcfeature_id, 
      FL.feature_id, 
      FL.fmin, 
      FL.fmax, 
      FL.strand, 
      AF.analysis_id, 
      (SELECT name FROM {analysis} Where analysis_id = AF.analysis_id) AS genome,
      (SELECT value FROM {analysisprop} Where analysis_id = AF.analysis_id AND type_id = (SELECT cvterm_id FROM {cvterm} WHERE name = 'Short Name' AND cv_id = (SELECT cv_id FROM {cv} WHERE name = 'analysis_property'))) AS short_name 
    FROM {featureloc} FL
    INNER JOIN {analysisfeature} AF ON AF.feature_id = FL.srcfeature_id WHERE FL.feature_id = :feature_id";

  $counter = 0;$option = 0;  
  foreach ($res as $b) {
    $counter ++;
      // filter the reference organism
      // b1 and b2 are selected org
      $loc1 = chado_query($sql_loc, array(':feature_id'=>$b->b1))->fetchObject();
      $loc2 = chado_query($sql_loc, array(':feature_id'=>$b->b2))->fetchObject();
      
      // ignore the genomes that are not selected for comparsion
      if (!key_exists($loc1->analysis_id, $ref_genome) && !key_exists($loc2->analysis_id, $ref_genome)) {
        continue;
      }
      
      //if ($counter == 1) {dpm(array('genome1' => $loc1->analysis_id, 'genome2' => $loc2->analysis_id));}
      if ($loc1->analysis_id == $analysis_id and $loc2->analysis_id == $analysis_id) 
      {
        // if ($option <> 1) {dpm('OPTION1: b1 an b2 are both from selected genome');$option = 1;}
        $b->b1_genome    = $loc1->genome;
        $b->b1_sid    = $_SESSION['tripal_synview_search']['REF'][$loc1->analysis_id][$loc1->srcfeature_id];
        $b->b1_len    = $_SESSION['tripal_synview_search']['RLEN'][$loc1->analysis_id][$loc1->srcfeature_id];
        $b->b1_fmin   = $loc1->fmin;
        $b->b1_fmax   = $loc1->fmax;
        $b->b1_strand = $loc1->strand;

        $b->b2_genome    = $loc2->genome;
        $b->b2_sid    = $_SESSION['tripal_synview_search']['REF'][$loc2->analysis_id][$loc2->srcfeature_id];
        $b->b2_len    = $_SESSION['tripal_synview_search']['RLEN'][$loc2->analysis_id][$loc2->srcfeature_id];
        $b->b2_fmin   = $loc2->fmin;
        $b->b2_fmax   = $loc2->fmax;
        $b->b2_strand = $loc2->strand;
        $blocks[$b->blockid] = $b;

        // build array for json
        if (!array_key_exists($loc1->analysis_id, $jdata) ) {
          $jdata[$loc1->analysis_id] = array();
          $jdata[$loc1->analysis_id]['name'] = $loc1->genome;
          $jdata[$loc1->analysis_id]['short_name'] = $loc1->short_name;
          $jdata[$loc1->analysis_id]['canvas'] = 'canvas' . $loc1->analysis_id;
          $jdata[$loc1->analysis_id]['ideoCollection'] = array();
          $jdata[$loc1->analysis_id]['bedCollection']  = array();
          $jdata[$loc1->analysis_id]['linkCollection'] = array(); 
          $jdata[$loc1->analysis_id]['labCollection']  = array();
        }

        if (!array_key_exists($b->b1_sid, $jdata[$loc1->analysis_id]['ideoCollection']) ) {
          $jdata[$loc1->analysis_id]['ideoCollection'][$b->b1_sid] = array();
          $jdata[$loc1->analysis_id]['ideoCollection'][$b->b1_sid]['id'] = $b->b1_sid;
          $jdata[$loc1->analysis_id]['ideoCollection'][$b->b1_sid]['length'] = $b->b1_len / 1000000;
          $loc1->srcfeature_id == $_SESSION['tripal_synview_search']['SELECT_CHR'] ? $jdata[$loc1->analysis_id]['ideoCollection'][$b->b1_sid]['color'] = 'blue' : $jdata[$loc1->analysis_id]['ideoCollection'][$b->b1_sid]['color'] = 'red';
        }

        if (!array_key_exists($b->b2_sid, $jdata[$loc1->analysis_id]['ideoCollection']) ) {
          $jdata[$loc1->analysis_id]['ideoCollection'][$b->b2_sid] = array();
          $jdata[$loc1->analysis_id]['ideoCollection'][$b->b2_sid]['id'] = $b->b2_sid;
          $jdata[$loc1->analysis_id]['ideoCollection'][$b->b2_sid]['length'] = $b->b2_len / 1000000;
          $loc2->srcfeature_id == $_SESSION['tripal_synview_search']['SELECT_CHR'] ? $jdata[$loc1->analysis_id]['ideoCollection'][$b->b2_sid]['color'] = 'blue' : $jdata[$loc1->analysis_id]['ideoCollection'][$b->b2_sid]['color'] = 'red';
        }

        if (!array_key_exists($b->blockid, $jdata[$loc1->analysis_id]['bedCollection']) ) {
          $jdata[$loc1->analysis_id]['bedCollection'][] = array(
            'chr' => $b->b1_sid,
            'start' => $b->b1_fmin / 1000000, 
            'end' => $b->b1_fmax / 1000000, 
            'id' => $b->blockid, 'color' => 'green');
          $jdata[$loc1->analysis_id]['bedCollection'][] = array(
              'chr' => $b->b2_sid,        
              'start' => $b->b2_fmin / 1000000, 
              'end' => $b->b2_fmax / 1000000, 
              'id' => $b->blockid, 'color' => 'green');
          $jdata[$loc1->analysis_id]['linkCollection'][] = array(
            'bid' => $b->blockid,
            'source' => $jdata[$loc1->analysis_id]['bedCollection'][count($jdata[$loc1->analysis_id]['bedCollection'])-2], 
            'target' => $jdata[$loc1->analysis_id]['bedCollection'][count($jdata[$loc1->analysis_id]['bedCollection'])-1]);
        }
      }
      // b1 is ref orgs, b2 is select org
      elseif (array_key_exists($loc1->analysis_id, $ref_genome) and $loc2->analysis_id == $analysis_id ) 
      {
        // if ($option <> 2) {dpm('OPTION2: b1 is one of the reference genomes and b2 is from selected genome');$option = 2;}
        $r = $search_results[$b->b2];
        $b->b1_genome    = $loc1->genome;
        $b->b1_sid    = $_SESSION['tripal_synview_search']['REF'][$loc1->analysis_id][$loc1->srcfeature_id];
        $b->b1_len    = $_SESSION['tripal_synview_search']['RLEN'][$loc1->analysis_id][$loc1->srcfeature_id];
        $b->b1_fmin   = $loc1->fmin;
        $b->b1_fmax   = $loc1->fmax;
        $b->b1_strand = $loc1->strand;
        $b->b2_genome    = $loc2->genome;
        $b->b2_sid    = $_SESSION['tripal_synview_search']['REF'][$loc2->analysis_id][$r->srcfeature_id];
        $b->b2_len    = $_SESSION['tripal_synview_search']['RLEN'][$loc2->analysis_id][$r->srcfeature_id];
        $b->b2_fmin   = $r->fmin;
        $b->b2_fmax   = $r->fmax;
        $b->b2_strand = $r->strand;
        $blocks[$b->blockid] = $b;
        // build array for json
        if (!array_key_exists($loc1->analysis_id, $jdata) ) {
          $jdata[$loc1->analysis_id] = array();
          $jdata[$loc1->analysis_id]['name'] = $loc1->genome;
          $jdata[$loc1->analysis_id]['short_name'] = $loc1->short_name;
          $jdata[$loc1->analysis_id]['canvas'] = 'canvas' . $loc1->analysis_id;
          $jdata[$loc1->analysis_id]['ideoCollection'] = array();
          $jdata[$loc1->analysis_id]['bedCollection']  = array();
          $jdata[$loc1->analysis_id]['linkCollection'] = array();
          $jdata[$loc1->analysis_id]['labCollection']  = array();
        }

        if (!array_key_exists($b->b1_sid, $jdata[$loc1->analysis_id]['ideoCollection']) ) {
          $jdata[$loc1->analysis_id]['ideoCollection'][$b->b1_sid] = array();
          $jdata[$loc1->analysis_id]['ideoCollection'][$b->b1_sid]['id'] = $b->b1_sid;
          $jdata[$loc1->analysis_id]['ideoCollection'][$b->b1_sid]['length'] = $b->b1_len / 1000000;
          $loc1->srcfeature_id == $_SESSION['tripal_synview_search']['SELECT_CHR'] ? $jdata[$loc1->analysis_id]['ideoCollection'][$b->b1_sid]['color'] = 'blue' : $jdata[$loc1->analysis_id]['ideoCollection'][$b->b1_sid]['color'] = 'red';
        }

        if (!array_key_exists($b->b2_sid, $jdata[$loc1->analysis_id]['ideoCollection']) ) {
          $jdata[$loc1->analysis_id]['ideoCollection'][$b->b2_sid] = array();
          $jdata[$loc1->analysis_id]['ideoCollection'][$b->b2_sid]['id'] = $b->b2_sid;
          $jdata[$loc1->analysis_id]['ideoCollection'][$b->b2_sid]['length'] = $b->b2_len / 1000000;
          $r->srcfeature_id == $_SESSION['tripal_synview_search']['SELECT_CHR'] ? $jdata[$loc1->analysis_id]['ideoCollection'][$b->b2_sid]['color'] = 'blue' : $jdata[$loc1->analysis_id]['ideoCollection'][$b->b2_sid]['color'] = 'red';
        }

        if (!array_key_exists($b->blockid, $jdata[$loc1->analysis_id]['bedCollection']) ) {
          $jdata[$loc1->analysis_id]['bedCollection'][] = array(
            'chr' => $b->b1_sid,
            'start' => $b->b1_fmin / 1000000,
            'end' => $b->b1_fmax / 1000000,
            'id' => $b->blockid, 'color' => 'green');
          $jdata[$loc1->analysis_id]['bedCollection'][] = array(
            'chr' => $b->b2_sid,
            'start' => $b->b2_fmin / 1000000,
            'end' => $b->b2_fmax / 1000000,
            'id' => $b->blockid, 'color' => 'green');
          $jdata[$loc1->analysis_id]['linkCollection'][] = array(
            'bid' => $b->blockid,
            'source' => $jdata[$loc1->analysis_id]['bedCollection'][count($jdata[$loc1->analysis_id]['bedCollection'])-2],
            'target' => $jdata[$loc1->analysis_id]['bedCollection'][count($jdata[$loc1->analysis_id]['bedCollection'])-1]);
        }
      }
      elseif (array_key_exists($loc2->analysis_id, $ref_genome) and $loc1->analysis_id == $analysis_id )
      {
        // if ($option <> 3) {dpm('OPTION3: b2 is one of the reference genomes and b1 is from selected genome');$option = 3;}
        $r = $search_results[$b->b1];
        $b->b1_genome    = $loc1->genome;
        $b->b1_sid    = $_SESSION['tripal_synview_search']['REF'][$loc1->analysis_id][$r->srcfeature_id];
        $b->b1_len    = $_SESSION['tripal_synview_search']['RLEN'][$loc1->analysis_id][$r->srcfeature_id];
        $b->b1_fmin   = $r->fmin;
        $b->b1_fmax   = $r->fmax;
        $b->b1_strand = $r->strand;
        $b->b2_genome    = $loc2->genome;
        $b->b2_sid    = $_SESSION['tripal_synview_search']['REF'][$loc2->analysis_id][$loc2->srcfeature_id];
        $b->b2_len    = $_SESSION['tripal_synview_search']['RLEN'][$loc2->analysis_id][$loc2->srcfeature_id];
        $b->b2_fmin   = $loc2->fmin;
        $b->b2_fmax   = $loc2->fmax;
        $b->b2_strand = $loc2->strand;
        $blocks[$b->blockid] = $b;

        // build array for json
        if (!array_key_exists($loc2->analysis_id, $jdata) ) {
          $jdata[$loc2->analysis_id] = array();
          $jdata[$loc2->analysis_id]['name'] = $loc2->genome;
          $jdata[$loc2->analysis_id]['short_name'] = $loc2->short_name;
          $jdata[$loc2->analysis_id]['canvas'] = 'canvas' . $loc2->analysis_id;
          $jdata[$loc2->analysis_id]['ideoCollection'] = array();
          $jdata[$loc2->analysis_id]['bedCollection']  = array();
          $jdata[$loc2->analysis_id]['linkCollection'] = array();
          $jdata[$loc2->analysis_id]['labCollection']  = array();
        }

        if (!array_key_exists($b->b1_sid, $jdata[$loc2->analysis_id]['ideoCollection']) ) {
          $jdata[$loc2->analysis_id]['ideoCollection'][$b->b1_sid] = array();
          $jdata[$loc2->analysis_id]['ideoCollection'][$b->b1_sid]['id'] = $b->b1_sid;
          $jdata[$loc2->analysis_id]['ideoCollection'][$b->b1_sid]['length'] = $b->b1_len / 1000000;
          $r->srcfeature_id == $_SESSION['tripal_synview_search']['SELECT_CHR'] ? $jdata[$loc2->analysis_id]['ideoCollection'][$b->b1_sid]['color'] = 'blue' : $jdata[$loc2->analysis_id]['ideoCollection'][$b->b1_sid]['color'] = 'red';
        }

        if (!array_key_exists($b->b2_sid, $jdata[$loc2->analysis_id]['ideoCollection']) ) {
          $jdata[$loc2->analysis_id]['ideoCollection'][$b->b2_sid] = array();
          $jdata[$loc2->analysis_id]['ideoCollection'][$b->b2_sid]['id'] = $b->b2_sid;
          $jdata[$loc2->analysis_id]['ideoCollection'][$b->b2_sid]['length'] = $b->b2_len / 1000000;
          $loc2->srcfeature_id == $_SESSION['tripal_synview_search']['SELECT_CHR'] ? $jdata[$loc2->analysis_id]['ideoCollection'][$b->b2_sid]['color'] = 'blue' : $jdata[$loc2->analysis_id]['ideoCollection'][$b->b2_sid]['color'] = 'red';
        }

        if (!array_key_exists($b->blockid, $jdata[$loc2->analysis_id]['bedCollection']) ) {
          $jdata[$loc2->analysis_id]['bedCollection'][] = array(
            'chr' => $b->b1_sid,
            'start' => $b->b1_fmin / 1000000,
            'end' => $b->b1_fmax / 1000000,
            'id' => $b->blockid, 'color' => 'green');
          $jdata[$loc2->analysis_id]['bedCollection'][] = array(
            'chr' => $b->b2_sid,
            'start' => $b->b2_fmin / 1000000,
            'end' => $b->b2_fmax / 1000000,
            'id' => $b->blockid, 'color' => 'green');
          $jdata[$loc2->analysis_id]['linkCollection'][] = array(
            'bid' => $b->blockid,
            'source' => $jdata[$loc2->analysis_id]['bedCollection'][count($jdata[$loc2->analysis_id]['bedCollection'])-2],
            'target' => $jdata[$loc2->analysis_id]['bedCollection'][count($jdata[$loc2->analysis_id]['bedCollection'])-1]);
        }
      }
      else 
      {
      }
    }

  $jdata_tmp = array();
  foreach ($jdata as $id => $data) {
    $data['ideoCollection'] = array_values($data['ideoCollection']);
    $jdata_tmp[] = $data;
  }

  $json_data = json_encode($jdata_tmp);
  $json_data = "var data = $json_data";
  drupal_add_js($json_data, array('type'=>'inline', 'scope'=>'footer','weight' => 50));

  $cluster = array();
  return theme('synview_search_result', array('cluster'=> $cluster, 'blocks' => $blocks, 'jdata' => $jdata_tmp));
}

/**
 * load synteny blocks of synteny file into chado database
 * 
 * @param $node
 * 
 * generate job args, then trigger a tripal job for parsing synteny file and loading blocks
 */
function synteny_file_load_job($node) 
{
  global $user;
  if ($node->syn_name) {
    $job_args = array(
      tripal_synview_get_organism_id($node->syn_genome1),
      tripal_synview_get_organism_id($node->syn_genome2),
      $node->syn_path,
    );
    tripal_add_job("Parse synteny file: $node->syn_path", 'tripal_synview',
      'synview_parse_synfile', $job_args, $user->uid);
  }
}

/**
 * Adds custom templates to a node
 */
function synview_node_view_alter(&$build) {
  
  if ($build['#bundle'] == 'chado_feature') {
    //only show our template on full page views
    if ($build['#view_mode'] != 'full' OR array_key_exists('tripal_feature_synteny', $build) ) {
      return;
    }
    
    //add template to build
    $build['tripal_feature_synteny'] = array(
      '#theme' => 'tripal_feature_synteny',
      '#node' => $build['#node'],
      '#tripal_toc_id' => 'synteny',
      '#tripal_toc_title' => 'Synteny',
    );
  }
}