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bowringbowring
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Fixed #593 and refactored by Intellij (#608)
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‎common.gradle

+2-2
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ apply plugin: 'java'
66
apply plugin: 'maven'
77

88
String mavenGroupId = 'org.cirdles'
9-
String mavenVersion = '1.7.4'
9+
String mavenVersion = '1.7.5'
1010

1111
sourceCompatibility = '1.8'
1212
[compileJava, compileTestJava]*.options*.encoding = 'UTF-8'
@@ -97,4 +97,4 @@ if (JavaVersion.current().isJava8Compatible()) {
9797
}
9898
tasks.withType(JavaCompile) {
9999
options.encoding = 'UTF-8'
100-
}
100+
}

‎gradle.properties

+9
Original file line numberDiff line numberDiff line change
@@ -1,2 +1,11 @@
11
action.build.args=clean build test
22
action.clean.args=clean
3+
netbeans.de-funfried-netbeans-plugins-externalcodeformatter.enableIndentationSettings=true
4+
netbeans.de-funfried-netbeans-plugins-externalcodeformatter.overrideTabSizeValue=4
5+
netbeans.de-funfried-netbeans-plugins-externalcodeformatter.enabledFormatter_2e_JSON=netbeans-formatter
6+
netbeans.de-funfried-netbeans-plugins-externalcodeformatter.enabledFormatter_2e_JAVASCRIPT=netbeans-formatter
7+
netbeans.de-funfried-netbeans-plugins-externalcodeformatter.enabledFormatter_2e_XML=netbeans-formatter
8+
netbeans.de-funfried-netbeans-plugins-externalcodeformatter.overrideTabSize=false
9+
netbeans.de-funfried-netbeans-plugins-externalcodeformatter.enabledFormatter_2e_JAVA=netbeans-formatter
10+
netbeans.de-funfried-netbeans-plugins-externalcodeformatter.showNotifications=false
11+
netbeans.de-funfried-netbeans-plugins-externalcodeformatter.useProjectSettings=true

‎squidApp/src/main/java/org/cirdles/squid/gui/dataViews/MassStationAuditViewForShrimp.java

+5-6
Original file line numberDiff line numberDiff line change
@@ -401,7 +401,7 @@ public void paint(GraphicsContext g2d) {
401401

402402
g2d.setFont(Font.font("SansSerif", 7));
403403
Text text = new Text(String.valueOf(runIndices[i]));
404-
text.setFont(Font.font("SansSerif", 7)); // applyCss();
404+
text.setFont(Font.font("SansSerif", 7));
405405
g2d.setFill(Paint.valueOf("BLACK"));
406406
g2d.fillText(String.valueOf(runIndices[i]), mapX(myOnPeakNormalizedAquireTimes[i]) - text.getLayoutBounds().getWidth() + 2.0f, height - 1.5);
407407
g2d.setStroke(Paint.valueOf("BLACK"));
@@ -441,16 +441,16 @@ public void paint(GraphicsContext g2d) {
441441
mapY(peakTukeysMeanAndUnct[0]));
442442

443443
g2d.setFill(Paint.valueOf("BLUE"));
444-
g2d.fillText("mean = " + (new BigDecimal(peakTukeysMeanAndUnct[0])).setScale(4, RoundingMode.HALF_UP).toPlainString(),
444+
g2d.fillText("mean = " + (BigDecimal.valueOf(peakTukeysMeanAndUnct[0])).setScale(4, RoundingMode.HALF_UP).toPlainString(),
445445
(float) mapX(minX) - 150f,
446446
(float) mapY(peakTukeysMeanAndUnct[0]) + verticalTextShift);
447-
g2d.fillText(" 95% = " + (new BigDecimal(peakTukeysMeanAndUnct[2])).setScale(6, RoundingMode.HALF_UP).toEngineeringString(),
447+
g2d.fillText(" 95% = " + (BigDecimal.valueOf(peakTukeysMeanAndUnct[2])).setScale(6, RoundingMode.HALF_UP).toEngineeringString(),
448448
(float) mapX(minX) - 150f,
449449
(float) mapY(peakTukeysMeanAndUnct[0]) + 15f);
450-
g2d.fillText(" max = " + (new BigDecimal(maxMassAMU)).setScale(3, RoundingMode.HALF_UP).toPlainString(),
450+
g2d.fillText(" max = " + (BigDecimal.valueOf(maxMassAMU)).setScale(3, RoundingMode.HALF_UP).toPlainString(),
451451
(float) mapX(minX) - 150f,
452452
(float) mapY(maxMassAMU) + verticalTextShift);
453-
g2d.fillText(" min = " + (new BigDecimal(minMassAMU)).setScale(3, RoundingMode.HALF_UP).toPlainString(),
453+
g2d.fillText(" min = " + (BigDecimal.valueOf(minMassAMU)).setScale(3, RoundingMode.HALF_UP).toPlainString(),
454454
(float) mapX(minX) - 150f,
455455
(float) mapY(minMassAMU) + verticalTextShift);
456456

@@ -465,7 +465,6 @@ public void paint(GraphicsContext g2d) {
465465

466466
private void showSpotLabelOnGraph(GraphicsContext g2d, int spotIndex) {
467467
if (countOfScansCumulative.length > spotIndex) {
468-
//g2d.setFont(Font.font("SansSerif", FontWeight.BOLD, 11));
469468
g2d.setFont(Font.font("SansSerif", 11));
470469
g2d.setFill(Paint.valueOf("BLUE"));
471470
Text text = new Text(prawnFileRuns.get(spotIndex).getPar().get(0).getValue());

‎squidApp/src/main/java/org/cirdles/squid/gui/squidReportTable/SquidReportTableHelperMethods.java

+19-4
Original file line numberDiff line numberDiff line change
@@ -1,32 +1,47 @@
11
package org.cirdles.squid.gui.squidReportTable;
22

3+
import java.util.HashMap;
34
import org.cirdles.squid.shrimp.ShrimpFractionExpressionInterface;
45
import org.cirdles.squid.squidReports.squidReportTables.SquidReportTable;
56
import org.cirdles.squid.squidReports.squidReportTables.SquidReportTableInterface;
67

78
import java.util.List;
9+
import java.util.Map;
810
import org.cirdles.squid.constants.Squid3Constants;
911

1012
import static org.cirdles.squid.gui.SquidUIController.squidProject;
13+
import org.cirdles.squid.tasks.Task;
1114

1215
public class SquidReportTableHelperMethods {
16+
1317
public static String[][] processReportTextArray(SquidReportTableLauncher.ReportTableTab tab, SquidReportTableInterface squidReportTable, String unknownSpot) {
1418
String[][] textArray = {};
1519

20+
Map<String, List<ShrimpFractionExpressionInterface>> reportSamplesMap = new HashMap<>();
1621
switch (tab) {
1722
case refMatCustom:
1823
if (squidReportTable == null) {
1924
squidReportTable = SquidReportTable.createDefaultSquidReportTableRefMat(squidProject.getTask());
2025
}
21-
textArray = squidReportTable.reportSpotsInCustomTable(squidReportTable, squidProject.getTask(), squidProject.getTask().getReferenceMaterialSpots());
26+
27+
reportSamplesMap.put(((Task) squidProject.getTask()).getFilterForRefMatSpotNames(), squidProject.getTask().getReferenceMaterialSpots());
28+
textArray = squidReportTable.reportSpotsInCustomTable(squidReportTable, squidProject.getTask(), reportSamplesMap, true);
2229
break;
2330
case unknownCustom:
2431
if (squidReportTable == null) {
2532
squidReportTable = SquidReportTable.createDefaultSquidReportTableUnknown(squidProject.getTask());
2633
}
27-
List<ShrimpFractionExpressionInterface> spots = squidProject.makeListOfUnknownsBySampleName();
28-
filterShrimpFractionsBySpot(spots, unknownSpot);
29-
textArray = squidReportTable.reportSpotsInCustomTable(squidReportTable, squidProject.getTask(), spots);
34+
35+
if (Squid3Constants.SpotTypes.UNKNOWN.getSpotTypeName().compareToIgnoreCase(unknownSpot) == 0) {
36+
for (Map.Entry<String, List<ShrimpFractionExpressionInterface>> entry : squidProject.getTask().getMapOfUnknownsBySampleNames().entrySet()) {
37+
if (entry.getKey().compareToIgnoreCase(Squid3Constants.SpotTypes.UNKNOWN.getSpotTypeName()) != 0) {
38+
reportSamplesMap.put(entry.getKey(), entry.getValue());
39+
}
40+
}
41+
} else {
42+
reportSamplesMap.put(unknownSpot, squidProject.getTask().getMapOfUnknownsBySampleNames().get(unknownSpot));
43+
}
44+
textArray = squidReportTable.reportSpotsInCustomTable(squidReportTable, squidProject.getTask(), reportSamplesMap, true);
3045
break;
3146

3247
default:

‎squidApp/src/main/java/org/cirdles/squid/gui/squidReportTable/TextArrayManager.java

+7-7
Original file line numberDiff line numberDiff line change
@@ -65,10 +65,10 @@ private static void initializeSelectionProperties() {
6565

6666
private static void initializeAliquots() {
6767
aliquots.clear();
68-
int i = Integer.parseInt(array[0][0]);
69-
String currentAliquot = array[i][1];
68+
int ii = Integer.parseInt(array[0][0]);
69+
String currentAliquot = array[ii][1];
7070
aliquots.add(currentAliquot);
71-
for (i = ++i; i < array.length; i++) {
71+
for (int i = ii + 1; i < array.length; i++) {
7272
if (!array[i][1].isEmpty() && !currentAliquot.equals(array[i][1])) {
7373
aliquots.add(array[i][1]);
7474
currentAliquot = array[i][1];
@@ -160,7 +160,7 @@ private static String getColumnName(int col, String[][] textArray) {
160160
}
161161

162162
if (col == textArray[0].length - 2) {
163-
retVal = "\n\n\nFractions";
163+
retVal = "\n\n\nSpot";
164164
}
165165

166166
return retVal;
@@ -171,7 +171,7 @@ private static void setTableItems() {
171171
int startSpot = Integer.parseInt(array[0][0]);
172172
String aliquot = null;
173173
for (int i = startSpot; i < array.length; i++) {
174-
if (Boolean.parseBoolean(array[i][0]) == true) {
174+
if (Boolean.parseBoolean(array[i][0])) {
175175
ObservableList<String> row = FXCollections.observableArrayList();
176176
if (controllerType == SquidReportTableLauncher.ReportTableTab.unknownCustom) {
177177
if (aliquot == null || !array[i][1].isEmpty()) {
@@ -197,8 +197,8 @@ private static void setTableItems() {
197197

198198
private static void setUpBoundCol() {
199199
boundCol.getColumns().clear();
200-
TableColumn<ObservableList<String>, String> header = new TableColumn<>("Squid");
201-
TableColumn<ObservableList<String>, String> col = new TableColumn<>("\n\n\nFractions");
200+
TableColumn<ObservableList<String>, String> header = new TableColumn<>("Squid3");
201+
TableColumn<ObservableList<String>, String> col = new TableColumn<>("\n\n\nSpot");
202202
col.setComparator(comparator);
203203
col.setPrefWidth(col.getPrefWidth() + 76);
204204
final int num = 1;

‎squidApp/src/main/java/org/cirdles/squid/gui/utilities/fileUtilities/FileHandler.java

+23-23
Original file line numberDiff line numberDiff line change
@@ -340,29 +340,29 @@ public static File selectExpressionXMLFile(Window ownerWindow)
340340
return retVal;
341341
}
342342

343-
public static File saveReportFileCSV(boolean rawOutput, String[][] report, Window ownerWindow)
344-
throws IOException {
345-
346-
File retVal = null;
347-
348-
FileChooser fileChooser = new FileChooser();
349-
fileChooser.setTitle("Save Report '.csv' file");
350-
fileChooser.setSelectedExtensionFilter(new FileChooser.ExtensionFilter("Report '.csv' files", "*.csv"));
351-
File mruFolder = new File("");//squidPersistentState.getMRUExpressionFolderPath());
352-
fileChooser.setInitialDirectory(mruFolder.isDirectory() ? mruFolder : null);
353-
fileChooser.setInitialFileName(report[0][1] + ".csv");
354-
355-
File reportFileCSV = fileChooser.showSaveDialog(ownerWindow);
356-
357-
if (reportFileCSV != null) {
358-
retVal = reportFileCSV;
359-
//squidPersistentState.updateExpressionListMRU(reportFileCSV);
360-
361-
ReportSerializerToCSV.writeCSVReport(rawOutput, reportFileCSV, report);
362-
}
363-
364-
return retVal;
365-
}
343+
//// public static File saveReportFileCSV(boolean rawOutput, String[][] report, Window ownerWindow)
344+
//// throws IOException {
345+
////
346+
//// File retVal = null;
347+
////
348+
//// FileChooser fileChooser = new FileChooser();
349+
//// fileChooser.setTitle("Save Report '.csv' file");
350+
//// fileChooser.setSelectedExtensionFilter(new FileChooser.ExtensionFilter("Report '.csv' files", "*.csv"));
351+
//// File mruFolder = new File("");//squidPersistentState.getMRUExpressionFolderPath());
352+
//// fileChooser.setInitialDirectory(mruFolder.isDirectory() ? mruFolder : null);
353+
//// fileChooser.setInitialFileName(report[0][1] + ".csv");
354+
////
355+
//// File reportFileCSV = fileChooser.showSaveDialog(ownerWindow);
356+
////
357+
//// if (reportFileCSV != null) {
358+
//// retVal = reportFileCSV;
359+
//// //squidPersistentState.updateExpressionListMRU(reportFileCSV);
360+
////
361+
//// ReportSerializerToCSV.writeCSVReport(rawOutput, reportFileCSV, report);
362+
//// }
363+
////
364+
//// return retVal;
365+
//// }
366366

367367
public static File getCustomExpressionFolder(Window ownerWindow) {
368368
File retVal;

‎squidCore/src/main/java/org/cirdles/squid/core/CalamariReportsEngine.java

+17-22
Original file line numberDiff line numberDiff line change
@@ -15,8 +15,8 @@
1515
*/
1616
package org.cirdles.squid.core;
1717

18+
import org.cirdles.squid.Squid;
1819
import org.cirdles.squid.parameters.parameterModels.ParametersModel;
19-
import org.cirdles.squid.parameters.util.DateHelper;
2020
import org.cirdles.squid.projects.SquidProject;
2121
import org.cirdles.squid.shrimp.ShrimpFraction;
2222
import org.cirdles.squid.shrimp.ShrimpFractionExpressionInterface;
@@ -41,7 +41,6 @@
4141
import static java.nio.charset.StandardCharsets.UTF_8;
4242
import static java.nio.file.StandardOpenOption.APPEND;
4343
import static java.util.Arrays.asList;
44-
import org.cirdles.squid.Squid;
4544
import static org.cirdles.squid.constants.Squid3Constants.DEFAULT_PRAWNFILE_NAME;
4645
import static org.cirdles.squid.squidReports.squidWeightedMeanReports.SquidWeightedMeanReportEngine.makeWeightedMeanReportHeaderAsCSV;
4746
import static org.cirdles.squid.utilities.conversionUtilities.RoundingUtilities.squid3RoundedToSize;
@@ -131,7 +130,7 @@ public void clearReports() {
131130
/**
132131
* ReportsEngine to test results
133132
*
134-
* @param shrimpFractions the value of shrimpFractions
133+
* @param shrimpFractions the value of shrimpFractions
135134
* @param doWriteReportFiles
136135
* @param summaryOnly
137136
* @throws java.io.IOException
@@ -145,9 +144,9 @@ public void produceReports(List<ShrimpFractionExpressionInterface> shrimpFractio
145144
}
146145
}
147146

148-
public String makeReportFolderStructure() throws IOException{
147+
public String makeReportFolderStructure() throws IOException {
149148
return folderToWriteCalamariReports.getCanonicalPath()
150-
+ File.separator + "Squid3ProjectReports-"
149+
+ File.separator + "Squid3ProjectReports-"
151150
+ squidProject.getProjectName().replaceAll("\\s", "_")
152151
+ File.separator;
153152
}
@@ -969,29 +968,27 @@ public String produceCalamariReportByFlavor(CalamariReportFlavors flavor) {
969968
break;
970969

971970
default:
972-
// throw exception
971+
// throw exception
973972
}
974973

975974
return report.toString();
976975
}
977976

978977
public File writeReportTableFiles(String[][] report, String baseReportTableName) throws IOException {
979-
String reportsPath
980-
= makeReportFolderStructure();
978+
String reportsPath = makeReportFolderStructure();
981979
File reportsFolder = new File(reportsPath);
982980
if (!reportsFolder.mkdirs()) {
983981
//throw new IOException("Failed to delete reports folder '" + reportsPath + "'");
984982
}
985983

986984
File reportTableFile = new File(reportsPath + baseReportTableName);
987-
ReportSerializerToCSV.writeCSVReport(false, reportTableFile, report);
985+
ReportSerializerToCSV.writeCSVReport(false, reportTableFile, report, true);
988986

989987
return reportTableFile;
990988
}
991989

992990
public File writeReportTableFilesPerSquid3(String[][] report, String baseReportTableName) throws IOException {
993-
String reportsPath
994-
= makeReportFolderStructure();
991+
String reportsPath = makeReportFolderStructure();
995992
File reportsFolder = new File(reportsPath);
996993
if (!reportsFolder.mkdirs()) {
997994
//throw new IOException("Failed to delete reports folder '" + reportsPath + "'");
@@ -1004,14 +1001,13 @@ public File writeReportTableFilesPerSquid3(String[][] report, String baseReportT
10041001
}
10051002

10061003
/**
1007-
*
10081004
* @throws IOException
10091005
*/
10101006
public File writeSummaryReportsForUnknowns() throws IOException {
10111007
File reportFile = getFileForSummaryCalc(
10121008
squidProject.getProjectName()
1013-
+ "_UnknownsSummaryReport"
1014-
+ ".csv");
1009+
+ "_UnknownsSummaryReport"
1010+
+ ".csv");
10151011
PrintWriter writer = new PrintWriter(reportFile, "UTF-8");
10161012
List<Expression> unknownExpressions = new ArrayList<>();
10171013
for (Expression exp : squidProject.getTask().getTaskExpressionsOrdered()) {
@@ -1028,15 +1024,14 @@ public File writeSummaryReportsForUnknowns() throws IOException {
10281024
}
10291025

10301026
/**
1031-
*
1032-
* @throws IOException
10331027
* @return the java.io.File
1028+
* @throws IOException
10341029
*/
10351030
public File writeSummaryReportsForReferenceMaterials() throws IOException {
10361031
File reportFile = getFileForSummaryCalc(
10371032
squidProject.getProjectName()
1038-
+ "_RefMatSummaryReport"
1039-
+ ".csv");
1033+
+ "_RefMatSummaryReport"
1034+
+ ".csv");
10401035
PrintWriter writer = new PrintWriter(reportFile, "UTF-8");
10411036
List<Expression> refMatExpressions = new ArrayList<>();
10421037
for (Expression exp : squidProject.getTask().getTaskExpressionsOrdered()) {
@@ -1077,9 +1072,9 @@ public File writeSummaryReportsForReferenceMaterials() throws IOException {
10771072
writer.println("name, value, one sigma ABS, one sigma PCT");
10781073
Arrays.asList(val.getValues()).forEach(valueModel -> writer.println(
10791074
valueModel.getName() + ","
1080-
+ valueModel.getValue() + ", "
1081-
+ valueModel.getOneSigmaABS().doubleValue() + ", "
1082-
+ valueModel.getOneSigmaPCT().doubleValue()));
1075+
+ valueModel.getValue() + ", "
1076+
+ valueModel.getOneSigmaABS().doubleValue() + ", "
1077+
+ valueModel.getOneSigmaPCT().doubleValue()));
10831078
});
10841079

10851080
writer.flush();
@@ -1230,7 +1225,7 @@ public void writeSquidWeightedMeanReportToFile(String weightedMeanReport, File r
12301225

12311226
/**
12321227
* @param aFolderToWriteCalamariReports the folderToWriteCalamariReports to
1233-
* set
1228+
* set
12341229
*/
12351230
public void setFolderToWriteCalamariReports(File aFolderToWriteCalamariReports) {
12361231
folderToWriteCalamariReports = aFolderToWriteCalamariReports;

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