Make SAINTexpress support upper and lower case "control".

fcyu · fcyu · commit a27674f01058 · 2023-01-12T20:55:29.000-05:00
diff --git a/MSFragger-GUI/src/com/dmtavt/fragpipe/cmd/CmdSaintExpress.java b/MSFragger-GUI/src/com/dmtavt/fragpipe/cmd/CmdSaintExpress.java
@@ -116,10 +116,10 @@ public static void reprintTsvToSaintInput(final Path inputPath, final Path outPa
       final String[] second_row = br.readLine().split("\t");
       for (int i = 0; i < IP.length; i++) {
         final String s = second_row[i + column_offset];
-        bait_names[i] = s.equals("CONTROL") ? IP[i] : s;
+        bait_names[i] = s.equalsIgnoreCase("CONTROL") ? IP[i] : s;
       }
       for (int i = 0; i < IP.length; ++i) {
-        bait_dat.add(IP[i] + "\t" + bait_names[i] + "\t" + (bait_names[i].startsWith("CONTROL") ? "C" : "T"));
+        bait_dat.add(IP[i] + "\t" + bait_names[i] + "\t" + (bait_names[i].toUpperCase().startsWith("CONTROL") ? "C" : "T"));
       }
       String line;
       while ((line = br.readLine()) != null) {

Original file line number	Diff line number	Diff line change
`@@ -116,10 +116,10 @@ public static void reprintTsvToSaintInput(final Path inputPath, final Path outPa`
`116`	`116`	`final String[] second_row = br.readLine().split("\t");`
`117`	`117`	`for (int i = 0; i < IP.length; i++) {`
`118`	`118`	`final String s = second_row[i + column_offset];`
`119`		`- bait_names[i] = s.equals("CONTROL") ? IP[i] : s;`
	`119`	`+ bait_names[i] = s.equalsIgnoreCase("CONTROL") ? IP[i] : s;`
`120`	`120`	`}`
`121`	`121`	`for (int i = 0; i < IP.length; ++i) {`
`122`		`- bait_dat.add(IP[i] + "\t" + bait_names[i] + "\t" + (bait_names[i].startsWith("CONTROL") ? "C" : "T"));`
	`122`	`+ bait_dat.add(IP[i] + "\t" + bait_names[i] + "\t" + (bait_names[i].toUpperCase().startsWith("CONTROL") ? "C" : "T"));`
`123`	`123`	`}`
`124`	`124`	`String line;`
`125`	`125`	`while ((line = br.readLine()) != null) {`