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Add RNA types #170

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Add RNA types #170

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121 changes: 53 additions & 68 deletions src/js/read-mijson.js
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Original file line number Diff line number Diff line change
@@ -1,21 +1,21 @@
import {Annotation} from "./viz/interactor/annotation";
import {Protein} from "./viz/interactor/protein";
import {BioactiveEntity} from "./viz/interactor/bioactive-entity";
import {BioactiveEntity} from "./viz/interactor/bioactive-entity";
import {Gene} from "./viz/interactor/gene";
import {DNA} from "./viz/interactor/dna";
import {RNA} from "./viz/interactor/rna";
import {Complex} from "./viz/interactor/complex";
import {ComplexSymbol} from "./viz/interactor/complex-symbol";
import {MoleculeSet} from "./viz/interactor/molecule-set";
import {MoleculeSet} from "./viz/interactor/molecule-set";
import {NaryLink} from "./viz/link/nary-link";
import {FeatureLink} from "./viz/link/feature-link";
import {SequenceDatum} from "./viz/sequence-datum";
import {SequenceDatum} from "./viz/sequence-datum";
import {BinaryLink} from "./viz/link/binary-link";
import {UnaryLink} from "./viz/link/unary-link";
import {UnaryLink} from "./viz/link/unary-link";
import {matrix} from "./expand";

// reads MI JSON format
export function readMijson (/*miJson*/miJson, /*App*/ app, expand = true) {
export function readMijson(/*miJson*/miJson, /*App*/ app, expand = true) {
//check that we've got a parsed javascript object here, not a String
miJson = (typeof miJson === "object") ? miJson : JSON.parse(miJson);
miJson.data = miJson.data.reverse();
Expand Down Expand Up @@ -215,6 +215,7 @@ export function readMijson (/*miJson*/miJson, /*App*/ app, expand = true) {

function newParticipant(interactor, participantId, interactorRef) {
let participant;

if (typeof interactor == "undefined" || interactor.type.id === "MI:1302") {
//must be a previously unencountered complex -
// MI:0314 - interaction?, MI:0317 - complex? and its many subclasses
Expand All @@ -227,75 +228,59 @@ export function readMijson (/*miJson*/miJson, /*App*/ app, expand = true) {
}
}


if (interactionExists) {
participant = new Complex(participantId, app, interactorRef);
complexes.set(participantId, participant);
} else {
participant = new ComplexSymbol(participantId, app, interactorRef, interactor);
}
}else if (interactor.type.id === "MI:1304" //molecule set
||
interactor.type.id === "MI:1305" //molecule set - candidate set
||
interactor.type.id === "MI:1307" //molecule set - defined set
||
interactor.type.id === "MI:1306" //molecule set - open set
) {
participant = new MoleculeSet(participantId, app, interactor, interactor.label);
} else if (interactor.type.id === "MI:1100" // bioactive entity
||
interactor.type.id === "MI:0904" // bioactive entity - polysaccharide
||
interactor.type.id === "MI:0328" //bioactive entity - small mol
) {
participant = new BioactiveEntity(participantId, app, interactor, interactor.label);
} else if (interactor.type.id === "MI:0326" || interactor.type.id === "MI:0327") { // proteins, peptides
participant = new Protein(participantId, app, interactor, interactor.label, interactor.sequence);
} else if (interactor.type.id === "MI:0250") { //genes
participant = new Gene(participantId, app, interactor, interactor.label);
} else if (interactor.type.id === "MI:0320" // RNA
||
interactor.type.id === "MI:0321" // RNA - catalytic
||
interactor.type.id === "MI:0322" // RNA - guide
||
interactor.type.id === "MI:0323" // RNA - heterogeneous nuclear
||
interactor.type.id === "MI:2190" // RNA - long non-coding
||
interactor.type.id === "MI:0324" // RNA - messenger
||
interactor.type.id === "MI:0679" // RNA - poly adenine
||
interactor.type.id === "MI:0608" // RNA - ribosomal
||
interactor.type.id === "MI:0611" // RNA - signal recognition particle
||
interactor.type.id === "MI:0610" // RNA - small interfering
||
interactor.type.id === "MI:0607" // RNA - small nuclear
||
interactor.type.id === "MI:0609" // RNA - small nucleolar
||
interactor.type.id === "MI:0325" // RNA - transfer
||
interactor.type.id === "IA:2966" // RNA - double stranded ribonucleic acid
||
interactor.type.id === "MI:0318" // nucleic acid
) {
participant = new RNA(participantId, app, interactor, interactor.label);
} else if (interactor.type.id === "MI:0319" // DNA
||
interactor.type.id === "MI:0681" // DNA - double stranded
||
interactor.type.id === "MI:0680" // DNA - single stranded
) {
participant = new DNA(participantId, app, interactor, interactor.label);
} else {
// MI:0329 - unknown participant ?
// MI:0383 - biopolymer ?
alert("Unrecognised type:" + interactor.type.name);
} else switch (interactor.type.id) {
case "MI:1304": // molecule set
case "MI:1305": // molecule set - candidate set
case "MI:1307": // molecule set - defined set
case "MI:1306": // molecule set - open set
participant = new MoleculeSet(participantId, app, interactor, interactor.label);
break;
case "MI:1100": // bioactive entity
case "MI:0904": // bioactive entity - polysaccharide
case "MI:0328": // bioactive entity - small molecule
case "MI:2258": // bioactive entity - xenobiotic
participant = new BioactiveEntity(participantId, app, interactor, interactor.label);
break;
case "MI:0326": // proteins
case "MI:0327": // peptides
participant = new Protein(participantId, app, interactor, interactor.label, interactor.sequence);
break;
case "MI:0250": // genes
participant = new Gene(participantId, app, interactor, interactor.label);
break;
case "MI:0318": // Nucleic Acid
case "MI:0320": // RNA
case "MI:0321": // RNA - catalytic RNA
case "MI:0322": // RNA - guide RNA
case "MI:0323": // RNA - heterogeneous nuclear rna
case "MI:0324": // RNA - messenger rna
case "MI:0325": // RNA - transfer rna
case "MI:0607": // RNA - small nuclear rna
case "MI:0608": // RNA - ribosomal rna
case "MI:0609": // RNA - small nucleolar rna
case "MI:0610": // RNA - small interfering rna
case "MI:0611": // RNA - signal recognition particle rna
case "MI:0679": // RNA - poly adenine
case "MI:2190": // RNA - long non-coding ribonucleic acid
case "MI:2204": // RNA - micro rna
case "MI:2359": // RNA - ds rna
participant = new RNA(participantId, app, interactor, interactor.label);
break;
case "MI:0319": // DNA
case "MI:0681": // DNA - double stranded
case "MI:0680": // DNA - single stranded
participant = new DNA(participantId, app, interactor, interactor.label);
break;
default:
// MI:0329 - unknown participant ?
// MI:0383 - biopolymer ?
alert("Unrecognised type:" + interactor.type.name);
}
return participant;
}
Expand Down