-
Notifications
You must be signed in to change notification settings - Fork 26
/
index.html
4719 lines (4372 loc) · 227 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<!DOCTYPE html><html lang="en" xmlns="http://www.w3.org/1999/html"><head>
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async="" src="https://www.googletagmanager.com/gtag/js?id=UA-109049087-1"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag() {
dataLayer.push(arguments);
}
gtag("js", new Date());
gtag("config", "UA-109049087-1");
</script>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=Edge">
<title>Newt Editor</title>
<link rel="icon" href="app/img/newt-icon.png" type="image/png">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link href="node_modules/bootstrap/dist/css/bootstrap.css" rel="stylesheet">
<link href="node_modules/intro.js/introjs.css" rel="stylesheet" type="text/css">
<!--cytoscape.js plugins -->
<link href="node_modules/cytoscape-panzoom/cytoscape.js-panzoom.css" rel="stylesheet" type="text/css">
<link href="node_modules/cytoscape-panzoom/font-awesome-4.0.3/css/font-awesome.css" rel="stylesheet" type="text/css">
<!-- <link href="node_modules/qtip2/dist/jquery.qtip.css" rel="stylesheet" type="text/css" /> -->
<link href="node_modules/cytoscape-context-menus/cytoscape-context-menus.css" rel="stylesheet" type="text/css">
<!-- app's style -->
<link href="app/css/chise.css" rel="stylesheet">
<script src="app/bundle.js"></script>
<!-- libraries -->
<!-- <script src="node_modules/qtip2/dist/jquery.qtip.js"></script> -->
</head>
<body>
<div class="read-mode-off">
<div class="nav-menu sbgn-nav-menu">
<nav class="navbar navbar-default sbgn-nav-bar" role="navigation">
<div>
<ul class="nav navbar-nav navbar-left">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
File
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<input id="file-input" type="file" style="display: none">
<li><a href="#" type="file" id="new-file">New</a></li>
<li><a href="#" type="file" id="load-file">Open...</a></li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Samples
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu">
<li>
<a class="title"><i>PD</i></a>
</li>
<li class="divider" style="margin-top: 0"></li>
<li>
<a href="#" id="load-sample1">Neuronal muscle signaling</a>
</li>
<li>
<a href="#" id="load-sample2">CaM-CaMK dependent signaling to nucleus</a>
</li>
<li>
<a href="#" id="load-sample3">ATM mediated phosphorylation of repair proteins</a>
</li>
<li>
<a href="#" id="load-sample4">Activated STAT1alpha induction of the IRF1 gene</a>
</li>
<li>
<a href="#" id="load-sample5">Vitamins B6 activation to pyridoxal phosphate</a>
</li>
<li>
<a href="#" id="load-sample6">Insulin-like growth factor (IGF) signaling</a>
</li>
<li>
<a href="#" id="load-sample7">PolyQ proteins interference</a>
</li>
<li><a href="#" id="load-sample8">Glycolysis</a></li>
<li><a href="#" id="load-sample9">MAPK cascade</a></li>
<li>
<a href="#" id="load-sample10">Drosophila cell cycle</a>
</li>
<li>
<a href="#" id="load-sample11">Mammalian cholesterol biosynthesis</a>
</li>
<li>
<a href="#" id="load-sample12">Two gene system behavior</a>
</li>
<li>
<a href="#" id="load-sample19">PD Learner's Reference Card</a>
</li>
<li class="divider" style="margin-bottom: 0"></li>
<li>
<a class="title"><i>AF</i></a>
</li>
<li class="divider" style="margin-top: 0"></li>
<li>
<a href="#" id="load-sample13">Transforming growth factor beta (TGFB) signaling</a>
</li>
<li><a href="#" id="load-sample14">Repressilator</a></li>
<li>
<a href="#" id="load-sample15">Epidermal growth factor receptor</a>
</li>
<li>
<a href="#" id="load-sample16">Regulation of TGF-beta induced metastasis</a>
</li>
<li>
<a href="#" id="load-sample20">AF Learner's Reference Card</a>
</li>
<li class="divider" style="margin-bottom: 0"></li>
<li>
<a class="title"><i>SIF</i></a>
</li>
<li class="divider" style="margin-top: 0"></li>
<li>
<a href="#" id="load-sample17">RTN4 controllers and binding proteins</a>
</li>
<li>
<a href="#" id="load-sample18">Signaling downstream of AKT2/3</a>
</li>
<li class="divider" style="margin-bottom: 0"></li>
<li>
<a class="title"><i>SBML</i></a>
</li>
<li class="divider" style="margin-top: 0"></li>
<li>
<a href="#" id="load-sample21">RUNX1 regulates transcription of genes in WNT signaling</a>
</li>
<li>
<a href="#" id="load-sample22">PTK6 activates STAT3
</a>
</li>
<li>
<a href="#" id="load-sample23">Pharmacokinetics of PFOA and PFOS in the monkey
</a>
</li>
<li>
<a href="#" id="load-sample24">
Interaction topologies of MAPK cascade (M1_K2_PSEQ)</a>
</li>
</ul>
</li>
<li><a href="#" id="save-as-nwt">Save...</a></li>
<li><a href="#" type="file" id="close-file">Close</a></li>
<li class="divider"></li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Import
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu">
<input id="simple-af-file-input" type="file" style="display: none">
<input id="sif-file-input" type="file" style="display: none">
<input id="sif-style-input" type="file" style="display: none">
<input id="sif-layout-input" type="file" style="display: none">
<input id="sbml-file" type="file" style="display: none">
<input id="celldesigner-file-input" type="file" style="display: none">
<input id="gpml-file-input" type="file" style="display: none">
<li>
<a href="#" id="import-simple-af-file">Simple AF</a>
</li>
<li><a href="#" id="import-sif-file">SIF</a></li>
<li><a href="#" id="import-sif-style">SIF Style</a></li>
<li><a href="#" id="import-sif-layout">SIF Layout</a></li>
<li><a href="#" id="import-SBML-file">SBML</a></li>
<li>
<a href="#" id="import-celldesigner-file">CellDesigner</a>
</li>
<li><a href="#" id="import-GPML-file">GPML</a></li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Export
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu">
<li>
<a href="#" id="export-as-sbgnml-plain-file">SBGN-ML Plain</a>
</li>
<li>
<a href="#" id="export-as-sbgnml3-plain-file">SBGN-ML Plain 0.3</a>
</li>
<li><a href="#" id="export-as-nwt3-file">NWT 0.3</a></li>
<li><a href="#" id="export-to-plain-sif">SIF</a></li>
<li>
<a href="#" id="export-to-sif-layout">SIF Layout</a>
</li>
<li><a href="#" id="export-as-sbml">SBML</a></li>
<li>
<a href="#" id="export-as-celldesigner-file">CellDesigner</a>
</li>
<li><a href="#" id="export-as-gpml">GPML</a></li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Export as Image
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu">
<li><a href="#" id="save-as-png">PNG</a></li>
<li><a href="#" id="save-as-jpg">JPG</a></li>
<li><a href="#" id="save-as-svg">SVG</a></li>
</ul>
</li>
<li class="divider"></li>
<input id="user-preferences-file-input" type="file" style="display: none">
<li>
<a href="#" id="load-user-preferences">Open Preferences...</a>
</li>
<li>
<a href="#" id="save-user-preferences">Save Preferences...</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Edit
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<li>
<a href="#" id="add-complex-for-selected">Add Complex for Selected</a>
</li>
<li>
<a href="#" id="add-compartment-for-selected">Add Compartment for Selected</a>
</li>
<li>
<a href="#" id="add-submap-for-selected">Add Submap for Selected</a>
</li>
<li>
<a href="#" id="open-sbgn-bricks-modal">Add Using SBGN Bricks...</a>
</li>
<li><a href="#" id="clone-selected">Clone Selected</a></li>
<li class="divider"></li>
<li>
<a href="#" id="delete-selected-simple">Delete Selected Simple</a>
</li>
<li>
<a href="#" id="delete-selected-smart">Delete Selected Smart</a>
</li>
<li class="divider"></li>
<li>
<a href="#" id="resize-nodes-to-content">Resize Nodes To Content</a>
</li>
<li>
<a href="#" id="highlight-errors-of-validation">
Validate Map...</a>
</li>
<li>
<a href="#" id="highlight-errors-of-pd2af">
Convert PD map to AF map</a>
</li>
<li class="divider"></li>
<li class="disabled">
<a href="#" id="undo-last-action">Undo</a>
</li>
<li class="disabled">
<a href="#" id="redo-last-action">Redo</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
View
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Select
</a>
<ul class="dropdown-menu">
<li>
<a href="#" id="select-all">All Nodes and Edges</a>
</li>
<li><a href="#" id="select-all-nodes">All Nodes</a></li>
<li><a href="#" id="select-all-edges">All Edges</a></li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Zoom
</a>
<ul class="dropdown-menu">
<li>
<a href="#" id="zoom-to-selected">Zoom to Selected</a>
</li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Hide/Show
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu">
<li>
<a href="#" id="hide-selected-simple">Hide Selected Simple</a>
</li>
<li>
<a href="#" id="hide-selected-smart">Hide Selected Smart</a>
</li>
<li><a href="#" id="show-selected">Show Selected</a></li>
<li>
<a href="#" id="show-hidden-neighbors-of-selected">Show Hidden Neighbors of Selected</a>
</li>
<li><a href="#" id="show-all">Show All</a></li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Collapse/Expand
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu">
<li>
<a href="#" id="collapse-selected">Collapse Selected</a>
</li>
<li>
<a href="#" id="expand-selected">Expand Selected</a>
</li>
<li>
<a href="#" id="collapse-complexes">Collapse Complexes</a>
</li>
<li>
<a href="#" id="expand-complexes">Expand Complexes</a>
</li>
<li><a href="#" id="collapse-all">Collapse All</a></li>
<li><a href="#" id="expand-all">Expand All</a></li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" id="add-node-menu-option" class="dropdown-toggle" data-toggle="dropdown">
Align
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu" id="add-node-submenu">
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Horizontal
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu">
<li><a href="#" id="align-horizontal-top">Top</a></li>
<li>
<a href="#" id="align-horizontal-middle">Middle</a>
</li>
<li>
<a href="#" id="align-horizontal-bottom">Bottom</a>
</li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Vertical
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu">
<li><a href="#" id="align-vertical-left">Left</a></li>
<li>
<a href="#" id="align-vertical-center">Center</a>
</li>
<li>
<a href="#" id="align-vertical-right">Right</a>
</li>
</ul>
</li>
</ul>
</li>
<li>
<a href="#" id="grid-properties" style="padding-right: 30px">Grid and Guidelines...</a>
</li>
<li>
<a href="#" id="general-properties">Map Properties...</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Highlight
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<li>
<a href="#" id="highlight-search-menu-item">Search...</a>
</li>
<li><a href="#" id="highlight-selected">Selected</a></li>
<li>
<a href="#" id="highlight-neighbors-of-selected">Neighbors of Selected</a>
</li>
<li>
<a href="#" id="highlight-processes-of-selected">Processes of Selected</a>
</li>
<li>
<a href="#" id="remove-highlights">Remove Highlights</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Experiment
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<li><a href="#" id="import-experimental-data">Open...</a></li>
<input id="overlay-data" type="file" style="display: none">
<li>
<a href="#" id="sample-experiment-data">Open Sample</a>
</li>
<li class="divider"></li>
<li>
<a href="#" value="true" id="experiment-data-hide-all">Hide/Show All</a>
</li>
<li>
<a href="#" id="experiment-data-remove-all">Remove All</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Layout
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<li><a href="#" id="perform-layout">Perform Layout</a></li>
<li>
<a href="#" id="perform-static-layout">Perform Static Layout</a>
</li>
<li>
<a href="#" id="layout-properties">Layout Properties...</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Query
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<li class="dropdown-submenu">
<a href="#" id="query-pathwaycommons" class="dropdown-toggle" data-toggle="dropdown">Pathway Commons</a>
<ul class="dropdown-menu">
<li>
<a href="#" id="query-pathsbetween">Paths Between...</a>
</li>
<li>
<a href="#" id="query-pathsfromto">Paths From To...</a>
</li>
<li>
<a href="#" id="query-commonstream">Common Stream...</a>
</li>
<li>
<a href="#" id="query-neighborhood">Neighborhood...</a>
</li>
<li><a href="#" id="query-pathsbyURI">By URI...</a></li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" id="query-wikipathways" class="dropdown-toggle" data-toggle="dropdown">WikiPathways</a>
<ul class="dropdown-menu">
<li>
<a href="#" id="query-mapbyWPID">By WPID...</a>
</li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" id="query-reactome" class="dropdown-toggle" data-toggle="dropdown">Reactome</a>
<ul class="dropdown-menu">
<li>
<a href="#" id="query-mapbyReactomeID">By Reactome ID...</a>
</li>
</ul>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Legend
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<li><a href="#" id="PD-legend">Process Description</a></li>
<li><a href="#" id="AF-legend">Activity Flow</a></li>
<li><a href="#" id="SIF-legend">SIF</a></li>
<li><a href="#" id="SBML-legend">SBML</a></li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Help
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<li><a href="#" id="quick-help">Quick Help</a></li>
<li><a href="#" id="quick-tutorial">Quick Tutorial</a></li>
<li><a href="#" id="ui-guide">UI Guide</a></li>
<li><a href="#" id="about">About</a></li>
</ul>
</li>
</ul>
<a href="http://newteditor.org" target="_blank"><img class="newt-logo" height="25" width="auto" src="app/img/newt-logo.png"></a>
<span class="input-file" id="displayed-file-name"></span>
<span class="input-file" id="file-name"></span>
</div>
</nav>
</div>
<div id="sbgn-toolbar" class="read-mode-off">
<div class="inside-menu">
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="new-file-icon" src="app/img/toolbar/new.svg" title="New: Create a blank map">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="load-file-icon" src="app/img/toolbar/load.svg" title="Open: Open a map from a Newt file">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="save-icon" src="app/img/toolbar/save.svg" title="Save: Save current map to a Newt file">
</div>
</div>
<div class="menu-break-large sbgn-toolbar-element"> </div>
<div class="inside-menu">
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="select-mode-icon" src="app/img/toolbar/select.svg" title="Select / Edit">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="add-node-mode-icon" src="app/img/nodes/unspecified-entity.svg" title="Create a new Unspecified Entity" style="width: 36px; object-fit: contain;">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="add-edge-mode-icon" src="app/img/edges/consumption.svg" title="Create a new Consumption">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="marquee-zoom-mode-icon" src="app/img/toolbar/marquee.svg" title="Marquee Zoom: Zoom to area specified by Shift + left click and drag">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="lasso-mode-icon" src="app/img/toolbar/lasso.svg" title="Lasso Tool: Select nodes / edges in free form">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="sbgn-bricks-icon" src="app/img/toolbar/sbgnbricks-logo.svg" title="SBGN Bricks: Add using SBGN bricks">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="delete-selected-simple-icon" src="app/img/toolbar/delete-simple.svg" title="Delete Selected Simple: Delete selected nodes and edges">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="delete-selected-smart-icon" src="app/img/toolbar/delete-smart.svg" title="Delete Selected Smart: Delete selected nodes and any processes they are involved in">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="highlight-errors-of-validation-icon" src="app/img/toolbar/check.svg" title="Validate Map: Validate SBGN PD map and fix problems">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="undo-icon" src="app/img/toolbar/undo.svg" title="Undo: Undo the last operation">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="redo-icon" src="app/img/toolbar/redo.svg" title="Redo: Redo the last undone operation">
</div>
</div>
<div class="menu-break-large sbgn-toolbar-element"> </div>
<div class="inside-menu">
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="hide-selected-simple-icon" src="app/img/toolbar/hide-selected-simple.svg" title="Hide Selected Simple: Hide selected nodes and edges">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="hide-selected-smart-icon" src="app/img/toolbar/hide-selected-smart.svg" title="Hide Selected Smart: Hide selected nodes and any processes they are involved in">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="show-selected-icon" src="app/img/toolbar/show-all.svg" title="Show Selected: Show selected nodes and any processes they are involved in, hiding the remaining nodes and their edges">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="collapse-selected-icon" src="app/img/toolbar/collapse-selected.svg" title="Collapse Selected: Collapse selected compound node to hide its members">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="expand-selected-icon" src="app/img/toolbar/expand-selected.svg" title="Expand Selected: Expand selected collapsed node to show its members">
</div>
<div class="btn-group sbgn-toolbar-element sbgn-dd-list" role="group" id="align-list">
<button id="align-button" style="padding: 3px" title="Align to First Selected: Align positions of selected nodes based on the first (if any) selected node" type="button" class="btn" aria-haspopup="true" aria-expanded="false">
<div style="height: 16px">
<img style="height: 16px; width: auto" id="sbgn-align-img" src="app/img/align/align.svg">
<!--<span style="float: right;" class="caret"></span>-->
</div>
</button>
<button id="align-dd-button" style="padding: 3px; padding-top: 4px" type="button" class="btn dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
<div style="height: 16px">
<span class="caret"></span>
<span class="sr-only"></span>
</div>
</button>
<ul id="align-menu" class="dropdown-menu">
<li>
<a class="dd-list-href" href="#" id="align-horizontal-top-icon"> <img src="app/img/align/align-horizontal-top.svg"> Align Horizontal Top</a>
</li>
<li>
<a class="dd-list-href" href="#" id="align-horizontal-middle-icon"> <img src="app/img/align/align-horizontal-middle.svg"> Align Horizontal Middle</a>
</li>
<li>
<a class="dd-list-href" href="#" id="align-horizontal-bottom-icon"> <img src="app/img/align/align-horizontal-bottom.svg"> Align Horizontal Bottom</a>
</li>
<li>
<a class="dd-list-href" href="#" id="align-vertical-left-icon"> <img src="app/img/align/align-vertical-left.svg"> Align Vertical Left</a>
</li>
<li>
<a class="dd-list-href" href="#" id="align-vertical-center-icon"> <img src="app/img/align/align-vertical-center.svg"> Align Vertical Center</a>
</li>
<li>
<a class="dd-list-href" href="#" id="align-vertical-right-icon"> <img src="app/img/align/align-vertical-right.svg"> Align Vertical Right</a>
</li>
</ul>
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="toggle-grid-snapping-icon" src="app/img/toolbar/grid.svg" title="Enable Grid: Show and snap to grid during drag">
</div>
<img id="toggle-guidelines-snapping-icon" class="sbgn-toolbar-element" src="app/img/toolbar/guidelines.svg" title="Enable Guidelines: Enable and snap to alignment guidelines during drag">
<img id="properties-icon" class="sbgn-toolbar-element" src="app/img/toolbar/settings.svg" title="Map Properties: Modify general properties of current SBGN map">
</div>
<div class="menu-break-large sbgn-toolbar-element"> </div>
<div class="inside-menu">
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="search-by-label-icon" src="app/img/toolbar/search.svg" title="Search: Search (case insensitive) and highlight all nodes with specified label text">
</div>
<input id="search-by-label-text-box" class="sbgn-toolbar-element" type="label">
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="highlight-selected-icon" src="app/img/toolbar/highlight-selected.svg" title="Highlight Selected: Highlight selected nodes and edges">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="remove-highlights-icon" src="app/img/toolbar/remove-highlights.svg" title="Remove Highlights: Remove any highlights">
</div>
</div>
<div class="menu-break-large sbgn-toolbar-element"> </div>
<div class="inside-menu">
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="perform-layout-icon" src="app/img/toolbar/layout-cose.svg" title="Perform Layout: Perform a force-directed layout of current map, maintaining compound structures">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="perform-static-layout-icon" src="app/img/toolbar/layout-static.svg" title="Perform Static Layout: Re-calculate layout of current map from scratch, ignoring current positions and maintaining compound structures">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="layout-properties-icon" src="app/img/toolbar/layout-properties.svg" title="Layout Properties: Modify parameters used during layout">
</div>
</div>
<div class="menu-break-large sbgn-toolbar-element"> </div>
<div class="inside-menu">
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="query-pathsbetween-icon" src="app/img/toolbar/PC-logo.svg" title="Perform PC Query: Perform a PathwayCommons query to get a map of interest between specified genes">
</div>
</div>
<div class="menu-break-large sbgn-toolbar-element"> </div>
<div class="inside-menu">
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="quick-help-icon" src="app/img/toolbar/quick-help.svg" title="Quick Help">
</div>
<div style="padding: 1px" class="sbgn-toolbar-element">
<img id="about-icon" src="app/img/toolbar/about.svg" title="About">
</div>
</div>
</div>
</div>
<table id="sbgn-inspector-and-canvas">
<tbody>
<tr>
<td>
<div id="network-panels-container" class="tab-content read-mode-off"></div>
</td>
<td>
<div id="sbgn-inspector">
<ul class="nav nav-tabs">
<li id="inspector-style-tab" class="chise-tab validation-mode-tab">
<a data-toggle="tab" href="#sbgn-inspector-style"><img width="18px" height="18px" src="app/img/tabs/properties.svg"> Object</a>
</li>
<li id="inspector-map-tab" class="chise-tab validation-mode-tab">
<a data-toggle="tab" href="#sbgn-inspector-map"><img width="18px" height="18px" src="app/img/toolbar/settings.svg"> Map</a>
</li>
<li id="inspector-palette-tab" class="chise-tab active validation-mode-tab">
<a data-toggle="tab" href="#sbgn-inspector-palette"><img width="18px" height="18px" src="app/img/tabs/palette.svg"> Palette</a>
</li>
<li id="inspector-console-tab" class="chise-tab validation-mode-tab" style="display: none">
<a data-toggle="tab" href="#sbgn-inspector-console"><img width="18px" height="18px" src="app/img/tabs/console.svg"> Console</a>
</li>
</ul>
<div class="tab-content">
<div id="sbgn-inspector-style" class="tab-pane fade">
<div id="sbgn-inspector-style-panel-group" class="panel-group"></div>
</div>
<div id="sbgn-inspector-map" class="tab-pane fade">
<div class="panel-group">
<div class="panel">
<div class="panel-heading" data-toggle="collapse" data-target="#sbgn-inspector-map-properties-general">
<p class="panel-title accordion-toggle">General</p>
</div>
<div id="sbgn-inspector-map-properties-general" class="panel-collapse collapse in">
<div id="map-tab-general-container"></div>
</div>
</div>
<div class="panel">
<div class="panel-heading collapsed" data-toggle="collapse" data-target="#sbgn-inspector-map-properties-label">
<p class="panel-title accordion-toggle">Labels</p>
</div>
<div id="sbgn-inspector-map-properties-label" class="panel-collapse collapse">
<div id="map-tab-label-container"></div>
</div>
</div>
<div class="panel">
<div class="panel-heading collapsed" data-toggle="collapse" data-target="#sbgn-inspector-map-properties-rearrangement">
<p class="panel-title accordion-toggle">Arrangement</p>
</div>
<div id="sbgn-inspector-map-properties-rearrangement" class="panel-collapse collapse">
<div id="map-tab-rearrangement-container"></div>
</div>
</div>
<div class="panel">
<div id="sbgn-inspector-map-properties-experiment-heading" class="panel-heading collapsed" data-toggle="collapse" data-target="#sbgn-inspector-map-properties-experiment">
<p class="panel-title accordion-toggle">Experiment</p>
</div>
<div id="sbgn-inspector-map-properties-experiment" class="panel-collapse collapse">
<div id="map-tab-experiment-container"></div>
</div>
</div>
<div class="panel">
<div class="panel-heading collapsed" data-toggle="collapse" data-target="#sbgn-inspector-map-color-scheme">
<p class="panel-title accordion-toggle">Color Scheme</p>
</div>
<div id="sbgn-inspector-map-color-scheme" class="panel-collapse collapse">
<div id="color-scheme-template-container"></div>
</div>
</div>
</div>
</div>
<div id="sbgn-inspector-palette" class="tab-pane fade in active">
<div class="panel-group">
<div class="panel">
<div id="PD-palette-heading" class="panel-heading" data-toggle="collapse" data-target="#expand-collapse-pd-nodes-palette">
<p class="panel-title accordion-toggle">
Process Description
</p>
</div>
<div id="expand-collapse-pd-nodes-palette" class="panel-collapse collapse in">
<div class="panel-body palette-panel-body">
<p class="palette-label">Entity Pool Nodes</p>
<div id="pd-node-palette" class="element-palette node-palette">
<div class="paletteWrapper">
<div class="paletteCol">
<img src="app/img/nodes/macromolecule.svg" language="PD" value="macromolecule" title="Macromolecule">
</div>
<div class="paletteCol">
<img src="app/img/nodes/simple-chemical.svg" language="PD" value="simple-chemical" title="Simple Chemical">
</div>
<div class="paletteCol">
<img src="app/img/nodes/unspecified-entity.svg" language="PD" value="unspecified-entity" title="Unspecified Entity">
</div>
<div class="paletteCol">
<img src="app/img/nodes/nucleic-acid-feature.svg" language="PD" value="nucleic-acid-feature" title="Nucleic Acid Feature">
</div>
<div class="paletteCol">
<img src="app/img/nodes/perturbing-agent.svg" language="PD" value="perturbing-agent" title="Perturbing Agent">
</div>
<div class="paletteCol">
<img src="app/img/nodes/empty-set.svg" language="PD" value="empty-set" title="Empty Set">
</div>
<div class="paletteCol">
<img src="app/img/nodes/complex.svg" language="PD" value="complex" title="Complex">
</div>
</div>
</div>
</div>
<div class="panel-body palette-panel-body">
<p class="palette-label">Process Nodes</p>
<div id="pd-node-palette" class="element-palette node-palette">
<div class="paletteWrapper">
<div class="paletteCol">
<img src="app/img/nodes/process.svg" language="PD" value="process" title="Process">
</div>
<div class="paletteCol">
<img src="app/img/nodes/omitted-process.svg" language="PD" value="omitted-process" title="Omitted Process">
</div>
<div class="paletteCol">
<img src="app/img/nodes/uncertain-process.svg" language="PD" value="uncertain-process" title="Uncertain Process">
</div>
<div class="paletteCol">
<img src="app/img/nodes/association.svg" language="PD" value="association" title="Association">
</div>
<div class="paletteCol">
<img src="app/img/nodes/dissociation.svg" language="PD" value="dissociation" title="Dissociation">
</div>
<div class="paletteCol">
<img src="app/img/nodes/phenotype.svg" language="PD" value="phenotype" title="Phenotype">
</div>
</div>
</div>
</div>
<div class="panel-body palette-panel-body">
<p class="palette-label">Logical Operators</p>
<div id="pd-node-palette" class="element-palette node-palette">
<div class="paletteWrapper">
<div class="paletteCol">
<img src="app/img/nodes/and.svg" language="PD" value="and" title="AND">
</div>
<div class="paletteCol">
<img src="app/img/nodes/or.svg" language="PD" value="or" title="OR">
</div>
<div class="paletteCol">
<img src="app/img/nodes/not.svg" language="PD" value="not" title="NOT">
</div>
</div>
</div>
</div>
<div class="panel-body palette-panel-body">
<p class="palette-label">Other Nodes</p>
<div id="pd-node-palette" class="element-palette node-palette">
<div class="paletteWrapper">
<div class="paletteCol">
<img src="app/img/nodes/compartment.svg" language="PD" value="compartment" title="Compartment">
</div>
<div class="paletteCol">
<img src="app/img/nodes/submap.svg" language="PD" value="submap" title="Submap">
</div>
<div class="paletteCol">
<img src="app/img/nodes/tag.svg" language="PD" value="tag" title="Tag">
</div>
</div>
</div>
</div>
<div class="panel-body palette-panel-body" style="padding-bottom: 0px">
<p class="palette-label">Connecting Arcs</p>
<div id="pd-edge-palette" class="element-palette edge-palette">
<div class="paletteWrapper">
<div class="paletteCol">
<img src="app/img/edges/consumption.svg" language="PD" value="consumption" title="Consumption">
</div>
<div class="paletteCol">
<img src="app/img/edges/production.svg" language="PD" value="production" title="Production">
</div>
<div class="paletteCol">
<img src="app/img/edges/modulation.svg" language="PD" value="modulation" title="Modulation">
</div>
<div class="paletteCol">
<img src="app/img/edges/stimulation.svg" language="PD" value="stimulation" title="Stimulation">
</div>
<div class="paletteCol">
<img src="app/img/edges/catalysis.svg" language="PD" value="catalysis" title="Catalysis">
</div>
<div class="paletteCol">
<img src="app/img/edges/inhibition.svg" language="PD" value="inhibition" title="Inhibition">
</div>
<div class="paletteCol">
<img src="app/img/edges/necessary-stimulation.svg" language="PD" value="necessary stimulation" title="Necessary Stimulation">
</div>
<div class="paletteCol">
<img src="app/img/edges/consumption.svg" language="PD" value="logic arc" title="Logic Arc">
</div>
<div class="paletteCol">
<img src="app/img/edges/consumption.svg" language="PD" value="equivalence arc" title="Equivalence Arc">
</div>
</div>
</div>
</div>
</div>
</div>
<!-- AF Nodes Panel -->
<div class="panel">
<div id="AF-palette-heading" class="panel-heading collapsed" data-toggle="collapse" data-target="#expand-collapse-af-nodes-palette">
<p class="panel-title accordion-toggle">
Activity Flow
</p>
</div>
<div id="expand-collapse-af-nodes-palette" class="panel-collapse collapse">
<div class="panel-body palette-panel-body" style="padding-bottom: 0px">
<p class="palette-label">Activity Nodes</p>
<div id="af-node-palette" class="element-palette node-palette">
<div class="paletteWrapper">
<div class="paletteCol">
<img src="app/img/nodes/BA-plain.svg" language="AF" value="BA-plain" title="Biological Activity">
</div>
<div class="paletteCol">
<img src="app/img/nodes/phenotype.svg" language="AF" value="phenotype" title="Phenotype">
</div>
</div>
</div>
</div>
<div class="panel-body palette-panel-body" style="padding-bottom: 0px">
<p class="palette-label">Auxiliary Units</p>
<div id="af-node-palette" class="element-palette node-palette">
<div class="paletteWrapper">
<div class="paletteCol">
<img src="app/img/nodes/BA-macromolecule.svg" language="AF" value="BA-macromolecule" title="Macromolecule">
</div>
<div class="paletteCol">
<img src="app/img/nodes/BA-simple-chemical.svg" language="AF" value="BA-simple-chemical" title="Simple Chemical">
</div>
<div class="paletteCol">
<img src="app/img/nodes/BA-nucleic-acid-feature.svg" language="AF" value="BA-nucleic-acid-feature" title="Nucleic Acid Feature">
</div>
<div class="paletteCol">
<img src="app/img/nodes/BA-unspecified-entity.svg" language="AF" value="BA-unspecified-entity" title="Unspecified Entity">
</div>
<div class="paletteCol">
<img src="app/img/nodes/BA-complex.svg" language="AF" value="BA-complex" title="Complex">
</div>
<div class="paletteCol">
<img src="app/img/nodes/BA-perturbing-agent.svg" language="AF" value="BA-perturbing-agent" title="Perturbing Agent">
</div>
</div>
</div>
</div>
<div class="panel-body palette-panel-body" style="padding-bottom: 0px">
<p class="palette-label">Logical Operators</p>
<div id="af-node-palette" class="element-palette node-palette">
<div class="paletteWrapper">
<div class="paletteCol">
<img src="app/img/nodes/and.svg" language="AF" value="and" title="AND">
</div>
<div class="paletteCol">
<img src="app/img/nodes/or.svg" language="AF" value="or" title="OR">
</div>
<div class="paletteCol">
<img src="app/img/nodes/not.svg" language="AF" value="not" title="NOT">
</div>
<div class="paletteCol">
<img src="app/img/nodes/delay.svg" language="AF" value="delay" title="Delay">
</div>
</div>
</div>
</div>
<div class="panel-body palette-panel-body" style="padding-bottom: 0px">
<p class="palette-label">Other Nodes</p>
<div id="af-node-palette" class="element-palette node-palette">
<div class="paletteWrapper">
<div class="paletteCol">
<img src="app/img/nodes/compartment.svg" language="AF" value="compartment" title="Compartment">
</div>
<div class="paletteCol">
<img src="app/img/nodes/submap.svg" language="AF" value="submap" title="Submap">
</div>
<div class="paletteCol">
<img src="app/img/nodes/tag.svg" language="AF" value="tag" title="Tag">
</div>
</div>
</div>
</div>
<!-- AF Edges Panel -->
<div class="panel-body palette-panel-body" style="padding-bottom: 0px">
<p class="palette-label">Connecting Arcs</p>
<div id="af-edge-palette" class="element-palette edge-palette">
<div class="paletteWrapper">
<div class="paletteCol">
<img src="app/img/edges/stimulation.svg" language="AF" value="positive influence" title="Positive Influence">
</div>
<div class="paletteCol">
<img src="app/img/edges/inhibition.svg" language="AF" value="negative influence" title="Negative Influence">
</div>
<div class="paletteCol">
<img src="app/img/edges/modulation.svg" language="AF" value="unknown influence" title="Unknown Influence">
</div>
<div class="paletteCol">
<img src="app/img/edges/necessary-stimulation.svg" language="AF" value="necessary stimulation" title="Necessary Stimulation">
</div>
<div class="paletteCol">
<img src="app/img/edges/consumption.svg" language="AF" value="logic arc" title="Logic Arc">
</div>
<div class="paletteCol">
<img src="app/img/edges/consumption.svg" language="AF" value="equivalence arc" title="Equivalence Arc">
</div>
</div>
</div>