forked from ConesaLab/tappAS
-
Notifications
You must be signed in to change notification settings - Fork 0
/
DlgHelp.java
371 lines (358 loc) · 22.3 KB
/
DlgHelp.java
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
/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package tappas;
import javafx.fxml.FXMLLoader;
import javafx.scene.Node;
import javafx.scene.control.ButtonBar;
import javafx.scene.control.ButtonType;
import javafx.scene.control.Dialog;
import javafx.scene.input.MouseButton;
import javafx.scene.web.WebEngine;
import javafx.scene.web.WebView;
import javafx.stage.Modality;
import javafx.stage.StageStyle;
import javafx.stage.Window;
import java.nio.file.Paths;
import java.util.HashMap;
/**
*
* @author Hector del Risco - [email protected] & Pedro Salguero - [email protected]
*/
public class DlgHelp {
static HashMap<String, DlgHelpData> dlgs = new HashMap<>();
Dialog dialog;
WebView web;
WebEngine engine;
public void show(String title, String htmlFile, Window window) {
App app = Tappas.getApp();
// check if help dialog is already opened, try to give focus if so
if(dlgs.containsKey(htmlFile)) {
DlgHelpData data = dlgs.get(htmlFile);
try {
// return if OK, otherwise will flow to creating a new dialog
data.dlg.getDialogPane().getScene().getWindow().requestFocus();
return;
}
catch(Exception e) { dlgs.remove(htmlFile); }
}
// create help dialog
dialog = new Dialog();
dialog.setTitle(title);
dlgs.put(htmlFile, new DlgHelpData(title, dialog));
dialog.initModality(Modality.NONE);
dialog.initStyle(StageStyle.DECORATED);
dialog.initOwner(window);
dialog.setResizable(true);
dialog.getDialogPane().autosize();
dialog.setOnHidden((event) -> { dlgs.remove(htmlFile); });
try {
// get help content or use Help_NA.html if none available
Node node = (Node) FXMLLoader.load(Tappas.class.getResource("/tappas/dialogs/Help.fxml"));
dialog.getDialogPane().setContent(node);
web = (WebView) node.getParent().lookup("#webHelp");
engine = web.getEngine();
String content = app.data.getFileContentFromResource("/tappas/resources/web/" + htmlFile);
if(content.isEmpty())
content = app.data.getFileContentFromResource("/tappas/resources/web/Help_NA.html");
// handle includes and special tags
content = replaceSharedSections(content);
content = app.resources.replaceHTMLAllResources(content);
// display contents
engine.loadContent(content);
web.setOnMouseClicked((event) -> {
if(event.getButton() == MouseButton.PRIMARY) {
String cmd = (String) web.getEngine().executeScript("getCmdRequest()");
if(!cmd.trim().isEmpty()) {
showPage(cmd);
dialog.close();
}
}
});
ButtonType btnOK = new ButtonType("Close", ButtonBar.ButtonData.OK_DONE);
dialog.getDialogPane().getButtonTypes().addAll(btnOK);
dialog.show();
} catch(Exception e) {
app.logError("Unable to create help dialog: " + e.getMessage());
}
}
//
// Internal Functions
//
private void showPage(String url) {
App app = Tappas.getApp();
// handle web and local content accordingly
if(url.startsWith("http"))
Tappas.getHost().showDocument(url);
else {
String filepath = Paths.get(app.data.getAppDataFolder(), "web", url).toString();
app.logger.logDebug("web FP: " + filepath);
String weburl;
if(Utils.isWindowsOS()) {
// need an additional slash when using drive letters
weburl = "/" + filepath.replaceAll("\\\\", "/");
System.out.println("fp: " + url);
}
else
weburl = filepath;
weburl = "file://" + weburl;
app.logger.logDebug("Web URL: " + weburl);
Tappas.getHost().showDocument(weburl);
}
}
private String replaceSharedSections(String html) {
String newHtml = "";
String lines[] = html.split("\\n");
for(String line : lines) {
if(line.contains("<!-- RowColumns -->"))
line = "<span class=\"notes\" style=\"padding-left:25px; padding-bottom:10px;\">All project data tables include row selection (<input type=\"checkbox\" style=\"vertical-align:middle; font-size:x-small;\" disabled>) and sequential id (#) columns</span><br/>";
else if(line.contains("<!-- HiddenColumns -->"))
line = "<p>The following table columns are NOT displayed by default:</p>\n";
else if(line.contains("<!-- DVReminders -->"))
line = "<p>" + replaceSharedSections("<!-- DVRemindersAdd -->") + "</p>";
else if(line.contains("<!-- DVRemindersAdd -->")) {
line = "Keep in mind that if your application window size is not big enough, the legend for some of the charts may not be displayed. ";
line += "Don't forget to take advantage of mouseover and context-sensitive menus for additional information and functionality.";
}
else if(line.contains("<!-- AddHelp:"))
line = getAddHelpHtml(line);
else if(line.contains("<!-- SubtabMenuBarHeader"))
line = "<br/><b><font color='#a2ca72'>Subtab Menu Bar</font></b><p>In addition to the Help button, the following menu buttons are provided:</p><table>";
else if(line.contains("<!-- SubtabMenuBar:"))
line = getSubtabMenuBarHtml(line, true);
else if(line.contains("<!-- SubtabMenuBarNoHeader:"))
line = getSubtabMenuBarHtml(line, false);
newHtml += line + "\n";
}
return newHtml;
}
private String getAddHelpHtml(String line) {
String newLine = "<br/><b><font color='#a2ca72'>Additional Help</font></b><ul>";
String[] info = line.split(":");
if(info.length == 2) {
String[] fields = info[1].split(",");
for(String field : fields) {
String[] vals = field.split(" ");
switch (vals[0]) {
case "gui":
newLine += "\n<li>For overview of the application user interface see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageAppXface.html#Top')\">";
newLine += " Application Interface</span> section in Overview</li>\n";
break;
case "projects":
newLine += "\n<li>For overview of application projects see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageProjects.html#Top')\">";
newLine += " Projects</span> section in Overview</li>\n";
break;
case "afFormat":
newLine += "\n<li>For annotation file format see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageProjects.html#AnnotationFileFormat')\">";
newLine += " Annotation File Format</span> section in Overview</li>\n";
break;
case "emFormat":
newLine += "\n<li>For expression matrix file format see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageProjects.html#ExpMatrixFileFormat')\">";
newLine += " Expression Matrix File Format</span> section in Overview</li>\n";
break;
case "tips":
newLine += "\n<li>For tips on using the application see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageAppTips.html#Tips')\">";
newLine += " Application Tips</span> section in Overview</li>\n";
break;
case "tables":
newLine += "\n<li>For help with data tables see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageAppXface.html#Tables')\">";
newLine += " Application Interface - Tables</span> section in Overview</li>\n";
break;
case "query":
newLine += "\n<li>For help with searching and filtering data tables see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageQuery.html#Top')\">";
newLine += " Ad Hoc Query</span> section in Overview</li>\n";
break;
case "genedv":
newLine += "\n<li>For help with gene data visualization see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageDataViz.html#GeneDV')\">";
newLine += " Data Visualization</span> section in Overview</li>\n";
break;
case "export":
newLine += "\n<li>For help with exporting data tables see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageExport.html#Top')\">";
newLine += " Export Data and Images</span> section in Overview</li>\n";
break;
case "visual":
newLine += "\n<li>For help with visual display controls see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageAppXface.html#Visual')\">";
newLine += " Visual Display Controls</span> section in Overview</li>\n";
break;
case "menus":
newLine += "\n<li>For help with context-sensitive menus see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageAppXface.html#Menus')\">";
newLine += " Context-Sensitive Menus</span> section in Overview</li>\n";
break;
case "inpdata":
newLine += "\n<li>For help with input data and filtering see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageProjects.html#InputData')\">";
newLine += " Input Data and Filtering</span> section in Overview</li>\n";
break;
case "dea":
newLine += "\n<li>For help with DEA see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageDEA.html#Top')\">";
newLine += " Differential Expression Analysis</span> section in Overview</li>\n";
break;
case "diu":
newLine += "\n<li>For help with DIU see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageDIU.html#Top')\">";
newLine += " Differential Isoform Usage </span> section in Overview</li>\n";
break;
case "dfi":
newLine += "\n<li>For help with DFI see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageAFA.html#DFI')\">";
newLine += " Annotation Features DIU</span> section in Overview</li>\n";
break;
case "fda":
newLine += "\n<li>For help with FDA see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageAFA.html#FDA')\">";
newLine += " Functional Diversity Analysis</span> section in Overview</li>\n";
break;
case "fea":
newLine += "\n<li>For help with FEA see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageEA.html#FEA')\">";
newLine += " Functional Enrichment Analysis</span> section in Overview</li>\n";
break;
case "feaclusters":
newLine += "\n<li>For help with FEA clusters see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageEA.html#FEAClusters')\">";
newLine += " Enriched Features Cluster Analysis</span> section in Overview</li>\n";
break;
case "gsea":
newLine += "\n<li>For help with GSEA see the ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageEA.html#GSEA')\">";
newLine += " Gene Set Enrichment Analysis</span> section in Overview</li>\n";
break;
case "noiseq":
newLine += "\n<li>To see the <span class=\"fakeAnchor\" onclick=\"setCmdRequest('https://www.bioconductor.org/packages/release/bioc/html/NOISeq.html')\">NOISeq</span> package documentation, click ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('https://www.bioconductor.org/packages/release/bioc/html/NOISeq.html')\">here.</span></li>";
break;
case "edger":
newLine += "\n<li>To see the <span class=\"fakeAnchor\" onclick=\"setCmdRequest('https://www.bioconductor.org/packages/release/bioc/html/edgeR.html')\">edgeR</span> package documentation, click ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('https://www.bioconductor.org/packages/release/bioc/html/edgeR.html')\">here.</span></li>";
break;
case "dexseq":
newLine += "\n<li>To see the <span class=\"fakeAnchor\" onclick=\"setCmdRequest('https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html')\">DEXSeq</span> package documentation, click ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html')\">here.</span></li>";
break;
case "goseq":
newLine += "\n<li>To see the <span class=\"fakeAnchor\" onclick=\"setCmdRequest('https://www.bioconductor.org/packages/release/bioc/html/goseq.html')\">goseq</span> package documentation, click ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('https://www.bioconductor.org/packages/release/bioc/html/goseq.html')\">here.</span></li>";
break;
case "goglm":
newLine += "\n<li>To see the <span class=\"fakeAnchor\" onclick=\"setCmdRequest('https://github.com/gu-mi/GOglm')\">GOglm</span> package documentation, click ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('https://github.com/gu-mi/GOglm')\">here.</span></li>";
break;
case "gff3":
newLine += "\n<li>To see the <span class=\"fakeAnchor\" onclick=\"setCmdRequest('https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md')\">Generic Feature Format Version 3 (GFF3)</span> specifications, click ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md')\">here.</span></li>";
break;
case "go":
newLine += "\n<li>To see the <span class=\"fakeAnchor\" onclick=\"setCmdRequest('http://www.geneontology.org/')\">Gene Ontology</span> references, click ";
newLine += "<span class=\"fakeAnchor\" onclick=\"setCmdRequest('http://www.geneontology.org/')\">here.</span></li>";
break;
}
}
}
newLine += "</ul>";
return newLine;
}
private String getSubtabMenuBarHtml(String line, boolean header) {
String newLine = header? "<br/><b><font color='#a2ca72'>Subtab Menu Bar</font></b><p>In addition to the Help button, the following menu buttons are provided:</p><table>" : "<table>";
String[] info = line.split(":");
if(info.length == 2) {
String[] fields = info[1].split(",");
for(String field : fields) {
String[] vals = field.split(" ");
switch (vals[0]) {
case "optlog":
newLine += "\n<tr><td style=\"vertical-align:top;\">";
newLine += "<div class=\"subtabButton\"><img src=\"images/optionsButton.png\" width=\"28\" height=\"28\" alt=\"Menu selections...\"/></div>";
newLine += "</td>\n<td>";
newLine += " - menu with the following selections:<ul><li>View Analysis Log - displays the analysis log</li></ul>";
newLine += "\n</td></tr>";
break;
case "optdbg":
newLine += "\n<tr><td style=\"vertical-align:top;\">";
newLine += "<div class=\"subtabButton\"><img src=\"images/optionsButton.png\" width=\"28\" height=\"28\" alt=\"Menu selections...\"/></div>";
newLine += "</td>\n<td>";
newLine += " - menu with the following selections:<ul><li>Log debug messages - check to log application debug messages. WARNING do not turn this feature on unless needed and make sure to uncheck when done</li></ul>";
newLine += "\n</td></tr>";
break;
case "select":
newLine += "\n<tr><td>";
newLine += "<div class=\"subtabButton\"><img src=\"images/selectButton.png\" width=\"28\" height=\"28\" alt=\"Table row selection...\"/></div>";
newLine += "</td>\n<td>";
newLine += " - table row selection management menu. See <span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageQuery.html#Top')\">Ad Hoc Query</span> section in Overview";
newLine += "\n</td></tr>";
break;
case "export":
newLine += "\n<tr><td>";
newLine += "<div class=\"subtabButton\"><img src=\"images/exportButton.png\" width=\"28\" height=\"28\" alt=\"Export data or images...\"/></div>";
newLine += "</td>\n<td>";
newLine += " - export data or images to file. See <span class=\"fakeAnchor\" onclick=\"setCmdRequest('pageExport.html#Top')\">Export Data and Images</span> section in Overview";
newLine += "\n</td></tr>";
break;
case "dataViz":
newLine += "\n<tr><td>";
newLine += "<div class=\"subtabButton\"><img src=\"images/dataVizButton.png\" width=\"28\" height=\"28\" alt=\"Data visualization options...\"/></div>";
newLine += "</td>\n<td>";
newLine += " - data visualization menu will show menu selections for all relevant data visualization subtabs";
newLine += "\n</td></tr>";
break;
case "clusters":
newLine += "\n<tr><td>";
newLine += "<div class=\"subtabButton\"><img src=\"images/clustersDataButton.png\" width=\"28\" height=\"28\" alt=\"FEA Clusters...\"/></div>";
newLine += "</td>\n<td>";
newLine += " - FEA clusters menu with selections to view clusters or run cluster analysis";
newLine += "\n</td></tr>";
break;
case "sigLevel":
newLine += "\n<tr><td>";
newLine += "<div class=\"subtabButton\"><img src=\"images/sigLevelButton.png\" width=\"28\" height=\"28\" alt=\"Change significance level.\"/></div>";
newLine += "</td>\n<td>";
newLine += " - change significance level, will recalculate analysis results";
newLine += "\n</td></tr>";
break;
case "rerun":
newLine += "\n<tr><td>";
newLine += "<div class=\"subtabButton\"><img src=\"images/rerunButton.png\" width=\"28\" height=\"28\" alt=\"Rerun analysis...\"/></div>";
newLine += "</td>\n<td>";
newLine += " - rerun analysis, will allow changing analysis parameters";
newLine += "\n</td></tr>";
break;
case "zoom":
newLine += "\n<tr><td><div class=\"subtabButton\" style=\"height:90px;\">";
newLine += "<div class=\"subtabButton\"><img src=\"images/minusButton.png\" width=\"24\" height=\"24\" alt=\"Minus\"/></div>";
newLine += "<div class=\"subtabButton\"><img src=\"images/fitButton.png\" width=\"24\" height=\"24\" alt=\"Fit\"/></div>";
newLine += "<div class=\"subtabButton\"><img src=\"images/plusButton.png\" width=\"24\" height=\"24\" alt=\"Plus\"/></div>";
newLine += "</div></td>\n<td>";
newLine += " - use [-] to zoom out, [+] to zoom in, and [Fit] to display image so it fits in available space";
newLine += "\n</td></tr>";
break;
}
}
}
newLine += "</table>";
return newLine;
}
//
// Data Classes
//
public class DlgHelpData {
String title;
Dialog dlg;
public DlgHelpData(String title, Dialog dlg) {
this.title = title;
this.dlg = dlg;
}
}
}