From 1317a035459586589db40654cbb9fe4733bdca19 Mon Sep 17 00:00:00 2001
From: Elora-V <elora95.vigo@gmail.com>
Date: Mon, 16 Sep 2024 08:13:00 +0200
Subject: [PATCH] remove .value for all network
---
src/composables/CalculateRelationCycle.ts | 20 +++----
src/composables/CalculateSize.ts | 16 +++---
src/composables/ConvertFromNetwork.ts | 6 +--
src/composables/ConvertToNetwork.ts | 2 +-
src/composables/LayoutDrawCycle.ts | 54 +++++++++----------
src/composables/LayoutFindCycle.ts | 10 ++--
src/composables/LayoutMain.ts | 10 ++--
src/composables/LayoutMainChain.ts | 4 +-
src/composables/LayoutManageSideCompounds.ts | 30 +++++------
src/composables/LayoutReversibleReactions.ts | 6 +--
src/composables/LayoutSugiyamaForce.ts | 2 +-
src/composables/SubgraphForSubgraphNetwork.ts | 2 +-
src/composables/SubgraphForViz.ts | 2 +-
.../__tests__/CalculateRelationCycle.tests.ts | 5 +-
.../__tests__/CalculateSize.tests.ts | 17 +++---
src/types/SubgraphNetwork.ts | 4 +-
16 files changed, 94 insertions(+), 96 deletions(-)
diff --git a/src/composables/CalculateRelationCycle.ts b/src/composables/CalculateRelationCycle.ts
index 2ce533a..60cef57 100644
--- a/src/composables/CalculateRelationCycle.ts
+++ b/src/composables/CalculateRelationCycle.ts
@@ -133,10 +133,10 @@ export function neighborsGroupCycle(subgraphNetwork:SubgraphNetwork,cycleGroupId
*/
export function parentNodeNotInCycle(subgraphNetwork: SubgraphNetwork, listNodes: string[]): string[][] {
const parentNodes = listNodes.map((node: string) => {
- const parentNodesI = subgraphNetwork.network.value.links
+ const parentNodesI = subgraphNetwork.network.links
.filter(link => link.target.id === node) // get link with those node as child
.map(link => link.source.id) // get the other node
- .filter(id => !inCycle(subgraphNetwork.network.value, id)) // no node in a cycle
+ .filter(id => !inCycle(subgraphNetwork.network, id)) // no node in a cycle
return parentNodesI;
});
return parentNodes;
@@ -152,10 +152,10 @@ export function parentNodeNotInCycle(subgraphNetwork: SubgraphNetwork, listNodes
*/
export function childNodeNotInCycle(subgraphNetwork: SubgraphNetwork, listNodes: string[]): string[][] {
const childNodes = listNodes.map((node: string) => {
- const childNodesI = subgraphNetwork.network.value.links
+ const childNodesI = subgraphNetwork.network.links
.filter(link => link.source.id === node) // get link with those node as parent
.map(link => link.target.id) // get the other node
- .filter(id => !inCycle(subgraphNetwork.network.value, id)) // no node in a cycle
+ .filter(id => !inCycle(subgraphNetwork.network, id)) // no node in a cycle
return childNodesI;
});
@@ -321,7 +321,7 @@ export function sortLinksWithAllGroupCycle(subgraphNetwork:SubgraphNetwork,order
links=links.concat(resultSorting.linksOrdered);
});
// add other links
- Object.values(subgraphNetwork.network.value.links).forEach((link) => {
+ Object.values(subgraphNetwork.network.links).forEach((link) => {
if (!links.includes(link)){
links.push(link);
}
@@ -329,7 +329,7 @@ export function sortLinksWithAllGroupCycle(subgraphNetwork:SubgraphNetwork,order
return { subgraphNetwork:subgraphNetwork,linksOrdered:links };
}else{ // no change
- return { subgraphNetwork:subgraphNetwork,linksOrdered:subgraphNetwork.network.value.links };
+ return { subgraphNetwork:subgraphNetwork,linksOrdered:subgraphNetwork.network.links };
}
}
@@ -395,12 +395,12 @@ function sortLinksWithGroupCycle(subgraphNetwork:SubgraphNetwork,groupCycle:stri
function getLinksNodeGroupCycle(subgraphNetwork:SubgraphNetwork,nodeId:string,groupCycleId:string,source:"node"|"groupCycle"):LinkLayout[]{
if (source==="node"){
// node to group cycle
- return Object.values(subgraphNetwork.network.value.links).filter((link) => {
+ return Object.values(subgraphNetwork.network.links).filter((link) => {
return link.source.id === nodeId && link.target.metadataLayout && TypeSubgraph.CYCLEGROUP in link.target.metadataLayout && link.target.metadataLayout[TypeSubgraph.CYCLEGROUP] === groupCycleId;
});
}else{
// group cycle to node
- return Object.values(subgraphNetwork.network.value.links).filter((link) => {
+ return Object.values(subgraphNetwork.network.links).filter((link) => {
return link.target.id === nodeId && link.source.metadataLayout && TypeSubgraph.CYCLEGROUP in link.source.metadataLayout && link.source.metadataLayout[TypeSubgraph.CYCLEGROUP] === groupCycleId;
});
}
@@ -441,7 +441,7 @@ export function getListNodeLinksForCycleGroup(subgraphNetwork:SubgraphNetwork,gr
:{nodes:{ id: string,fx?:number, fy?:number,x?:number,y?:number }[],links:{source:string,target:string}[]}{
const nodesGroupCycle=getNodesPlacedInGroupCycle(subgraphNetwork,groupCycleName,positionAsFixed);
const nodesGroupCycleName=Object.values(nodesGroupCycle).map(node=>node.id);
- const linksGroupCycle=getLinksForListNodes(subgraphNetwork.network.value,nodesGroupCycleName);
+ const linksGroupCycle=getLinksForListNodes(subgraphNetwork.network,nodesGroupCycleName);
return {nodes:nodesGroupCycle,links:linksGroupCycle};
}
@@ -457,7 +457,7 @@ export function getListNodeLinksForCycleGroupAsObject(subgraphNetwork:SubgraphNe
:{nodes:{[key:string]:{ x:number,y:number }},links:{source:string,target:string}[]}{
const nodesGroupCycle=getNodesPlacedInGroupCycleAsObject(subgraphNetwork,groupCycleName);
const nodesGroupCycleName=Object.keys(nodesGroupCycle);
- const linksGroupCycle=getLinksForListNodes(subgraphNetwork.network.value,nodesGroupCycleName);
+ const linksGroupCycle=getLinksForListNodes(subgraphNetwork.network,nodesGroupCycleName);
return {nodes:nodesGroupCycle,links:linksGroupCycle};
}
diff --git a/src/composables/CalculateSize.ts b/src/composables/CalculateSize.ts
index b1366aa..c564f7c 100644
--- a/src/composables/CalculateSize.ts
+++ b/src/composables/CalculateSize.ts
@@ -290,8 +290,8 @@ export function rectangleSize(listCoordinates:Coordinate[],listID?:string[],subg
minX = -defaultWidthNode/2;
} else {
const minXNode = listID[minXIndex];
- if (!(minXNode in subgraphNetwork.network.value.nodes)) throw new Error("Node not in network");
- const sizeMinXNode = getSizeNodePixel(subgraphNetwork.network.value.nodes[minXNode],subgraphNetwork.networkStyle.value);
+ if (!(minXNode in subgraphNetwork.network.nodes)) throw new Error("Node not in network");
+ const sizeMinXNode = getSizeNodePixel(subgraphNetwork.network.nodes[minXNode],subgraphNetwork.networkStyle);
minX = minX - sizeMinXNode.width/2;
}
@@ -300,8 +300,8 @@ export function rectangleSize(listCoordinates:Coordinate[],listID?:string[],subg
maxX = defaultWidthNode/2;
}else {
const maxXNode = listID[maxXIndex];
- if (!(maxXNode in subgraphNetwork.network.value.nodes)) throw new Error("Node not in network");
- const sizeMaxXNode = getSizeNodePixel(subgraphNetwork.network.value.nodes[maxXNode],subgraphNetwork.networkStyle.value);
+ if (!(maxXNode in subgraphNetwork.network.nodes)) throw new Error("Node not in network");
+ const sizeMaxXNode = getSizeNodePixel(subgraphNetwork.network.nodes[maxXNode],subgraphNetwork.networkStyle);
maxX = maxX + sizeMaxXNode.width/2;
}
@@ -310,8 +310,8 @@ export function rectangleSize(listCoordinates:Coordinate[],listID?:string[],subg
minY = -defaultHeightNode/2;
} else {
const minYNode = listID[minYIndex];
- if (!(minYNode in subgraphNetwork.network.value.nodes)) throw new Error("Node not in network");
- const sizeMinYNode = getSizeNodePixel(subgraphNetwork.network.value.nodes[minYNode],subgraphNetwork.networkStyle.value);
+ if (!(minYNode in subgraphNetwork.network.nodes)) throw new Error("Node not in network");
+ const sizeMinYNode = getSizeNodePixel(subgraphNetwork.network.nodes[minYNode],subgraphNetwork.networkStyle);
minY = minY - sizeMinYNode.height/2;
}
@@ -320,8 +320,8 @@ export function rectangleSize(listCoordinates:Coordinate[],listID?:string[],subg
maxY = defaultHeightNode/2;
} else {
const maxYNode = listID[maxYIndex];
- if (!(maxYNode in subgraphNetwork.network.value.nodes)) throw new Error("Node not in network");
- const sizeMaxYNode = getSizeNodePixel(subgraphNetwork.network.value.nodes[maxYNode],subgraphNetwork.networkStyle.value);
+ if (!(maxYNode in subgraphNetwork.network.nodes)) throw new Error("Node not in network");
+ const sizeMaxYNode = getSizeNodePixel(subgraphNetwork.network.nodes[maxYNode],subgraphNetwork.networkStyle);
maxY = maxY + sizeMaxYNode.height/2;
}
}
diff --git a/src/composables/ConvertFromNetwork.ts b/src/composables/ConvertFromNetwork.ts
index af84107..6fd32ac 100644
--- a/src/composables/ConvertFromNetwork.ts
+++ b/src/composables/ConvertFromNetwork.ts
@@ -290,7 +290,7 @@ export function networkToViz(subgraphNetwork:SubgraphNetwork,cycle:boolean=true,
// insert nodes
if (addNodes){
- Object.entries(subgraphNetwork.network.value.nodes)
+ Object.entries(subgraphNetwork.network.nodes)
.sort(([keyA], [keyB]) => keyA.localeCompare(keyB))
.forEach(([key, node])=> {
const nodeViz=nodeForViz(subgraphNetwork,node,cycle,groupOrCluster);
@@ -379,10 +379,10 @@ export function networkToViz(subgraphNetwork:SubgraphNetwork,cycle:boolean=true,
*/
function nodeForViz(subgraphNetwork:SubgraphNetwork,node:NodeLayout,cycle:boolean,groupOrCluster:"group"|"cluster"):{name:string,attributes:AttributesViz}|undefined{
// if cycle not taken into account or not in cycle
- if (!cycle || !inCycle(subgraphNetwork.network.value,node.id)){
+ if (!cycle || !inCycle(subgraphNetwork.network,node.id)){
const attributes:AttributesViz={};
// size of node in inches
- const sizeNode= getSizeNodePixel(node,subgraphNetwork.networkStyle.value);
+ const sizeNode= getSizeNodePixel(node,subgraphNetwork.networkStyle);
attributes.height=pixelsToInches(sizeNode.height);
attributes.width=pixelsToInches(sizeNode.width);
attributes.fixedsize=true;
diff --git a/src/composables/ConvertToNetwork.ts b/src/composables/ConvertToNetwork.ts
index 76bd682..4b0f600 100644
--- a/src/composables/ConvertToNetwork.ts
+++ b/src/composables/ConvertToNetwork.ts
@@ -88,7 +88,7 @@ export function networkLayoutToNetwork(networkLayout: NetworkLayout): Network {
* @param assignRank boolean that indicates if rank and order need to be infered and assigned to nodes
*/
export async function changeNetworkFromViz(json: JsonViz, subgraphNetwork: SubgraphNetwork, assignRank:boolean=false): Promise<SubgraphNetwork> {
- const network=subgraphNetwork.network.value;
+ const network=subgraphNetwork.network;
const unique_y:Array<number> =[];
json["objects"].forEach((node) => {
diff --git a/src/composables/LayoutDrawCycle.ts b/src/composables/LayoutDrawCycle.ts
index 7d55213..8ab2523 100644
--- a/src/composables/LayoutDrawCycle.ts
+++ b/src/composables/LayoutDrawCycle.ts
@@ -38,7 +38,7 @@ import { childNodeNotInCycle, getListNodeLinksForCycleGroup, getListNodeLinksFor
*/
export async function coordinateAllCycles(subgraphNetwork:SubgraphNetwork,allowInterncircle:boolean=false):Promise<SubgraphNetwork> {
- const network = subgraphNetwork.network.value;
+ const network = subgraphNetwork.network;
const cycles = subgraphNetwork.cycles? Object.values(subgraphNetwork.cycles):undefined;
let i=0
let newGroup=true;
@@ -142,7 +142,7 @@ function addNewCycleGroup(subgraphNetwork:SubgraphNetwork, groupName:string):Sub
* @returns A number indicating the sorting order.
*/
function sortingCycleForDrawing(subgraphNetwork:SubgraphNetwork,a:Subgraph,b:Subgraph,fullConstraint:boolean=false):number{
- const network=subgraphNetwork.network.value;
+ const network=subgraphNetwork.network;
// first sort by number of fixed nodes
const fixedNodesA = a.nodes.filter(node => network.nodes[node].metadata && network.nodes[node].metadata.fixedCycle).length;
@@ -188,7 +188,7 @@ function sortingCycleForDrawing(subgraphNetwork:SubgraphNetwork,a:Subgraph,b:Sub
* @returns The updated subgraph network with the nodes placed in the cycle.
*/
async function coordinateCycle(subgraphNetwork:SubgraphNetwork, cycleToDrawID:string,groupCycleName:string,allowInterncircle:boolean=true):Promise<SubgraphNetwork>{
- const network = subgraphNetwork.network.value;
+ const network = subgraphNetwork.network;
// Get nodes to place
let cycle:string[]=[];
@@ -241,11 +241,11 @@ async function coordinateCycle(subgraphNetwork:SubgraphNetwork, cycleToDrawID:st
}
async function independentCycleCoordinates(subgraphNetwork:SubgraphNetwork,cycleToDrawID:string,groupCycleName:string):Promise<SubgraphNetwork>{
- const network = subgraphNetwork.network.value;
+ const network = subgraphNetwork.network;
const cycle=subgraphNetwork.cycles[cycleToDrawID].nodes;
// radius and centroid
- const radius = await getRadiusSize(cycle,network,subgraphNetwork.networkStyle.value);
+ const radius = await getRadiusSize(cycle,network,subgraphNetwork.networkStyle);
// first cycle centered at 0,0
const centroidX=0;
const centroidY=0;
@@ -263,7 +263,7 @@ async function independentCycleCoordinates(subgraphNetwork:SubgraphNetwork,cycle
}
async function tangentCycleCoordinates(subgraphNetwork:SubgraphNetwork,cycleToDrawID:string,groupCycleName:string,nodeFixed:Node,nodesPlaced:string[],allowInterncircle:boolean=false):Promise<SubgraphNetwork>{
- const network = subgraphNetwork.network.value;
+ const network = subgraphNetwork.network;
const cycle=subgraphNetwork.cycles[cycleToDrawID].nodes;
// get fixed node coordinates (in the group cycle)
@@ -276,7 +276,7 @@ async function tangentCycleCoordinates(subgraphNetwork:SubgraphNetwork,cycleToDr
const shiftedCycle = cycleCopy.splice(firstIndex).concat(cycleCopy);
// radius
- const radius = await getRadiusSize(cycle,network,subgraphNetwork.networkStyle.value);
+ const radius = await getRadiusSize(cycle,network,subgraphNetwork.networkStyle);
subgraphNetwork.cycles[cycleToDrawID].metadata.radius=radius;
//centroid depending on fixed cycle
@@ -365,7 +365,7 @@ async function getRadiusSize(cycle:string[],network:Network,styleNetwork:GraphSt
function cycleNodesCoordinates(cycleName:string,cycle:string[],centroidX:number,centroidY:number,radius:number,subgraphNetwork:SubgraphNetwork,
shiftAngle:number=-Math.PI/2,groupcycle?:string,):{subgraphNetwork:SubgraphNetwork,positionBefore:{[key:string]:{x:number,y:number}}}{
- const network=subgraphNetwork.network.value;
+ const network=subgraphNetwork.network;
let positionBefore:{[key:string]:{x:number,y:number}}={};
cycle.forEach((node, i) => {
@@ -396,12 +396,12 @@ function cycleNodesCoordinates(cycleName:string,cycle:string[],centroidX:number,
}
} else if (node in subgraphNetwork.network.value.nodes) {
// get position before drawing cycle
- const xBefore=subgraphNetwork.network.value.nodes[node].x;
- const yBefore=subgraphNetwork.network.value.nodes[node].x;
+ const xBefore=subgraphNetwork.network.nodes[node].x;
+ const yBefore=subgraphNetwork.network.nodes[node].x;
positionBefore[node]={x:xBefore,y:yBefore};
// assign new position
- subgraphNetwork.network.value.nodes[node].x=x;
- subgraphNetwork.network.value.nodes[node].y=y;
+ subgraphNetwork.network.nodes[node].x=x;
+ subgraphNetwork.network.nodes[node].y=y;
} else{
console.error("Node not in network or groupcycle not provided")
}
@@ -436,12 +436,12 @@ function undoIfOverlap(subgraphNetwork:SubgraphNetwork,groupCycleName:string,pos
function isOverlapCycles(subgraphNetwork:SubgraphNetwork,groupCycleName:string):boolean{
const graph =getListNodeLinksForCycleGroupAsObject(subgraphNetwork,groupCycleName);
// intersection of edges :
- const intersectionEdges=isIntersectionGraph(graph.nodes ,graph.links,subgraphNetwork.network.value,subgraphNetwork.networkStyle.value);
+ const intersectionEdges=isIntersectionGraph(graph.nodes ,graph.links,subgraphNetwork.network,subgraphNetwork.networkStyle.value);
if (intersectionEdges){
return true;
}else{
// overlap of nodes
- const nodesOverlap=isOverlapNodes(graph.nodes,subgraphNetwork.network.value,subgraphNetwork.networkStyle.value);
+ const nodesOverlap=isOverlapNodes(graph.nodes,subgraphNetwork.network,subgraphNetwork.networkStyle.value);
if (nodesOverlap){
return true;
}else{
@@ -467,7 +467,7 @@ function isOverlapCycles(subgraphNetwork:SubgraphNetwork,groupCycleName:string):
function getUnfixedIntervals(nodes:string[],subgraphNetwork:SubgraphNetwork) {
let intervals:number[][] = [];
let start = null;
- const network=subgraphNetwork.network.value;
+ const network=subgraphNetwork.network;
nodes.forEach((nodeID,i) => {
const node=network.nodes[nodeID];
if (node.metadata && !node.metadata.fixedInCycle) {
@@ -508,7 +508,7 @@ function getUnfixedIntervals(nodes:string[],subgraphNetwork:SubgraphNetwork) {
*/
function lineNodesCoordinates(start: {x: number, y: number}, end: {x: number, y: number}, nodes: string[],
subgraphNetwork:SubgraphNetwork,groupCycleName?:string):{subgraphNetwork:SubgraphNetwork,positionBefore:{[key:string]:{x:number,y:number}}} {
- const network=subgraphNetwork.network.value;
+ const network=subgraphNetwork.network;
let positionBefore:{[key:string]:{x:number,y:number}}={};
// Calculate direction vector
@@ -550,14 +550,14 @@ function lineNodesCoordinates(start: {x: number, y: number}, end: {x: number, y:
} else {
console.error("CycleGroup not in subgraphNetwork");
}
- } else if (node in subgraphNetwork.network.value.nodes) {
+ } else if (node in subgraphNetwork.network.nodes) {
// get position before drawing cycle
- const xBefore=subgraphNetwork.network.value.nodes[node].x;
- const yBefore=subgraphNetwork.network.value.nodes[node].x;
+ const xBefore=subgraphNetwork.network.nodes[node].x;
+ const yBefore=subgraphNetwork.network.nodes[node].x;
positionBefore[node]={x:xBefore,y:yBefore};
// assign new position
- subgraphNetwork.network.value.nodes[node].x=x;
- subgraphNetwork.network.value.nodes[node].y=y;
+ subgraphNetwork.network.nodes[node].x=x;
+ subgraphNetwork.network.nodes[node].y=y;
} else{
console.error("Node not in network or groupcycle not provided")
}
@@ -585,7 +585,7 @@ function lineNodesCoordinates(start: {x: number, y: number}, end: {x: number, y:
* @returns An object containing the updated subgraph network and group number.
*/
async function updateGroupCycles(remainingCycles: Subgraph[], subgraphNetwork: SubgraphNetwork, group: number, groupCycleName: string): Promise<{subgraphNetwork: SubgraphNetwork, group: number}> {
- const network = subgraphNetwork.network.value;
+ const network = subgraphNetwork.network;
const groupCycleIsDraw = isRemainingCycleIndepOfDrawing(remainingCycles, subgraphNetwork);
if (groupCycleIsDraw && subgraphNetwork.cyclesGroup[groupCycleName].metadata) {
@@ -630,7 +630,7 @@ async function forceGroupCycle(subgraphNetwork:SubgraphNetwork, groupCycleName:s
}
// get attributes for force layout
- const distanceLinks=medianEdgeLength(subgraphNetwork.network.value,false);
+ const distanceLinks=medianEdgeLength(subgraphNetwork.network,false);
const strengthManyBody=-distanceLinks*10;
// applying force layout
@@ -668,7 +668,7 @@ async function forceGroupCycle(subgraphNetwork:SubgraphNetwork, groupCycleName:s
*/
function isRemainingCycleIndepOfDrawing(remainingCycles:Subgraph[], subgraphNetwork:SubgraphNetwork):boolean{
- const network = subgraphNetwork.network.value;
+ const network = subgraphNetwork.network;
if (remainingCycles.every(cycle =>
cycle.nodes.every(node =>
@@ -762,7 +762,7 @@ function findTopCycleNode(subgraphNetwork: SubgraphNetwork, cycleNodes:string[])
* @returns An array of indices representing lists containing minimum y-coordinate nodes.
*/
function getNodesAssociatedMinY(subgraphNetwork: SubgraphNetwork, associatedListNodes: string[][]): number[] {
- const network=subgraphNetwork.network.value;
+ const network=subgraphNetwork.network;
let minY=Infinity;
let minNodes: number[] = [];
associatedListNodes.forEach((listNodes,i) => {
@@ -788,7 +788,7 @@ function getNodesAssociatedMinY(subgraphNetwork: SubgraphNetwork, associatedList
* @returns An array of indices representing lists containing maximum y-coordinate nodes.
*/
function getNodesAssociatedMaxY(subgraphNetwork: SubgraphNetwork, associatedListNodes: string[][]): number[] {
- const network=subgraphNetwork.network.value;
+ const network=subgraphNetwork.network;
let maxY=-Infinity;
let maxNodes:number[]=[];
associatedListNodes.forEach((listNodes,i) => {
@@ -814,7 +814,7 @@ function getNodesAssociatedMaxY(subgraphNetwork: SubgraphNetwork, associatedList
* @returns The name of the node with the median x-coordinate.
*/
function nodeMedianX(subgraphNetwork: SubgraphNetwork, listNodes: string[]): string {
- const network=subgraphNetwork.network.value;
+ const network=subgraphNetwork.network;
let xValues = listNodes.map(node => [node,network.nodes[node].x]);
xValues.sort((a, b) => Number(a[1]) - Number(b[1])); // sort by x
diff --git a/src/composables/LayoutFindCycle.ts b/src/composables/LayoutFindCycle.ts
index cde82c8..a0bba17 100644
--- a/src/composables/LayoutFindCycle.ts
+++ b/src/composables/LayoutFindCycle.ts
@@ -23,7 +23,7 @@ export function addDirectedCycleToSubgraphNetwork(subgraphNetwork:SubgraphNetwor
let existingCycle=true;
let i=0;
while (existingCycle && i< cycle[1].length){
- if (!(cycle[1][i] in subgraphNetwork.network.value.nodes)){
+ if (!(cycle[1][i] in subgraphNetwork.network.nodes)){
existingCycle=false;
}
i++;
@@ -32,7 +32,7 @@ export function addDirectedCycleToSubgraphNetwork(subgraphNetwork:SubgraphNetwor
if (existingCycle){
// update metada node : add cycle information
cycle[1].forEach(node=>{
- updateNodeMetadataSubgraph(subgraphNetwork.network.value,node,cycle[0],TypeSubgraph.CYCLE);
+ updateNodeMetadataSubgraph(subgraphNetwork.network,node,cycle[0],TypeSubgraph.CYCLE);
});
// remove reversible version of node in cycle, to only keep the one in the direction of cycle
const toRename=keepFirstReversibleNode(subgraphNetwork,cycle[1],false) as {[key: string]: string};
@@ -85,10 +85,10 @@ export function addDirectedCycleToSubgraphNetwork(subgraphNetwork:SubgraphNetwor
function getJohnsonCycles(subNetwork:SubgraphNetwork,onlyDirectedCycle:boolean=true,minsize:number=4):{[key:string]:string[]} {
// get graph structure for johnson algorithm
- const nodes=Object.keys(subNetwork.network.value.nodes).sort();
- const graph=graphForJohnson(subNetwork.network.value,nodes,onlyDirectedCycle);
+ const nodes=Object.keys(subNetwork.network.nodes).sort();
+ const graph=graphForJohnson(subNetwork.network,nodes,onlyDirectedCycle);
// apply johnson algorithm : get cycle
- return JohnsonAlgorithm(graph,nodes,"All",onlyDirectedCycle,minsize,subNetwork.network.value);
+ return JohnsonAlgorithm(graph,nodes,"All",onlyDirectedCycle,minsize,subNetwork.network);
}
diff --git a/src/composables/LayoutMain.ts b/src/composables/LayoutMain.ts
index 40f012f..05b65c4 100644
--- a/src/composables/LayoutMain.ts
+++ b/src/composables/LayoutMain.ts
@@ -63,8 +63,8 @@ export async function algorithmOnNetwork(network:Network,networkStyle:GraphStyle
// initialize the subgraphNetwork object
let subgraphNetwork:SubgraphNetwork={
- network:ref<NetworkLayout>(networkLayout),
- networkStyle:ref<GraphStyleProperties>(networkStyle)
+ network:networkLayout,
+ networkStyle:networkStyle
}
@@ -72,7 +72,7 @@ export async function algorithmOnNetwork(network:Network,networkStyle:GraphStyle
// change coordinates of the network with the algorithm
await allSteps(subgraphNetwork,parameters,true,true);
// convert networkLayout to network
- return networkLayoutToNetwork(subgraphNetwork.network.value);
+ return networkLayoutToNetwork(subgraphNetwork.network);
} catch(err){
console.log(" Error during execution of algorithm : " + err);
@@ -92,8 +92,8 @@ export async function algorithmOnNetwork(network:Network,networkStyle:GraphStyle
*/
export async function allSteps(subgraphNetwork: SubgraphNetwork,parameters:Parameters,shiftCoord:boolean=true,printNameStep:boolean=false):Promise<SubgraphNetwork> {
- let network=subgraphNetwork.network.value;
- let networkStyle=subgraphNetwork.networkStyle.value;
+ let network=subgraphNetwork.network;
+ let networkStyle=subgraphNetwork.networkStyle;
if (printNameStep){
console.log('_____________________________________________');
diff --git a/src/composables/LayoutMainChain.ts b/src/composables/LayoutMainChain.ts
index 36950fa..bd130f8 100644
--- a/src/composables/LayoutMainChain.ts
+++ b/src/composables/LayoutMainChain.ts
@@ -39,7 +39,7 @@ export function addMainChainFromSources(subgraphNetwork:SubgraphNetwork, sources
):SubgraphNetwork{
//console.log('create main chain from longest path');
- const network=subgraphNetwork.network.value;
+ const network=subgraphNetwork.network;
subgraphNetwork[TypeSubgraph.MAIN_CHAIN]={};
// get sources
@@ -76,7 +76,7 @@ export function addMainChainFromSources(subgraphNetwork:SubgraphNetwork, sources
*/
export function addMiniBranchToMainChain(subgraphNetwork:SubgraphNetwork):SubgraphNetwork{
//console.log('add mini branch to main chain');
- const network=subgraphNetwork.network.value;
+ const network=subgraphNetwork.network;
const graph=networkToGDSGraph(network);
// for each main chain :
Object.entries(subgraphNetwork.mainChains).forEach(([mainChainID,mainChain]:[string,Subgraph]) => {
diff --git a/src/composables/LayoutManageSideCompounds.ts b/src/composables/LayoutManageSideCompounds.ts
index 908c587..34416e9 100644
--- a/src/composables/LayoutManageSideCompounds.ts
+++ b/src/composables/LayoutManageSideCompounds.ts
@@ -150,7 +150,7 @@ import { error } from "console";
export async function addSideCompoundAttributeFromList(subgraphNetwork:SubgraphNetwork, pathListSideCompounds:string):Promise<void>{
const listIDSideCompounds = await getIDSideCompoundsInNetworkFromFile(subgraphNetwork,pathListSideCompounds);
listIDSideCompounds.forEach((sideCompoundID) => {
- setAsSideCompound(subgraphNetwork.network.value,sideCompoundID);
+ setAsSideCompound(subgraphNetwork.network,sideCompoundID);
});
}
@@ -162,7 +162,7 @@ export async function addSideCompoundAttributeFromList(subgraphNetwork:SubgraphN
*/
async function getIDSideCompoundsInNetworkFromFile(subgraphNetwork:SubgraphNetwork,pathListSideCompounds:string):Promise<string[]>{
let listIDSideCompounds:string[];
- const network = subgraphNetwork.network.value;
+ const network = subgraphNetwork.network;
try {
listIDSideCompounds = await getIDSideCompoundsFromFile(pathListSideCompounds);
const sideCompoundInNetwork = Object.keys(network.nodes).filter(id => listIDSideCompounds.includes(id));
@@ -256,8 +256,8 @@ export async function putDuplicatedSideCompoundAside(subgraphNetwork:SubgraphNet
* @returns void
*/
export async function duplicateSideCompound(subgraphNetwork:SubgraphNetwork):Promise<void>{
- const network = subgraphNetwork.network.value;
- const networkStyle = subgraphNetwork.networkStyle.value;
+ const network = subgraphNetwork.network;
+ const networkStyle = subgraphNetwork.networkStyle;
// duplication of side compounds
duplicateAllNodesByAttribut(network, networkStyle, sideCompoundAttribute);
// add attributes to side compounds duplicates
@@ -271,10 +271,10 @@ export async function duplicateSideCompound(subgraphNetwork:SubgraphNetwork):Pro
* @returns void
*/
function sideCompoundAttributeOnDuplicate(subgraphNetwork:SubgraphNetwork):void{
- const network = subgraphNetwork.network.value;
+ const network = subgraphNetwork.network;
Object.keys(network.nodes).forEach((nodeID)=>{
if(isDuplicate(network,nodeID)){
- setAsSideCompound(subgraphNetwork.network.value,nodeID);
+ setAsSideCompound(subgraphNetwork.network,nodeID);
}
});
}
@@ -289,7 +289,7 @@ function sideCompoundAttributeOnDuplicate(subgraphNetwork:SubgraphNetwork):void{
*/
function removeSideCompoundsFromNetwork(subgraphNetwork:SubgraphNetwork): SubgraphNetwork{
- const network = subgraphNetwork.network.value;
+ const network = subgraphNetwork.network;
subgraphNetwork.sideCompounds={};
const sideCompounds = subgraphNetwork.sideCompounds;
const listIDCoftactors:string[]=[];
@@ -336,7 +336,7 @@ export async function reinsertionSideCompounds(subgraphNetwork:SubgraphNetwork,f
const sideCompounds = subgraphNetwork.sideCompounds
// get information for length of edge for side compounds :
// get the min length of edge in the network (if not, use default value)
- let minLength=minEdgeLength(subgraphNetwork.network.value,false);
+ let minLength=minEdgeLength(subgraphNetwork.network,false);
// get the default value : min lenght if there is no link in the network (when side compounds are removed) :
if (isNaN(minLength)){
console.warn('Minimal edge length by default');
@@ -368,8 +368,8 @@ export async function reinsertionSideCompounds(subgraphNetwork:SubgraphNetwork,f
* @returns The calculated minimum edge length.
*/
async function minEdgeLengthDefault(subgraphNetwork:SubgraphNetwork,factorMinEdgeLength:number):Promise<number>{
- const network = subgraphNetwork.network.value;
- const networkStyle = subgraphNetwork.networkStyle.value;
+ const network = subgraphNetwork.network;
+ const networkStyle = subgraphNetwork.networkStyle;
const meanSize=await getMeanNodesSizePixel(Object.values(network.nodes),networkStyle, false);
const defaultSep=(meanSize.height+meanSize.width)/2;
if(subgraphNetwork.attributs){
@@ -387,7 +387,7 @@ async function minEdgeLengthDefault(subgraphNetwork:SubgraphNetwork,factorMinEdg
* @returns subgraphNetwork updated
*/
async function updateSideCompoundsReversibleReaction(subgraphNetwork:SubgraphNetwork):Promise<SubgraphNetwork>{
- const network = subgraphNetwork.network.value;
+ const network = subgraphNetwork.network;
if (subgraphNetwork.sideCompounds){
let sideCompounds=subgraphNetwork.sideCompounds;
Object.keys(sideCompounds).forEach((reactionID)=>{
@@ -450,7 +450,7 @@ async function motifStampSideCompound(subgraphNetwork:SubgraphNetwork,reactionID
* @throws Error if the reaction is not found in the network.
*/
async function initializeReactionSideCompounds(subgraphNetwork:SubgraphNetwork,idReaction:string):Promise<Reaction>{
- const network = subgraphNetwork.network.value;
+ const network = subgraphNetwork.network;
if (network.nodes[idReaction] && subgraphNetwork.sideCompounds && subgraphNetwork.sideCompounds[idReaction]){
try {
// position of reaction
@@ -493,7 +493,7 @@ async function initializeReactionSideCompounds(subgraphNetwork:SubgraphNetwork,i
* @returns An array of objects representing the metabolites, each containing an ID and a type.
*/
async function getMetaboliteFromReaction(subgraphNetwork: SubgraphNetwork, idReaction: string): Promise<{ id: string; type: MetaboliteType }[]> {
- const network = subgraphNetwork.network.value;
+ const network = subgraphNetwork.network;
return network.links
.filter((link) => link.source.id === idReaction || link.target.id === idReaction)
.map((link) => ({
@@ -731,7 +731,7 @@ async function giveCoordAllSideCompounds(subgraphNetwork:SubgraphNetwork,reactio
if (subgraphNetwork.sideCompounds){
const distance=calculateDistance(subgraphNetwork, factorLength);
const sideCompounds=subgraphNetwork.sideCompounds[reaction.id];
- const reactionCoord=subgraphNetwork.network.value.nodes[reaction.id];
+ const reactionCoord=subgraphNetwork.network.nodes[reaction.id];
// Reactants Placement
if (sideCompounds.reactants && sideCompounds.reactants.length>0){
await placeSideCompounds(sideCompounds.reactants, reaction, reactionCoord, distance, true);
@@ -866,7 +866,7 @@ function insertAllSideCompoundsInNetwork(subgraphNetwork:SubgraphNetwork,reactio
* @param typeSideCompound - The type of the side compound (reactant or product).
*/
function insertSideCompoundInNetwork(subgraphNetwork:SubgraphNetwork,reactionID:string,sideCompound:Node,typeSideCompound:MetaboliteType):void{
- const network = subgraphNetwork.network.value;
+ const network = subgraphNetwork.network;
// insert node
network.nodes[sideCompound.id]=sideCompound;
// insert link
diff --git a/src/composables/LayoutReversibleReactions.ts b/src/composables/LayoutReversibleReactions.ts
index 1bbe991..ba48db0 100644
--- a/src/composables/LayoutReversibleReactions.ts
+++ b/src/composables/LayoutReversibleReactions.ts
@@ -272,7 +272,7 @@ export async function chooseReversibleReaction(
nodeOrderFunction: (network: Network, sources: Array<string> | StartNodesType) => Promise<string[]> = BFSWithSources
): Promise<SubgraphNetwork> {
let nodeOrder: string[] = [];
- const network = subgraphNetwork.network.value;
+ const network = subgraphNetwork.network;
// get node order
nodeOrder = await nodeOrderFunction(network,sources);
// keep the first node seen only, for duplicated nodes
@@ -288,7 +288,7 @@ export async function chooseReversibleReaction(
* @param nodeOrder The order of nodes to consider for keeping the first reversible node.
*/
export function keepFirstReversibleNode(subgraphNetwork:SubgraphNetwork,nodeOrder:string[],doRename:boolean=true):SubgraphNetwork |{[key: string]: string}{
- const network = subgraphNetwork.network.value;
+ const network = subgraphNetwork.network;
const reactionToRemove:Array<string>=[];
const nodeToRename:{[key: string]: string}={};
@@ -336,7 +336,7 @@ export function keepFirstReversibleNode(subgraphNetwork:SubgraphNetwork,nodeOrde
* @returns The modified subgraph network.
*/
export function renameAllIDNode(subgraphNetwork:SubgraphNetwork,nodesToRename:{[key: string]: string}):SubgraphNetwork{
- const network = subgraphNetwork.network.value;
+ const network = subgraphNetwork.network;
// Modify nodes
Object.keys(network.nodes).forEach(ID => {
diff --git a/src/composables/LayoutSugiyamaForce.ts b/src/composables/LayoutSugiyamaForce.ts
index 4defdab..3d8725d 100644
--- a/src/composables/LayoutSugiyamaForce.ts
+++ b/src/composables/LayoutSugiyamaForce.ts
@@ -68,7 +68,7 @@ export async function vizLayout(subgraphNetwork:SubgraphNetwork,assignRank:boole
await instance().then( async viz => {
// attributes for viz
- const sep =await getSepAttributesInches(subgraphNetwork.network.value,subgraphNetwork.networkStyle.value,factorLenghtEdge);
+ const sep =await getSepAttributesInches(subgraphNetwork.network,subgraphNetwork.networkStyle,factorLenghtEdge);
subgraphNetwork.attributs={rankdir: "BT" , newrank:true, compound:true,splines:false,ranksep:sep.rankSep,nodesep:sep.nodeSep,dpi:dpi};
const dot=networkToDOT(subgraphNetwork,cycle,addNodes,groupOrCluster,orderChange);
if(printDot) console.log(dot);
diff --git a/src/composables/SubgraphForSubgraphNetwork.ts b/src/composables/SubgraphForSubgraphNetwork.ts
index 1ad6b23..2f2c288 100644
--- a/src/composables/SubgraphForSubgraphNetwork.ts
+++ b/src/composables/SubgraphForSubgraphNetwork.ts
@@ -56,7 +56,7 @@ export function addSubgraphToNetwork(subgraphNetwork:SubgraphNetwork,subgraph:Su
subgraphNetwork[type][subgraph.name]=subgraph;
// node matadata update
subgraph.nodes.forEach(node=>{
- updateNodeMetadataSubgraph(subgraphNetwork.network.value, node, subgraph.name, type);
+ updateNodeMetadataSubgraph(subgraphNetwork.network, node, subgraph.name, type);
});
// if subgraph associated with another subgraph : add to associatedSubgraphs of the "parent" subgraph
if (subgraph.parentSubgraph){
diff --git a/src/composables/SubgraphForViz.ts b/src/composables/SubgraphForViz.ts
index 797ccd5..1732e11 100644
--- a/src/composables/SubgraphForViz.ts
+++ b/src/composables/SubgraphForViz.ts
@@ -84,7 +84,7 @@ export function addMainChainForViz(vizGraph: Graph, nameMainChain: string, subgr
* @throws {Error} If a node is not found in the network.
*/
function changeCycleMetanodes(subgraphNetwork:SubgraphNetwork,listNodeBefore:string[]):string[]{
- const network=subgraphNetwork.network.value;
+ const network=subgraphNetwork.network;
const listNodeAfter:string[]=[];
// for each nodes :
listNodeBefore.forEach(node =>{
diff --git a/src/composables/__tests__/CalculateRelationCycle.tests.ts b/src/composables/__tests__/CalculateRelationCycle.tests.ts
index 3a00b87..2d33809 100644
--- a/src/composables/__tests__/CalculateRelationCycle.tests.ts
+++ b/src/composables/__tests__/CalculateRelationCycle.tests.ts
@@ -11,7 +11,6 @@ import * as GetSetAttributsNodes from "../GetSetAttributsNodes";
// General imports
-import { ref } from 'vue'; // Import the 'ref' function from the 'vue' module
import { link } from 'fs';
@@ -49,8 +48,8 @@ describe('CalculateRelationCycle', () => {
const networkStyle: GraphStyleProperties = {};
subgraphNetwork = {
- network: ref<NetworkLayout>(network),
- networkStyle: ref<GraphStyleProperties>(networkStyle),
+ network: network,
+ networkStyle: networkStyle,
};
});
diff --git a/src/composables/__tests__/CalculateSize.tests.ts b/src/composables/__tests__/CalculateSize.tests.ts
index f344418..c15ce78 100644
--- a/src/composables/__tests__/CalculateSize.tests.ts
+++ b/src/composables/__tests__/CalculateSize.tests.ts
@@ -13,7 +13,6 @@ import * as GetSetAttributsNodes from "../GetSetAttributsNodes";
import * as CalculateSize from "../CalculateSize";
// General imports
-import { ref } from 'vue'; // Import the 'ref' function from the 'vue' module
@@ -341,8 +340,8 @@ describe('CalculateSize', () => {
// DATA
const subgraphNetwork:SubgraphNetwork = {
- network: ref<NetworkLayout>(network3Edges),
- networkStyle: ref<GraphStyleProperties>(networkStyle)
+ network: network3Edges,
+ networkStyle: networkStyle
};
const listID = ["node1","node2"]
const coordinates: Coordinate[] = [
@@ -364,8 +363,8 @@ describe('CalculateSize', () => {
// DATA
const subgraphNetwork:SubgraphNetwork = {
- network: ref<NetworkLayout>(network3Edges),
- networkStyle: ref<GraphStyleProperties>(networkStyle)
+ network: network3Edges,
+ networkStyle: networkStyle
};
const listID = ["node1","nodeNotNetwork"]
const coordinates: Coordinate[] = [
@@ -399,8 +398,8 @@ describe('CalculateSize', () => {
}
};
let subgraphNetwork:SubgraphNetwork = {
- network: ref<NetworkLayout>(network3Edges),
- networkStyle: ref<GraphStyleProperties>(networkStyle),
+ network: network3Edges,
+ networkStyle: networkStyle,
[TypeSubgraph.CYCLEGROUP]:{
"groupCycle_0": subgraph0,
"groupCycle_1":subgraph1
@@ -408,8 +407,8 @@ describe('CalculateSize', () => {
};
const subgraphNetworkExpected:SubgraphNetwork = {
- network: ref<NetworkLayout>(network3Edges),
- networkStyle: ref<GraphStyleProperties>(networkStyle),
+ network: network3Edges,
+ networkStyle: networkStyle,
[TypeSubgraph.CYCLEGROUP]:{
"groupCycle_0": {
...subgraph0,
diff --git a/src/types/SubgraphNetwork.ts b/src/types/SubgraphNetwork.ts
index bd52a5d..59b8486 100644
--- a/src/types/SubgraphNetwork.ts
+++ b/src/types/SubgraphNetwork.ts
@@ -10,8 +10,8 @@ import { NetworkLayout } from "./NetworkLayout";
*/
export interface SubgraphNetwork {
- network: Ref<NetworkLayout>;
- networkStyle: Ref<GraphStyleProperties>;
+ network: NetworkLayout;
+ networkStyle: GraphStyleProperties;
stats?:{minEdgeLengthPixel?:number};
--
GitLab