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bowringbowring
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Merge pull request #750 from bowring/refactor
Solved issue #613 for review
2 parents a29ad73 + 5de372c commit 1cab35c

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‎README.md

+100-60
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‎common.gradle

+1-1
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@ apply plugin: 'maven-publish'
77

88

99
String mavenGroupId = 'org.cirdles'
10-
String mavenVersion = '1.10.8'
10+
String mavenVersion = '2.0.1'
1111

1212
[compileJava, compileTestJava]*.options*.encoding = 'UTF-8'
1313

‎squidApp/src/main/java/org/cirdles/squid/gui/AboutSquidController.java

+2-3
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,6 @@
1515
*/
1616
package org.cirdles.squid.gui;
1717

18-
import javafx.event.ActionEvent;
1918
import javafx.fxml.FXML;
2019
import javafx.scene.control.Label;
2120
import org.cirdles.squid.Squid;
@@ -53,12 +52,12 @@ void initialize() {
5352
}
5453

5554
@FXML
56-
private void visitSquidOnCirdlesAction(ActionEvent event) {
55+
private void visitSquidOnCirdlesAction() {
5756
BrowserControl.showURI("http://cirdles.org/projects/squid/");
5857
}
5958

6059
@FXML
61-
private void visitUsOnGithubAction(ActionEvent event) {
60+
private void visitUsOnGithubAction() {
6261
BrowserControl.showURI("https://github.com/CIRDLES/Squid");
6362
}
6463

‎squidApp/src/main/java/org/cirdles/squid/gui/IsotopesManagerController.java

+47-54
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,6 @@
2121
import javafx.beans.value.ObservableValue;
2222
import javafx.collections.FXCollections;
2323
import javafx.collections.ObservableList;
24-
import javafx.event.ActionEvent;
2524
import javafx.event.EventHandler;
2625
import javafx.fxml.FXML;
2726
import javafx.fxml.Initializable;
@@ -228,63 +227,57 @@ public TableRow<MassStationDetail> call(TableView<MassStationDetail> tableView)
228227
final TableRow<MassStationDetail> row = new TableRow<>();
229228
final ContextMenu contextMenu = new ContextMenu();
230229
final MenuItem selectAsBackgroundMenuItem = new MenuItem("Select as Background Isotope");
231-
selectAsBackgroundMenuItem.setOnAction(new EventHandler<ActionEvent>() {
232-
@Override
233-
public void handle(ActionEvent event) {
234-
if (!row.getItem().getIsBackground()) {
235-
task.setIndexOfBackgroundSpecies(row.getItem().getMassStationIndex());
236-
task.setIndexOfTaskBackgroundMass(row.getItem().getMassStationIndex());
237-
238-
row.getItem().setIsBackground(true);
239-
row.getItem().setIsotopeLabel(DEFAULT_BACKGROUND_MASS_LABEL);
240-
row.getItem().updateTaskIsotopeLabelForBackground(((Task) task).findNominalMassOfTaskBackgroundMass());
241-
row.getItem().setNumeratorRole(false);
242-
row.getItem().setDenominatorRole(false);
243-
244-
SquidSpeciesModel ssm
245-
= task.getSquidSpeciesModelList()
246-
.get(row.getItem().getMassStationIndex());
247-
int previousIndex = task.selectBackgroundSpeciesReturnPreviousIndex(ssm);
248-
if (previousIndex >= 0) {
249-
MassStationDetail previousMassStationDetail = massStationsData.get(previousIndex);
250-
previousMassStationDetail.setIsotopeLabel(
251-
task.getSquidSpeciesModelList().get(previousIndex).getIsotopeName());
252-
previousMassStationDetail.setTaskIsotopeLabel(task.getNominalMasses().get(previousIndex));
253-
previousMassStationDetail.setNumeratorRole(false);
254-
previousMassStationDetail.setDenominatorRole(false);
255-
256-
SquidSpeciesModel previousSsm = task.getSquidSpeciesModelList().get(previousIndex);
257-
previousSsm.setIsBackground(false);
258-
//previousSsm.setNumeratorRole(false);
259-
//previousSsm.setDenominatorRole(false);
260-
}
261-
task.setChanged(true);
262-
isotopesTableView.refresh();
263-
updateBackgroundStatusLabel();
230+
selectAsBackgroundMenuItem.setOnAction(event -> {
231+
if (!row.getItem().getIsBackground()) {
232+
task.setIndexOfBackgroundSpecies(row.getItem().getMassStationIndex());
233+
task.setIndexOfTaskBackgroundMass(row.getItem().getMassStationIndex());
234+
235+
row.getItem().setIsBackground(true);
236+
row.getItem().setIsotopeLabel(DEFAULT_BACKGROUND_MASS_LABEL);
237+
row.getItem().updateTaskIsotopeLabelForBackground(((Task) task).findNominalMassOfTaskBackgroundMass());
238+
row.getItem().setNumeratorRole(false);
239+
row.getItem().setDenominatorRole(false);
240+
241+
SquidSpeciesModel ssm
242+
= task.getSquidSpeciesModelList()
243+
.get(row.getItem().getMassStationIndex());
244+
int previousIndex = task.selectBackgroundSpeciesReturnPreviousIndex(ssm);
245+
if (previousIndex >= 0) {
246+
MassStationDetail previousMassStationDetail = massStationsData.get(previousIndex);
247+
previousMassStationDetail.setIsotopeLabel(
248+
task.getSquidSpeciesModelList().get(previousIndex).getIsotopeName());
249+
previousMassStationDetail.setTaskIsotopeLabel(task.getNominalMasses().get(previousIndex));
250+
previousMassStationDetail.setNumeratorRole(false);
251+
previousMassStationDetail.setDenominatorRole(false);
252+
253+
SquidSpeciesModel previousSsm = task.getSquidSpeciesModelList().get(previousIndex);
254+
previousSsm.setIsBackground(false);
255+
//previousSsm.setNumeratorRole(false);
256+
//previousSsm.setDenominatorRole(false);
264257
}
258+
task.setChanged(true);
259+
isotopesTableView.refresh();
260+
updateBackgroundStatusLabel();
265261
}
266262
});
267263
contextMenu.getItems().add(selectAsBackgroundMenuItem);
268264

269265
final MenuItem deSelectAsBackgroundMenuItem = new MenuItem("De-select as Background Isotope");
270-
deSelectAsBackgroundMenuItem.setOnAction(new EventHandler<ActionEvent>() {
271-
@Override
272-
public void handle(ActionEvent event) {
273-
if (row.getItem().getIsBackground()) {
274-
SquidSpeciesModel ssm
275-
= task.getSquidSpeciesModelList()
276-
.get(row.getItem().getMassStationIndex());
277-
task.setIndexOfBackgroundSpecies(-1);
278-
task.setIndexOfTaskBackgroundMass(-1);
279-
task.setChanged(true);
280-
ssm.setIsBackground(false);
281-
row.getItem().setIsBackground(false);
282-
row.getItem().setIsotopeLabel(ssm.getIsotopeName());
283-
row.getItem().setTaskIsotopeLabel(task.getNominalMasses().get(row.getItem().getMassStationIndex()));
284-
285-
isotopesTableView.refresh();
286-
updateBackgroundStatusLabel();
287-
}
266+
deSelectAsBackgroundMenuItem.setOnAction(event -> {
267+
if (row.getItem().getIsBackground()) {
268+
SquidSpeciesModel ssm
269+
= task.getSquidSpeciesModelList()
270+
.get(row.getItem().getMassStationIndex());
271+
task.setIndexOfBackgroundSpecies(-1);
272+
task.setIndexOfTaskBackgroundMass(-1);
273+
task.setChanged(true);
274+
ssm.setIsBackground(false);
275+
row.getItem().setIsBackground(false);
276+
row.getItem().setIsotopeLabel(ssm.getIsotopeName());
277+
row.getItem().setTaskIsotopeLabel(task.getNominalMasses().get(row.getItem().getMassStationIndex()));
278+
279+
isotopesTableView.refresh();
280+
updateBackgroundStatusLabel();
288281
}
289282
});
290283
contextMenu.getItems().add(deSelectAsBackgroundMenuItem);
@@ -306,7 +299,7 @@ public void handle(ActionEvent event) {
306299
}
307300

308301
@FXML
309-
private void applyTaskIsotopeLabelsAction(ActionEvent event) {
302+
private void applyTaskIsotopeLabelsAction() {
310303
try {
311304
task.applyTaskIsotopeLabelsToMassStationsAndUpdateTask();
312305
} catch (SquidException squidException) {
@@ -316,7 +309,7 @@ private void applyTaskIsotopeLabelsAction(ActionEvent event) {
316309
}
317310

318311
@FXML
319-
private void applyMassStationIsotopeLabelsAction(ActionEvent event) {
312+
private void applyMassStationIsotopeLabelsAction() {
320313
try {
321314
task.applyMassStationLabelsToTask();
322315
} catch (SquidException squidException) {

‎squidApp/src/main/java/org/cirdles/squid/gui/MassesAuditController.java

+10-10
Original file line numberDiff line numberDiff line change
@@ -265,7 +265,7 @@ private void setupMassStationDetailsListViews() throws SquidException {
265265
}
266266

267267
@FXML
268-
private void normalizeTimeAxisCheckBoxAction(ActionEvent event) {
268+
private void normalizeTimeAxisCheckBoxAction() {
269269
showTimeNormalized = normalizeTimeAxisCheckBox.isSelected();
270270
squidProject.getTask().setShowTimeNormalized(showTimeNormalized);
271271
try {
@@ -275,7 +275,7 @@ private void normalizeTimeAxisCheckBoxAction(ActionEvent event) {
275275
}
276276

277277
@FXML
278-
private void showPrimaryBeamCheckBoxAction(ActionEvent event) {
278+
private void showPrimaryBeamCheckBoxAction() {
279279
showPrimaryBeam = showPrimaryBeamCheckBox.isSelected();
280280
squidProject.getTask().setShowPrimaryBeam(showPrimaryBeam);
281281
try {
@@ -285,7 +285,7 @@ private void showPrimaryBeamCheckBoxAction(ActionEvent event) {
285285
}
286286

287287
@FXML
288-
private void showQt1yCheckBoxAction(ActionEvent event) {
288+
private void showQt1yCheckBoxAction() {
289289
showQt1y = showQt1yCheckBox.isSelected();
290290
squidProject.getTask().setShowQt1y(showQt1y);
291291
try {
@@ -295,7 +295,7 @@ private void showQt1yCheckBoxAction(ActionEvent event) {
295295
}
296296

297297
@FXML
298-
private void showQt1zCheckBoxAction(ActionEvent event) {
298+
private void showQt1zCheckBoxAction() {
299299
showQt1z = showQt1zCheckBox.isSelected();
300300
squidProject.getTask().setShowQt1z(showQt1z);
301301
try {
@@ -324,7 +324,7 @@ public int[] getCountOfScansCumulative(List<Run> prawnFileRuns) {
324324
}
325325

326326
@FXML
327-
private void displaySpotLabelsCheckBoxAction(ActionEvent event) {
327+
private void displaySpotLabelsCheckBoxAction() {
328328
showSpotLabels = displaySpotLabelsCheckBox.isSelected();
329329
squidProject.getTask().setShowSpotLabels(showSpotLabels);
330330
try {
@@ -411,7 +411,7 @@ private ComboBox<MassStationDetail> addMassComboFactory(ObservableList<MassStati
411411
}
412412

413413
@FXML
414-
private void displayMassesAction(ActionEvent actionEvent) {
414+
private void displayMassesAction() {
415415
countsRadioButtonChoice = 0b00;
416416
try {
417417
displayMassStationsForReview();
@@ -420,7 +420,7 @@ private void displayMassesAction(ActionEvent actionEvent) {
420420
}
421421

422422
@FXML
423-
private void displayTotalCountsAction(ActionEvent actionEvent) {
423+
private void displayTotalCountsAction() {
424424
countsRadioButtonChoice = 0b10;
425425
try {
426426
displayMassStationsForReview();
@@ -429,7 +429,7 @@ private void displayTotalCountsAction(ActionEvent actionEvent) {
429429
}
430430

431431
@FXML
432-
private void displayTotalSBMAction(ActionEvent actionEvent) {
432+
private void displayTotalSBMAction() {
433433
countsRadioButtonChoice = 0b01;
434434
try {
435435
displayMassStationsForReview();
@@ -438,7 +438,7 @@ private void displayTotalSBMAction(ActionEvent actionEvent) {
438438
}
439439

440440
@FXML
441-
private void displayBothCountsAction(ActionEvent actionEvent) {
441+
private void displayBothCountsAction() {
442442
countsRadioButtonChoice = 0b11;
443443
try {
444444
displayMassStationsForReview();
@@ -1010,7 +1010,7 @@ public void updateSpotsInGraphs() throws SquidException {
10101010
}
10111011

10121012
@FXML
1013-
private void resetMassesAuditGraphs(ActionEvent actionEvent) throws SquidException {
1013+
private void resetMassesAuditGraphs() throws SquidException {
10141014
((Task) squidProject.getTask()).resetMassStationGraphViews();
10151015
SquidUIController primaryStageController = (SquidUIController) primaryStageWindow.getScene().getUserData();
10161016
primaryStageController.launchMassesAudit();

‎squidApp/src/main/java/org/cirdles/squid/gui/ProjectManagerController.java

+12-12
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,6 @@
1717

1818
import javafx.beans.value.ObservableValue;
1919
import javafx.collections.FXCollections;
20-
import javafx.event.ActionEvent;
2120
import javafx.fxml.FXML;
2221
import javafx.fxml.Initializable;
2322
import javafx.scene.control.*;
@@ -256,6 +255,7 @@ private void setupListeners() {
256255
case PB_208:
257256
pb208RadioButton.setSelected(true);
258257
break;
258+
default:
259259
}
260260

261261
autoExcludeSpotsCheckBox.setSelected(squidProject.isSquidAllowsAutoExclusionOfSpots());
@@ -329,7 +329,7 @@ private void extractSummaryStatsFromPrawnFile() {
329329
}
330330

331331
@FXML
332-
private void yesSBMRadioButtonAction(ActionEvent event) {
332+
private void yesSBMRadioButtonAction() {
333333
squidProject.setUseSBM(true);
334334
SquidProject.setProjectChanged(true);
335335
task.setUseSBM(true);
@@ -345,7 +345,7 @@ private void yesSBMRadioButtonAction(ActionEvent event) {
345345
}
346346

347347
@FXML
348-
private void noSBMRadioButtonActions(ActionEvent event) {
348+
private void noSBMRadioButtonActions() {
349349
squidProject.setUseSBM(false);
350350
SquidProject.setProjectChanged(true);
351351
task.setUseSBM(false);
@@ -358,7 +358,7 @@ private void noSBMRadioButtonActions(ActionEvent event) {
358358
}
359359

360360
@FXML
361-
private void linearRegressionRatioCalcRadioButtonAction(ActionEvent event) {
361+
private void linearRegressionRatioCalcRadioButtonAction() {
362362
squidProject.setUserLinFits(true);
363363
SquidProject.setProjectChanged(true);
364364
task.setUserLinFits(true);
@@ -371,7 +371,7 @@ private void linearRegressionRatioCalcRadioButtonAction(ActionEvent event) {
371371
}
372372

373373
@FXML
374-
private void spotAverageRatioCalcRadioButtonAction(ActionEvent event) {
374+
private void spotAverageRatioCalcRadioButtonAction() {
375375
squidProject.setUserLinFits(false);
376376
SquidProject.setProjectChanged(true);
377377
task.setUserLinFits(false);
@@ -384,28 +384,28 @@ private void spotAverageRatioCalcRadioButtonAction(ActionEvent event) {
384384
}
385385

386386
@FXML
387-
private void pb204RadioButtonAction(ActionEvent event) throws SquidException {
387+
private void pb204RadioButtonAction() throws SquidException {
388388
squidProject.setSelectedIndexIsotope(Squid3Constants.IndexIsoptopesEnum.PB_204);
389389
SquidProject.setProjectChanged(true);
390390
task.setChanged(true);
391391
}
392392

393393
@FXML
394-
private void pb207RadioButtonAction(ActionEvent event) throws SquidException {
394+
private void pb207RadioButtonAction() throws SquidException {
395395
squidProject.setSelectedIndexIsotope(Squid3Constants.IndexIsoptopesEnum.PB_207);
396396
SquidProject.setProjectChanged(true);
397397
task.setChanged(true);
398398
}
399399

400400
@FXML
401-
private void pb208RadioButtonAction(ActionEvent event) throws SquidException {
401+
private void pb208RadioButtonAction() throws SquidException {
402402
squidProject.setSelectedIndexIsotope(Squid3Constants.IndexIsoptopesEnum.PB_208);
403403
SquidProject.setProjectChanged(true);
404404
task.setChanged(true);
405405
}
406406

407407
@FXML
408-
private void autoExcludeSpotsCheckBoxAction(ActionEvent event) {
408+
private void autoExcludeSpotsCheckBoxAction() {
409409
// this will cause weighted mean expressions to be changed with boolean flag
410410
squidProject.setSquidAllowsAutoExclusionOfSpots(autoExcludeSpotsCheckBox.isSelected());
411411
SquidProject.setProjectChanged(true);
@@ -417,7 +417,7 @@ private void autoExcludeSpotsCheckBoxAction(ActionEvent event) {
417417
}
418418

419419
@FXML
420-
private void parametersSetDefaultsOnAction(ActionEvent actionEvent) {
420+
private void parametersSetDefaultsOnAction() {
421421
taskDesign.setUseSBM(yesSBMRadioButton.isSelected());
422422

423423
taskDesign.setUserLinFits(linearRegressionRatioCalcRadioButton.isSelected());
@@ -448,13 +448,13 @@ private void parametersSetDefaultsOnAction(ActionEvent actionEvent) {
448448
}
449449

450450
@FXML
451-
void useCommonPbModelForUnkownsAction(ActionEvent event) {
451+
void useCommonPbModelForUnkownsAction() {
452452
squidProject.setCommonLeadForUnknownsMethodSelected(useCommonPbModelForUnknownsCheckBox.isSelected() ? METHOD_COMMON_LEAD_MODEL : METHOD_STACEY_KRAMER);
453453
DEFAULT_COMMON_LEAD_METHOD_FOR_UNKNOWNS = useCommonPbModelForUnknownsCheckBox.isSelected() ? METHOD_COMMON_LEAD_MODEL : METHOD_STACEY_KRAMER;
454454
}
455455

456456
@FXML
457-
private void refreshModelsAction(ActionEvent event) {
457+
private void refreshModelsAction() {
458458
try {
459459
task.refreshParametersFromModels(squidProject.isTypeGeochron(), true, false);
460460
physConstModelComboBox.setItems(FXCollections.observableArrayList(squidLabData.getPhysicalConstantsModels()));

‎squidApp/src/main/java/org/cirdles/squid/gui/SessionAuditController.java

+1-5
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,6 @@
2020
import javafx.beans.value.ObservableValue;
2121
import javafx.collections.FXCollections;
2222
import javafx.collections.ObservableList;
23-
import javafx.event.ActionEvent;
2423
import javafx.fxml.FXML;
2524
import javafx.fxml.Initializable;
2625
import javafx.scene.control.*;
@@ -70,9 +69,6 @@ public class SessionAuditController implements Initializable {
7069
private ComboBox<String> delimiterComboBox;
7170
private String sampleNameDelimiter;
7271

73-
public SessionAuditController() {
74-
}
75-
7672
/**
7773
* Initializes the controller class.
7874
*
@@ -349,7 +345,7 @@ private void lockParentsForRefMat(CheckBoxTreeItem<SampleNameTreeNodeInterface>
349345
* Calls method displaying appropriate tree dependent on the state of the
350346
* CheckBox
351347
*/
352-
private void duplicatesChecked(ActionEvent event) {
348+
private void duplicatesChecked() {
353349
setUpPrawnAuditTreeView(checkbox.isSelected());
354350
}
355351

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