Fix columns selection bug

pom.xml

@@ -5,7 +5,7 @@
     <groupId>PDV</groupId>
     <artifactId>PDV</artifactId>
     <packaging>jar</packaging>
-    <version>1.7.0</version>
+    <version>1.7.1</version>
     <name>PDV</name>
     <url>https://github.com/wenbostar/PDV</url>
     <description>An integrative proteomics viewer</description>

src/main/java/PDVGUI/fileimport/FragePipeImport.java

@@ -27,6 +27,7 @@
 import java.sql.PreparedStatement;
 import java.sql.SQLException;
 import java.sql.Statement;
+import java.text.DecimalFormat;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -92,6 +93,10 @@ public class FragePipeImport {
      * Progress dialog
      */
     private ProgressDialogX progressDialog;
+    /**
+     * Decimal
+     */
+    DecimalFormat df = new DecimalFormat("####0.000");
 
     /**
      * Main constructor
@@ -271,7 +276,7 @@ private void parseResultMzML() throws IOException, SQLException {
                     peptideSequence = lineSplit[peptideSequenceIndex];
                     caculatedMZ = Double.valueOf(lineSplit[caculatedMZIndex]);
                     observedMZ = Double.valueOf(lineSplit[observedMZIndex]);
-                    massError = caculatedMZ - observedMZ;
+                    massError = Double.valueOf(df.format(observedMZ - caculatedMZ));
                     assignedMod = lineSplit[assignenModIndex];
 
                     if (count == 0){
@@ -499,7 +504,7 @@ private void parseResultMGF() throws IOException, SQLException, ClassNotFoundExc
             peptideSequence = lineSplit[peptideSequenceIndex];
             caculatedMZ = Double.valueOf(lineSplit[caculatedMZIndex]);
             observedMZ = Double.valueOf(lineSplit[observedMZIndex]);
-            massError = caculatedMZ - observedMZ;
+            massError = observedMZ - caculatedMZ;
             assignedMod = lineSplit[assignenModIndex];
 
             if (count == 0){

src/main/java/PDVGUI/fileimport/MzIDFileImport.java

@@ -301,8 +301,9 @@ private void parseMzID() throws SQLException, IOException {
         }
 
         ArrayList<String> fileInFactory = spectrumFactory.getMgfFileNames();
+        String spectrumFileNotInMzID = "";
 
-        Integer matchFileNum = 0;
+        int matchFileNum = 0;
 
         for(String id: spectrumFileMap.keySet()){
 
@@ -312,18 +313,27 @@ private void parseMzID() throws SQLException, IOException {
                     matchFileNum++;
                 }
 
-             } else if (spectrumFileType.equals("mzml") || spectrumFileType.equals("mzxml")){
+            } else if (spectrumFileType.equals("mzml") || spectrumFileType.equals("mzxml")){
                 matchFileNum++;
             }
         }
 
         if (matchFileNum == 0){
             System.out.println("No matching file");
-            JOptionPane.showMessageDialog(
-                    null, "The spectrum file cannot match it in mzIdentML",
-                    "Error Matching", JOptionPane.ERROR_MESSAGE);
-            Thread.currentThread().interrupt();
-            progressDialog.setRunFinished();
+            spectrumFileNotInMzID = spectrumFactory.getMgfFileNames().get(0); //No Match mgf in MzID. Select first input mgf of user input
+
+            int value = JOptionPane.showConfirmDialog(
+                    null, "The spectrum file cannot match it in mzIdentML. Do you want to continue?",
+                    "Error Matching",
+                    JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+            if (value == JOptionPane.YES_OPTION) {
+                //Nothing
+            } else if (value == JOptionPane.NO_OPTION) {
+                Thread.currentThread().interrupt();
+                progressDialog.setRunFinished();
+            }
+
         }
 
         int count = 0;
@@ -426,6 +436,10 @@ private void parseMzID() throws SQLException, IOException {
                     currentSpectrumFile = currentSpectrumFile.substring(currentSpectrumFile.lastIndexOf("/") + 1, currentSpectrumFile.length());
                 }
 
+                if (matchFileNum == 0){
+                    currentSpectrumFile = spectrumFileNotInMzID;
+                }
+
                 currentMatch = new SpectrumMatch(Spectrum.getSpectrumKey(currentSpectrumFile, spectrumIndex));
 
                 if (spectrumFileType.equals("mgf")) {

src/main/java/PDVGUI/gui/PDVMainClass.java

@@ -258,7 +258,7 @@ public class PDVMainClass extends JFrame {
     /**
      * Version
      */
-    private static final String VERSION = "1.7.0";
+    private static final String VERSION = "1.7.1";
 
     /**
      * Main class
@@ -3319,6 +3319,13 @@ private void columnSelectionJMenuItemActionPerformed(ActionEvent evt){
         }
         columnName.addAll(scoreName);
 
+        if(columnToSelected == null){
+            columnToSelected = new HashMap<>();
+            for (String eachColumn: columnName){
+                columnToSelected.put(eachColumn, true);
+            }
+        }
+
         new ColumnSelectionDialog(this, spectrumJTable, columnName);
     }
 

src/main/java/PDVGUI/gui/utils/SpectrumMainPanel.java

@@ -544,8 +544,8 @@ private void initComponents(){
         reporterIonsCheckMenuItem.addActionListener(this::reporterIonsCheckMenuItemAction);
         otherMenu.add(reporterIonsCheckMenuItem);
 
-        //glyconsCheckMenuItem.setSelected(true);
-        glyconsCheckMenuItem.setEnabled(false);
+        glyconsCheckMenuItem.setEnabled(true); // Just test for YC. This should be false.
+        //glyconsCheckMenuItem.setEnabled(false);
         glyconsCheckMenuItem.setText("Glycan");
         glyconsCheckMenuItem.setFont(menuFont);
         glyconsCheckMenuItem.addActionListener(this::glyconsCheckMenuItemAction);
@@ -1481,6 +1481,9 @@ public void updateSpectrum(){
                             }
                         }
 
+                        // Just for FC test. This should be deleted.
+                        glycanContain = true;
+                        /* Just for FC test. This should be enabled.
                         if (glycanProb >= 1){
                             glycanContain = true;
                             glyconsCheckMenuItem.setSelected(glycanSelected);
@@ -1489,7 +1492,7 @@ public void updateSpectrum(){
                             glycanContain = false;
                             glyconsCheckMenuItem.setSelected(false);
                             glyconsCheckMenuItem.setEnabled(false);
-                        }
+                        }*/
 
                         updateAnnotationSettings();
                         annotations = peptideSpectrumAnnotator.getSpectrumAnnotationFiter(annotationSettings, specificAnnotationSettings, currentSpectrum, currentPeptide, null, true);
@@ -2340,9 +2343,10 @@ private void updateAnnotationSettings() {
                 }
             }
 
+            /* Just test for FC. This should be enabled.
             if (glycanSelected & glycanContain){
                 glyconsCheckMenuItem.setSelected(true);
-            }
+            }*/
 
             if (glyconsCheckMenuItem.isSelected()){
                 glycanSelected = true;

src/main/java/PDVGUI/gui/utils/TableModel/FrageTableModel.java

@@ -103,7 +103,7 @@ public String getColumnName(int column) {
         }else if(column == 7){
             return "m/z";
         }else if(column == 8){
-            return "Mass error";
+            return "m/z error";
         }
         for(int index = 0; index < scoreName.size(); index++){
             int newColumn = index + 9;
@@ -195,7 +195,7 @@ public Object getValueAt(int row, int column) {
                     if(peptideAssumption.getScore() != null){
                         return peptideAssumption.getScore();
                     } else {
-                        return 0.0;
+                        return "-";
                     }
                 }
                 for(int index = 0; index < scoreName.size(); index++){