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docs, fixes, etc for 2.3
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@maxkfranz
maxkfranz committed Sep 17, 2014
1 parent 85807ea commit 7985655
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Showing 63 changed files with 2,059 additions and 831 deletions.
246 changes: 135 additions & 111 deletions documentation/api/cytoscape.js-2.3-beta/cytoscape.js
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16 changes: 8 additions & 8 deletions documentation/api/cytoscape.js-2.3-beta/cytoscape.min.js
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129 changes: 83 additions & 46 deletions documentation/api/cytoscape.js-latest/cytoscape.js
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*!
* This file is part of Cytoscape.js 2.2.14.
* This file is part of Cytoscape.js 2.3-beta.
*
* Cytoscape.js is free software: you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by the Free
Expand Down Expand Up @@ -29,7 +29,7 @@ var cytoscape;
return cytoscape.init.apply(cytoscape, arguments);
};

$$.version = '2.2.14';
$$.version = '2.3-beta';

// allow functional access to cytoscape.js
// e.g. var cyto = $.cytoscape({ selector: "#foo", ... });
Expand Down Expand Up @@ -9222,14 +9222,19 @@ var cytoscape;
var reconstructPath = function(start, end, cameFromMap, pathAcum) {
// Base case
if (start == end) {
pathAcum.push(end);
pathAcum.push( cy.getElementById(end) );
return pathAcum;
}

if (end in cameFromMap) {
// We know which node is before the last one
var previous = cameFromMap[end];
pathAcum.push(end)
var previousEdge = cameFromEdge[end];

pathAcum.push( cy.getElementById(end) );
pathAcum.push( cy.getElementById(previousEdge) );


return reconstructPath(start,
previous,
cameFromMap,
Expand Down Expand Up @@ -9295,8 +9300,9 @@ var cytoscape;
if (options.heuristic != null && $$.is.fn(options.heuristic)) {
var heuristic = options.heuristic;
} else {
$$$.util.error("Missing required parameter (heuristic)! Aborting.");
return;
var heuristic = function(){ return 0; }; // use constant if unspecified
// $$.util.error("Missing required parameter (heuristic)! Aborting.");
// return;
}

// Weight function - optional
Expand All @@ -9317,6 +9323,7 @@ var cytoscape;
var closedSet = [];
var openSet = [source.id()];
var cameFrom = {};
var cameFromEdge = {};
var gScore = {};
var fScore = {};

Expand Down Expand Up @@ -9347,7 +9354,7 @@ var cytoscape;
return {
found : true
, distance : gScore[cMin.id()]
, path : rPath
, path : new $$.Collection(cy, rPath)
, steps : steps
};
}
Expand Down Expand Up @@ -9389,6 +9396,7 @@ var cytoscape;
fScore[w.id()] = tempScore + heuristic(w);
openSet.push(w.id()); // Add node to openSet
cameFrom[w.id()] = cMin.id();
cameFromEdge[w.id()] = e.id();
logDebug(" not in openSet, adding it. ");
logDebug(" fScore(%s) = %s", w.id(), tempScore);
continue;
Expand Down Expand Up @@ -9486,13 +9494,20 @@ var cytoscape;
// Initialize matrix used for path reconstruction
// Initialize distance matrix
var next = [];
for (var i = 0; i < numNodes; i++) {
var newRow = new Array(numNodes);
for (var j = 0; j < numNodes; j++) {
newRow[j] = undefined;
var edgeNext = [];

var initMatrix = function(next){
for (var i = 0; i < numNodes; i++) {
var newRow = new Array(numNodes);
for (var j = 0; j < numNodes; j++) {
newRow[j] = undefined;
}
next.push(newRow);
}
next.push(newRow);
}

initMatrix(next);
initMatrix(edgeNext);

// Process edges
for (var i = 0; i < edges.length ; i++) {
Expand All @@ -9504,6 +9519,7 @@ var cytoscape;
if (dist[sourceIndex][targetIndex] > weight) {
dist[sourceIndex][targetIndex] = weight
next[sourceIndex][targetIndex] = targetIndex;
edgeNext[sourceIndex][targetIndex] = edges[i];
}
}

Expand All @@ -9516,8 +9532,9 @@ var cytoscape;

// Check if already process another edge between same 2 nodes
if (dist[sourceIndex][targetIndex] > weight) {
dist[sourceIndex][targetIndex] = weight
dist[sourceIndex][targetIndex] = weight;
next[sourceIndex][targetIndex] = targetIndex;
edgeNext[sourceIndex][targetIndex] = edges[i];
}
}
}
Expand All @@ -9541,7 +9558,7 @@ var cytoscape;
}

var res = {
distanceTo: function(from, to) {
distance: function(from, to) {
if ($$.is.string(from)) {
// from is a selector string
var fromId = (cy.filter(from)[0]).id();
Expand All @@ -9561,18 +9578,25 @@ var cytoscape;
return dist[id2position[fromId]][id2position[toId]];
},

pathTo : function(from, to) {
var reconstructPathAux = function(from, to, next, position2id) {
path: function(from, to) {
var reconstructPathAux = function(from, to, next, position2id, edgeNext) {
if (from === to) {
return [position2id[from]];
return cy.getElementById( position2id[from] );
}
if (next[from][to] === undefined) {
return undefined;
}
var path = [position2id[from]];

var path = [ cy.getElementById(position2id[from]) ];
var prev = from;
while (from !== to) {
prev = from;
from = next[from][to];
path.push(position2id[from]);

var edge = edgeNext[prev][from];
path.push( edge );

path.push( cy.getElementById(position2id[from]) );
}
return path;
};
Expand All @@ -9592,10 +9616,14 @@ var cytoscape;
// to is a node
var toId = to.id();
}
return reconstructPathAux(id2position[fromId],

var pathArr = reconstructPathAux(id2position[fromId],
id2position[toId],
next,
position2id);
position2id,
edgeNext);

return new $$.Collection( cy, pathArr );
},
};

Expand Down Expand Up @@ -9674,6 +9702,7 @@ var cytoscape;
// Initializations
var cost = [];
var predecessor = [];
var predEdge = [];

for (var i = 0; i < numNodes; i++) {
if (nodes[i].id() === source.id()) {
Expand All @@ -9697,6 +9726,7 @@ var cytoscape;
if (temp < cost[targetIndex]) {
cost[targetIndex] = temp;
predecessor[targetIndex] = sourceIndex;
predEdge[targetIndex] = edges[e];
flag = true;
}

Expand All @@ -9706,6 +9736,7 @@ var cytoscape;
if (temp < cost[sourceIndex]) {
cost[sourceIndex] = temp;
predecessor[sourceIndex] = targetIndex;
predEdge[sourceIndex] = edges[e];
flag = true;
}
}
Expand Down Expand Up @@ -9754,24 +9785,26 @@ var cytoscape;

pathTo : function(to) {

var reconstructPathAux = function(predecessor, fromPos, toPos, position2id, acumPath) {
// Add toId to path
acumPath.push(position2id[toPos]);
if (fromPos === toPos) {
// reached starting node
return acumPath;
}
// If no path exists, discart acumulated path and return undefined
var predPos = predecessor[toPos];
if (typeof predPos === "undefined") {
return undefined;
var reconstructPathAux = function(predecessor, fromPos, toPos, position2id, acumPath, predEdge) {
for(;;){
// Add toId to path
acumPath.push( cy.getElementById(position2id[toPos]) );
acumPath.push( predEdge[toPos] );

if (fromPos === toPos) {
// reached starting node
return acumPath;
}

// If no path exists, discart acumulated path and return undefined
var predPos = predecessor[toPos];
if (typeof predPos === "undefined") {
return undefined;
}

toPos = predPos;
}
// recursively compute path until predecessor of toId
return reconstructPathAux(predecessor,
fromPos,
predPos,
position2id,
acumPath);

};

if ($$.is.string(to)) {
Expand All @@ -9788,13 +9821,15 @@ var cytoscape;
id2position[source.id()],
id2position[toId],
position2id,
path);
path,
predEdge);

// Get it in the correct order and return it
if (res != null) {
res.reverse();
}
return res;

return new $$.Collection(cy, res);
},

hasNegativeWeightCycle: false
Expand Down Expand Up @@ -9964,7 +9999,7 @@ var cytoscape;


// Construct result
var resEdges = (minCut[0]).map(function(e) {return edges[e[0]].id();});
var resEdges = (minCut[0]).map(function(e){ return edges[e[0]]; });
var partition1 = [];
var partition2 = [];

Expand All @@ -9973,16 +10008,16 @@ var cytoscape;
for (var i = 0; i < minCut[1].length; i++) {
var partitionId = minCut[1][i];
if (partitionId === witnessNodePartition) {
partition1.push(nodes[i].id());
partition1.push(nodes[i]);
} else {
partition2.push(nodes[i].id());
partition2.push(nodes[i]);
}
}

var ret = {
cut: resEdges,
partition1: partition1,
partition2: partition2
cut: new $$.Collection(cy, resEdges),
partition1: new $$.Collection(cy, partition1),
partition2: new $$.Collection(cy, partition2)
};

return ret;
Expand Down Expand Up @@ -12130,6 +12165,8 @@ var cytoscape;
var updatedCompounds = this.updateCompoundBounds();
var toNotify = updatedCompounds.length > 0 ? this.add( updatedCompounds ) : this;
toNotify.rtrigger('style'); // let the renderer know we've updated style

return this; // chaining
},

show: function(){
Expand Down
18 changes: 9 additions & 9 deletions documentation/api/cytoscape.js-latest/cytoscape.min.js
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