-
Notifications
You must be signed in to change notification settings - Fork 2
/
DrillDownDPAData.java
209 lines (195 loc) · 8.13 KB
/
DrillDownDPAData.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
/*
* 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.beans.property.SimpleStringProperty;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.concurrent.Task;
import javafx.scene.control.*;
import javafx.scene.control.cell.PropertyValueFactory;
import javafx.scene.layout.Pane;
import javafx.stage.Window;
import java.util.ArrayList;
import java.util.HashMap;
/**
*
* @author Pedro Salguero - [email protected]
*/
public class DrillDownDPAData extends DlgBase {
static int id = 0;
Label lblHeader, lblDescription;
Button btnHelpTbl, btnExportTbl;
TableView tblMembers;
Pane paneMenu;
ProgressIndicator pi;
int toolId;
String idColName;
String gene;
String panel;
static String exportFilename = "";
ArrayList<String> shortIso, longIso;
TaskHandler.ServiceExt service = null;
ObservableList<DPADrillDownData> data = null;
public DrillDownDPAData(Project project, Window window) {
super(project, window);
toolId = ++id;
}
public HashMap<String, String> showAndWait(String gene, HashMap<String,ArrayList<String>> iso) {
if(createToolDialog("DrillDownDPAData.fxml", "DPA Features Drill Down Data", null)) {
this.gene = gene;
this.shortIso = iso.get("S");
this.longIso = iso.get("L");
panel = TabGeneDataViz.Panels.TRANS.name();
idColName = "Gene";
exportFilename = "tappAS_DPA_Isoforms_" + gene + ".tsv";
// get control objects
lblHeader = (Label) scene.lookup("#lblHeader");
lblDescription = (Label) scene.lookup("#lblDescription");
pi = (ProgressIndicator) scene.lookup("#piImage");
tblMembers = (TableView) scene.lookup("#tblMembers");
paneMenu = (Pane) scene.lookup("#paneMenu");
// setup dialog
dialog.setTitle("DPA Drill Down Data for " + gene);
lblHeader.setText("Gene " + gene + " contains next Isoforms");
lblDescription.setText("");
tblMembers.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
ObservableList<TableColumn> cols = tblMembers.getColumns();
//cols.get(0).setText(idColName);
cols.get(0).setCellValueFactory(new PropertyValueFactory<>("shortIso"));
cols.get(1).setCellValueFactory(new PropertyValueFactory<>("longIso"));
SubTabBase.addRowNumbersCol(tblMembers);
ContextMenu cm = new ContextMenu();
//addGeneDVItem(cm, tblMembers, panel);
app.export.setupTableExport(this, cm, true);
tblMembers.setContextMenu(cm);
app.export.addCopyToClipboardHandler(tblMembers);
// setup menu buttons
double yoffset = 3.0;
btnExportTbl = app.ctls.addImgButton(paneMenu, "export.png", "Export table data...", yoffset, 32, true);
btnExportTbl.setOnAction((event) -> { onButtonExport(); });
yoffset += 36;
btnHelpTbl = app.ctls.addImgButton(paneMenu, "help.png", "Help", yoffset, 32, true);
btnHelpTbl.setOnAction((event) -> { DlgHelp dlg = new DlgHelp(); dlg.show(title, "Help_DrillDownData_DPA.html", Tappas.getWindow()); });
// process dialog - modeless
dialog.setOnShown(e -> { runThread();});
dialog.showAndWait();
}
return null;
}
@Override
protected void onButtonExport() {
DlgExportData.Config cfg = new DlgExportData.Config(true, idColName + "s list (IDs only)", false, "");
DlgExportData.Params results = app.ctlr.getExportDataParams(cfg, null, null);
if(results != null) {
HashMap<String, String> hmColNames = new HashMap<>();
Export.ExportSelection selection = Export.ExportSelection.All;
if(results.dataSelection.equals(DlgExportData.Params.DataSelection.SELECTEDROWS))
selection = Export.ExportSelection.Highlighted;
if(results.dataType.equals(DlgExportData.Params.DataType.TABLEROWS.name()))
app.export.exportTableDataToFile(tblMembers, selection, exportFilename);
else if(results.dataType.equals(DlgExportData.Params.DataType.LIST.name())) {
hmColNames.put(idColName, "");
app.export.exportTableDataListToFile(tblMembers, selection, hmColNames, exportFilename);
}
}
}
//
// Data Load
//
private void runThread() {
// get script path and run service/task
service = new DataService();
service.initialize();
service.start();
}
private class DataService extends TaskHandler.ServiceExt {
@Override
public void initialize() {
data = null;
}
@Override
protected void onRunning() {
pi.setVisible(true);
}
@Override
protected void onStopped() {
pi.setVisible(false);
}
@Override
protected void onFailed() {
java.lang.Throwable e = getException();
if(e != null)
app.logWarning("DrillDownDPA - task aborted. Exception: " + e.getMessage());
else
app.logWarning("DrillDownDPA - task aborted.");
app.ctls.alertWarning("Drill Down", "DrillDownDPA - task aborted");
}
@Override
protected void onSucceeded() {
if(data != null) {
tblMembers.setItems(data);
if(!data.isEmpty())
tblMembers.getSelectionModel().select(1);
}
else
app.ctls.alertWarning("DPA Drill Down Data", "Unable to load drill down data.");
}
@Override
protected Task<Void> createTask() {
Task task = new Task<Void>() {
@Override
protected Void call() throws Exception {
try {
ObservableList<DPADrillDownData> lst = FXCollections.observableArrayList();
int max = Math.max(shortIso.size(),longIso.size());
for(int i=0;i<max;i++){
if(i<=shortIso.size()-1 && i <= longIso.size()-1)
lst.add(new DPADrillDownData(shortIso.get(i), longIso.get(i)));
else if(i>longIso.size()-1 && i <= shortIso.size()-1)
lst.add(new DPADrillDownData(shortIso.get(i), ""));
else
lst.add(new DPADrillDownData("", longIso.get(i)));
}
//FXCollections.sort(lst);
data = lst;
}
catch (Exception e) {
app.logError("Unable to load gene': " + gene + " " + e.getMessage());
}
return null;
}
};
taskInfo = new TaskHandler.TaskInfo("DPA Drill Down Data " + toolId, task);
return task;
}
}
//
// Data Classes
//
static public class DPADrillDownData implements Comparable<DPADrillDownData> {
//public SimpleStringProperty gene;
public SimpleStringProperty shortIso;
public SimpleStringProperty longIso;
public DPADrillDownData(String shortIso, String longIso) {
this.shortIso = new SimpleStringProperty(shortIso);
this.longIso = new SimpleStringProperty(longIso);
}
//public String getGene() { return gene.get(); }
public String getShortIso() {
return shortIso.get();
}
public String getLongIso() {
return longIso.get();
}
@Override
public int compareTo(DPADrillDownData td) {
return 1;
}
/*public int compareTo(DPADrillDownData td) {
return (gene.get().compareToIgnoreCase(td.gene.get()));
}*/
}
}