Update to 1.1.7; Fix razor protein mapping bug

Fix razor protein mapping bug
Nesvilab · Feb 6, 2024 · b2c1d72 · b2c1d72
1 parent b6af509
commit b2c1d72
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Showing 3 changed files with 21 additions and 4 deletions.
diff --git a/pom.xml b/pom.xml
@@ -7,7 +7,7 @@
     <packaging>jar</packaging>
     <groupId>org.example</groupId>
     <artifactId>FP-PDV</artifactId>
-    <version>1.1.5</version>
+    <version>1.1.7</version>
 
     <properties>
         <maven.compiler.source>8</maven.compiler.source>

diff --git a/src/main/java/GUI/GUIMainClass.java b/src/main/java/GUI/GUIMainClass.java
@@ -3768,7 +3768,7 @@ public void run() {
     private void updateSpectrumFactoryFirst(ProgressDialogX progressDialog, String firstTitle) {
         String spectrumFileName = firstTitle.split("\\.")[0];
         String spectralFilePath = spectrumFileMap.get(spectrumFileName);
-
+        System.out.println(spectrumFileMap);
         try {
             if (Files.exists(new File(spectralFilePath).toPath())) {
                 readSpectrumFile(spectralFilePath);
@@ -3808,8 +3808,10 @@ private void readSpectrumFile(String spectralFilePath) throws IOException, Class
             } else if (spectralFilePath.endsWith(".d")){
                 if (new File(spectralFilePath.replace(".d", "_uncalibrated.mzml")).exists()){
                     addOneMzML(spectrumName, spectralFilePath.replace(".d", "_uncalibrated.mzml"));
-                } else {
+                } else if (new File(spectralFilePath.replace(".d", "_calibrated.mzml")).exists()){
                     addOneMzML(spectrumName, spectralFilePath.replace(".d", "_calibrated.mzml"));
+                } else {
+                    addOneMzML(spectrumName + "_centric", spectralFilePath.replace(".d", "_centric.mzML"));
                 }
 
             } else if (spectralFilePath.toLowerCase().endsWith("mzml")){
@@ -3822,6 +3824,8 @@ private void readSpectrumFile(String spectralFilePath) throws IOException, Class
     }
 
     private void addOneMzML(String spectrumName, String spectralFilePath){
+        System.out.println(spectrumName);
+        System.out.println("Reading " + spectralFilePath);
         MZMLFile mzmlFile = new MZMLFile(spectralFilePath);
         mzmlFile.setNumThreadsForParsing(threadsNumber);
         ScanCollectionDefault scans = new ScanCollectionDefault();
@@ -3878,9 +3882,16 @@ public void displayResults(ProgressDialogX progressDialog) throws SQLException {
         updateAllProteinIndexes(sqliteConnection.getProteinList(expAllSelections));
 
         String initProtein = allProteinIndex.get(selectedProteinPageNum - 1).get(0);
+        if (sqliteConnection.getSpectrumListOneProtein(initProtein)[0].size() == 0){
+            for (String newProtein : allProteinIndex.get(selectedProteinPageNum - 1)){
+                if (sqliteConnection.getSpectrumListOneProtein(newProtein)[0].size() != 0){
+                    initProtein = newProtein;
+                    break;
+                }
+            }
+        }
 
         updateSpectrumFactoryFirst(progressDialog, sqliteConnection.getSpectrumOldTitle(sqliteConnection.getSpectrumListOneProtein(initProtein)[0].get(0)));
-        //System.out.println(initProtein);
         updateAllPSMIndexes(sqliteConnection.getSpectrumListOneProtein(initProtein));
         proteinCurrentSelections.add(initProtein);
 

diff --git a/src/main/java/GUI/utils/ImportData.java b/src/main/java/GUI/utils/ImportData.java
@@ -358,6 +358,9 @@ private void processManifestFile(File mainFestFile) throws IOException {
                                 }
                             }
                         }
+                    }else {
+                        String[] fileArr = lineSplit[0].split(pattern);
+                        spectrumFileMap.put(fileArr[fileArr.length-1].split("\\.d")[0]+"_centric", lineSplit[0]);
                     }
                 }
 
@@ -384,6 +387,9 @@ private void processManifestFile(File mainFestFile) throws IOException {
                                 }
                             }
                         }
+                    }else {
+                        String[] fileArr = lineSplit[0].split(pattern);
+                        spectrumFileMap.put(fileArr[fileArr.length-1].split("\\.d")[0]+"_centric", lineSplit[0]);
                     }
                 }
             }