src/Reader/MzIdentMlReader1r1.php
public function getProteinDetectionList()
    {
        $this->getSequenceCollection();

        $groups = array();

        if (! isset($this->xmlReader->DataCollection->AnalysisData->ProteinDetectionList->ProteinAmbiguityGroup)) {
            return null;
        }

        foreach ($this->xmlReader->DataCollection->AnalysisData->ProteinDetectionList->ProteinAmbiguityGroup as $proteinAmbiguityGroup) {
            $group = $this->getProteinAmbiguityGroup($proteinAmbiguityGroup);
            $groupId = $this->getAttributeId($proteinAmbiguityGroup);
            // Reprocess each group to change refs to element
            foreach ($group as $id => $value) {
                $group[$id]['protein'] = $this->proteins[$value['protein']];

                foreach ($value['peptides'] as $pepId => $peptide) {
                    $group[$id]['peptides'][$pepId] = $this->peptides[$this->evidence[$peptide['peptide']]['peptide']];
                }
            }

            $groups[$groupId] = $group;
        }

        return $groups;
    }
public function getProteinDetectionList()
    {
        $this->getSequenceCollection();

        $groups = array();

        if (! isset($this->xmlReader->DataCollection->AnalysisData->ProteinDetectionList->ProteinAmbiguityGroup)) {
            return null;
        }

        foreach ($this->xmlReader->DataCollection->AnalysisData->ProteinDetectionList->ProteinAmbiguityGroup as $proteinAmbiguityGroup) {
            $group = $this->getProteinAmbiguityGroup($proteinAmbiguityGroup);
            $groupId = $this->getAttributeId($proteinAmbiguityGroup);
            // Reprocess each group to change refs to element
            foreach ($group as $id => $value) {
                $group[$id]['protein'] = $this->proteins[$value['protein']];

                foreach ($value['peptides'] as $pepId => $peptide) {
                    $group[$id]['peptides'][$pepId] = $this->peptides[$this->evidence[$peptide['peptide']]['peptide']];
                }
            }

            $groups[$groupId] = $group;
        }

        return $groups;
    }
public function getProteinDetectionList ( ) { $ this -> getSequenceCollection ( ) ; $ groups = array ( ) ; if ( ! isset ( $ this -> xmlReader -> DataCollection -> AnalysisData -> ProteinDetectionList -> ProteinAmbiguityGroup ) ) { return null ; } foreach ( $ this -> xmlReader -> DataCollection -> AnalysisData -> ProteinDetectionList -> ProteinAmbiguityGroup as $ proteinAmbiguityGroup ) { $ group = $ this -> getProteinAmbiguityGroup ( $ proteinAmbiguityGroup ) ; $ groupId = $ this -> getAttributeId ( $ proteinAmbiguityGroup ) ; // Reprocess each group to change refs to element foreach ( $ group as $ id => $ value ) { $ group [ $ id ] [ 'protein' ] = $ this -> proteins [ $ value [ 'protein' ] ] ; foreach ( $ value [ 'peptides' ] as $ pepId => $ peptide ) { $ group [ $ id ] [ 'peptides' ] [ $ pepId ] = $ this -> peptides [ $ this -> evidence [ $ peptide [ 'peptide' ] ] [ 'peptide' ] ] ; } } $ groups [ $ groupId ] = $ group ; } return $ groups ; }
The protein list resulting from a protein detection process.
The protein list resulting from a protein detection process .