Improve MGF title parse and error output.

fcyu · Aug 21, 2017 · 145eb70 · 145eb70
1 parent 433b183
commit 145eb70
Showing 1 changed file with 13 additions and 5 deletions.
diff --git a/src/main/java/proteomics/Spectrum/PreSpectra.java b/src/main/java/proteomics/Spectrum/PreSpectra.java
@@ -20,7 +20,9 @@ public class PreSpectra {
 
     private static final Logger logger = LoggerFactory.getLogger(PreSpectra.class);
     private static final Pattern pattern = Pattern.compile("^[0-9]+$");
-    private static final Pattern scanNumPattern = Pattern.compile("Scan:([0-9]+) ");
+    private static final Pattern scanNumPattern1 = Pattern.compile("Scan:([0-9]+) ", Pattern.CASE_INSENSITIVE);
+    private static final Pattern scanNumPattern2 = Pattern.compile("scan=([0-9]+)", Pattern.CASE_INSENSITIVE);
+    private static final Pattern scanNumPattern3 = Pattern.compile("^[^.]+\\.([0-9]+)\\.[0-9]+\\.[0-9]");
 
     private Map<Integer, SpectrumEntry> num_spectrum_map = new HashMap<>();
     private Set<Integer> debug_scan_num_set = new HashSet<>();
@@ -111,11 +113,17 @@ public void write(int b) throws IOException {}
                 try {
                     if (ext.toLowerCase().contentEquals("mgf")) {
                         mgfTitle = ((Ms2Query) spectrum).getTitle();
-                        Matcher matcher = scanNumPattern.matcher(mgfTitle);
-                        if (matcher.find()) {
-                            scan_num = Integer.valueOf(matcher.group(1));
+                        Matcher matcher1 = scanNumPattern1.matcher(mgfTitle);
+                        Matcher matcher2 = scanNumPattern2.matcher(mgfTitle);
+                        Matcher matcher3 = scanNumPattern3.matcher(mgfTitle);
+                        if (matcher1.find()) {
+                            scan_num = Integer.valueOf(matcher1.group(1));
+                        } else if (matcher2.find()) {
+                            scan_num = Integer.valueOf(matcher2.group(1));
+                        } else if (matcher3.find()) {
+                            scan_num = Integer.valueOf(matcher3.group(1));
                         } else {
-                            logger.error("Cannot get scan number from the MGF file. PIPI only support the MGF files converted from ReAdw4Mascot4.");
+                            logger.error("Cannot get scan number from the MGF title {}. Please report your MGF title to the author.", mgfTitle);
                             System.exit(1);
                         }
                     } else {