<?
/**
 * Change Log:
 * Jul 14, 2023	Harman Singh	Migrated from PHP 5.3 to PHP 8.1
 */
#Transition: PHP 4.3 to PHP 5.16 to target PHP 5.3
#Testing environment: 	PHP 5.1.6
#Methods changed: 		updated genDataObjs, getAllRaw and getAllAln methods
#Methods Tested: 		getAllRaw, getRawBySeqid(620), getAlnBySeqid(620)
#Testing Performed: 	test/manager_test_scripts/NucSeqManager_test.php
#DAO called: 			NucSeqDao
#DB directly called:  	NO
#Functions: 			- retrieve SeqData objects by seqid, marker, date and so on
#						- insert and update SeqData object
#Transition closed
class NucSeqManager {

	function genDataObjs($dbresult) {
		$objlist=false;
		if (pg_result_error($dbresult)) return FALSE; //changed from DB:: to PEAR::
		while ($row=pg_fetch_assoc($dbresult)) {
			$nucSeq=new CodingSeq($row["seqid"]);
			$nucSeq->setSeq(strtoupper($row["seq"]));
			$nucSeq->setLength($row["length"]);
			$nucSeq->setCds($row["cds"]);
			$nucSeq->setUpdated($row["updated"]);
			$nucSeq->setAmbiguous($row["ambiguous"]);
			$nucSeq->setMarker($row["fk_marker"]);

			$objlist[]= $nucSeq;
		}
		/* single object result */
		if (count($objlist)==1)
			return $objlist[0];
		/* multiple object result */
		else return $objlist;
	}

	/**
    * added the parameters $limit and $offset on Dec 21, 2010
    */
	function getAllRaw($limit=false,$offset=false) {
	/*	$nucSeqDao= new NucSeqDao();
		$result=$nucSeqDao->searchAllRaw();
		return NucSeqManager::genDataObjs($result);*/

		$nucSeqArray=array();
		$seqDataArray=SeqDataManager::getAll($limit,$offset);
		return NucSeqManager::generateRaw($seqDataArray);
	}

	/**
    * added the parameters $limit and $offset on Dec 21, 2010
    */
	function getAllAln($limit=false,$offset=false) {
	/*	$nucSeqDao= new NucSeqDao();
		$result=$nucSeqDao->searchAllAln();
		return NucSeqManager::genDataObjs($result);*/

		$nucSeqArray=array();
		$seqDataArray=SeqDataManager::getAll($limit,$offset);
		return NucSeqManager::generateAln($seqDataArray);
	}

	function getAllAlnCount() {
		/*$nucSeqDao= new NucSeqDao();
		$result=$nucSeqDao->searchAllRaw();
		$row=$result->fetchRow(MDB2_FETCHMODE_ASSOC);
		return $row["count"];*/

		return SeqDataManager::countAllNucAln();
	}

	function getRawBySeqid($seqid) {
	/*	$nucSeqDao= new NucSeqDao();
		$result=$nucSeqDao->searchRawBySeqid($seqid);
		return NucSeqManager::genDataObjs($result);*/

		$seqData=SeqDataManager::getBySeqId($seqid);
		if($seqData!=NULL)
			$raw=NucSeqManager::generateRaw($seqData);
		return $raw;
	}

	function getRawBySeqidArray($seqids) {
	/*	$nucSeqDao= new NucSeqDao();
		$result=$nucSeqDao->searchRawBySeqid($seqid);
		return NucSeqManager::genDataObjs($result);*/

		$seqData=SeqDataManager::getBySeqidArray($seqids);
		if($seqData!=NULL)
			$raw=NucSeqManager::generateRaw($seqData);
		return $raw;
	}


	function getRawBySeqidMarker($seqid,$marker) {
		//echo "getting : '$seqid'  '$marker'\n";
		$seqData=SeqDataManager::getBySeqIdMarker($seqid,$marker);
		if($seqData!=NULL)
			$raw=NucSeqManager::generateRaw($seqData);
		return $raw;
	}

	function getRawLengthBySeqidMarker($seqid,$marker) {
		$seqData = SeqDataManager::getLengthsBySeqIdMarker($seqid, $marker);
		if ( $seqData == NULL ) return NULL;
			return $seqData->getNucRawLength();
	}

	function getAlnLengthBySeqidMarker($seqid,$marker) {
		$seqData = SeqDataManager::getLengthsBySeqIdMarker($seqid, $marker);
		if ( $seqData == NULL ) return NULL;
			return $seqData->getNucAlnLength();
	}




	function getAlnBySeqid($seqid) {
	/*	$nucSeqDao= new NucSeqDao();
		$result=$nucSeqDao->searchAlnBySeqid($seqid);
		return NucSeqManager::genDataObjs($result);*/

		$seqData=SeqDataManager::getBySeqId($seqid);
		if($seqData!=NULL)
			$aln=NucSeqManager::generateAln($seqData);
		return $aln;
	}

	function getAlnBySeqidMarker($seqid,$marker) {

		$seqData=SeqDataManager::getBySeqidMarker($seqid,$marker);
		if($seqData!=NULL)
			$aln=NucSeqManager::generateAln($seqData);
		return $aln;
	}

	function saveRawSeq($seqObj,$site=NULL) {
		//$nucSeqDao= new NucSeqDao();
		$seqDataManager=new SeqDataManager();
		//$nucSeqDao->deleteRawBySeqidMarker($seqObj->getId(), $seqObj->getMarker());
		//$nucSeqDao->deleteAlnBySeqidMarker($seqObj->getId(), $seqObj->getMarker() );
		$seqObj->calcLength();
		/*$nucSeqDao->insertRaw(
			$seqObj->getId(),
			$seqObj->getSeq(),
			$seqObj->getLength(),
			$seqObj->getCds(),
			$seqObj->getAmbiguous(),
			$seqObj->getMarker()
		);*/
		//insert data into seqdata table
		$seqData=new SeqData();
		$seqData->setSeqId($seqObj->getId());
		$seqData->setMarker($seqObj->getMarker());
		$seqData->setNucRaw($seqObj->getSeq());
		$seqData->setNucRawLength($seqObj->getLength());
		$seqData->setNucRawCds($seqObj->getCds());
		$seqData->setSite($site);
		$seqDataManager->saveNucRaw($seqData);
	}

	function saveAlnSeq($seqObj) {
		//$nucSeqDao= new nucSeqDao();
		$seqDataManager=new SeqDataManager();

		/*$nucSeqDao->deleteAlnBySeqidMarker($seqObj->getId(), $seqObj->getMarker());
		$nucSeqDao->insertAln(
			$seqObj->getId(),
			$seqObj->getSeq(),
			$seqObj->getLength(),"NULL",
			$seqObj->getAmbiguous(),
			$seqObj->getMarker()
		);*/
		$seqData=new SeqData();
		$seqData->setSeqId($seqObj->getId());
		$seqData->setNucAln($seqObj->getSeq());
		$seqData->setNucAlnLength($seqObj->getLength());
		$seqData->setNucAlnCds($seqObj->getCds());

		$seqDataManager->saveNucAln($seqData);
	}

	//deprecated Jun 14, 2011 (no ambigoug count stored in DB table anymore)
	function updateAmbiguousNucaln($seqidarray){
		/*$nucSeqDao= new nucSeqDao();
		$nucSeqDao->updateAmbiguousAln($seqidarray);*/
	}

	function getAlnByDate($start=NULL,$end=NULL){
	/*	$nucSeqDao = new NucSeqDao();
		$result=$nucSeqDao->getAlnByDate($start,$end);
		return NucSeqManager::genDataObjs($result);*/

		$nucSeqArray=array();
		$seqDataArray=SeqDataManager::getByDate($start,$end);
		return NucSeqManager::generateAln($seqDataArray);
	}

	function getAlnByDateMarker($start=NULL,$end=NULL,$marker){
	/*	$nucSeqDao = new NucSeqDao();
		$result=$nucSeqDao->getAlnByDate($start,$end);
		return NucSeqManager::genDataObjs($result);*/

		$nucSeqArray=array();
		$seqDataArray=SeqDataManager::getByDateMarker($start,$end,$marker);
		return NucSeqManager::generateAln($seqDataArray);
	}

	function getRawByDate($start=NULL,$end=NULL){
	/*	$nucSeqDao= new NucSeqDao();
		$result=$nucSeqDao->getAlnByDate($start,$end);
		return NucSeqManager::genDataObjs($result);*/

		$nucSeqArray=array();
		$seqDataArray=SeqDataManager::getByDate($start,$end);
		return NucSeqManager::generateRaw($seqDataArray);
	}

	function getRawByDateMarker($start=NULL,$end=NULL,$marker){

		$nucSeqArray=array();
		$seqDataArray=SeqDataManager::getByDateMarker($start,$end,$marker);
		return NucSeqManager::generateRaw($seqDataArray);
	}

	// FUNCTIONS FOR MULTIGENE TRANSITION
	function generateRaw($seqdataArray) {

		if ( !is_array ($seqdataArray) )
			$seqdataArray = array( $seqdataArray);

		foreach ( $seqdataArray as $seqdata )
		{
			$nucSeq=new CodingSeq($seqdata->getSeqId());
			$nucSeq->setSeq($seqdata->getNucRaw());
			$nucSeq->setLength($seqdata->getNucRawLength());
			$nucSeq->setCds($seqdata->getNucRawCds());
			$nucSeq->setUpdated($seqdata->getUpdate());
			$nucSeq->setAmbiguous($seqdata->getAmbiguous());
			$nucSeq->setMarker($seqdata->getMarker());
			$result[] = $nucSeq;
		}

		if ( count($result) == 1 )
			return $result[0];
		return $result;
	}

	function generateAln($seqdataArray) {
		if ( !is_array ($seqdataArray) )
			$seqdataArray = array( $seqdataArray);

		foreach ( $seqdataArray as $seqdata )
		{
			if ( count($seqdata->getNucAln()) == 0 )
				continue;
			$nucSeq=new CodingSeq($seqdata->getSeqId());
			$nucSeq->setSeq($seqdata->getNucAln());
			$nucSeq->setLength($seqdata->getNucRawLength());
			$nucSeq->setCds($seqdata->getNucAlnCds());
			$nucSeq->setUpdated($seqdata->getUpdate());
			$nucSeq->setAmbiguous($seqdata->getAmbiguous());
			$nucSeq->setMarker($seqdata->getMarker());
			$result[] = $nucSeq;
		}

		if ( count($result) == 1 )
			return $result[0];
		return $result;
	}
}



?>