Replace some string literals with global variables.

Author: fcyu

MSFragger-GUI/src/com/dmtavt/fragpipe/FragpipeRun.java

@@ -19,6 +19,8 @@
 
 import static com.dmtavt.fragpipe.messages.MessagePrintToConsole.toConsole;
 import static com.dmtavt.fragpipe.tabs.TabDatabase.databaseSizeLimit;
+import static com.dmtavt.fragpipe.tabs.TabWorkflow.manifestExt;
+import static com.dmtavt.fragpipe.tabs.TabWorkflow.workflowExt;
 import static com.github.chhh.utils.FileDelete.deleteFileOrFolder;
 
 import com.dmtavt.fragpipe.api.Bus;
@@ -508,7 +510,7 @@ public static int run(MessageRun m) {
         saveRuntimeConfig(wd);
 
         // save manifest file in both GUI and headless mode
-        Path path = wd.resolve("fragpipe-files.fp-manifest");
+        Path path = wd.resolve("fragpipe-files" + manifestExt);
         Bus.post(new MessageManifestSave(path, true));
 
         if (tabRun.isWriteSubMzml()) { // write sub workflow and manifest files for the second-pass
@@ -557,8 +559,8 @@ public static int run(MessageRun m) {
               newPrecursorTrueTolerance = Float.parseFloat(matcher.group(1));
             }
 
-            Path workflowFilePath = wd.resolve("fragpipe.workflow");
-            Path workflowFileSecondPassPath = wd.resolve("fragpipe-second-pass.workflow");
+            Path workflowFilePath = wd.resolve("fragpipe" + workflowExt);
+            Path workflowFileSecondPassPath = wd.resolve("fragpipe-second-pass" + workflowExt);
             if (Files.exists(workflowFilePath) && Files.isRegularFile(workflowFilePath) && Files.isReadable(workflowFilePath)) {
               BufferedReader reader = Files.newBufferedReader(workflowFilePath);
               BufferedWriter writer = Files.newBufferedWriter(workflowFileSecondPassPath);
@@ -600,8 +602,8 @@ public static int run(MessageRun m) {
               reader.close();
             }
 
-            Path manifestFilePath = wd.resolve("fragpipe-files.fp-manifest");
-            Path manifestFileSecondPassPath = wd.resolve("fragpipe-files-second-pass.fp-manifest");
+            Path manifestFilePath = wd.resolve("fragpipe-files" + manifestExt);
+            Path manifestFileSecondPassPath = wd.resolve("fragpipe-files-second-pass" + manifestExt);
             if (Files.exists(manifestFilePath) && Files.isRegularFile(manifestFilePath) && Files.isReadable(manifestFilePath)) {
               BufferedReader reader = Files.newBufferedReader(manifestFilePath);
               BufferedWriter writer = Files.newBufferedWriter(manifestFileSecondPassPath);
@@ -743,7 +745,7 @@ private static void printReference(TextConsole console) {
 
 
   public static void saveRuntimeConfig(Path wd) {
-    Path path = wd.resolve("fragpipe.workflow");
+    Path path = wd.resolve("fragpipe" + workflowExt);
     Bus.post(new MessageSaveUiState(path));
   }
 

MSFragger-GUI/src/com/dmtavt/fragpipe/cmd/ProcessBuilderInfo.java

@@ -18,6 +18,7 @@
 package com.dmtavt.fragpipe.cmd;
 
 import static com.dmtavt.fragpipe.messages.MessagePrintToConsole.toConsole;
+import static com.dmtavt.fragpipe.tabs.TabWorkflow.manifestExt;
 
 import com.dmtavt.fragpipe.Fragpipe;
 import com.dmtavt.fragpipe.FragpipeRun;
@@ -138,7 +139,7 @@ public static Runnable toRunnable(final ProcessBuilderInfo pbi, final Path wdPat
 
               if (!isDownstream) {
                 // save manifest file in both GUI and headless mode
-                Path path = wdPath.resolve("fragpipe-files.fp-manifest");
+                Path path = wdPath.resolve("fragpipe-files" + manifestExt);
                 Bus.post(new MessageManifestSave(path, true));
               }
 

MSFragger-GUI/src/com/dmtavt/fragpipe/tabs/TabWorkflow.java

@@ -152,7 +152,8 @@ public class TabWorkflow extends JPanelWithEnablement {
   private JButton btnFilesRemove;
   private JButton btnFilesClear;
   public static final String TAB_PREFIX = "workflow.";
-  private static final String manifestExt = ".fp-manifest";
+  public static final String manifestExt = ".fp-manifest";
+  public static final String workflowExt = ".workflow";
   public static final int maxProcessors = 128;
 
   private SimpleETable tableRawFiles;
@@ -807,8 +808,8 @@ public void on(MessageSaveAsWorkflow m) throws IOException {
     Fragpipe fp0 = Fragpipe.getStickyStrict(Fragpipe.class);
     final javax.swing.JFrame fp = fp0.toJFrame();
     Properties uiProps = FragpipeCacheUtils.tabsSave0(fp0.tabs, m.saveWithFieldTypes);
-    String workflowExt = ".workflow";
-    FileNameEndingFilter workflowEndingFilter = new FileNameEndingFilter("workflow files", ".workflow");
+
+    FileNameEndingFilter workflowEndingFilter = new FileNameEndingFilter("workflow files", workflowExt);
 
     Path saveDir;
     Path savePath = null;
@@ -861,7 +862,7 @@ public void on(MessageSaveAsWorkflow m) throws IOException {
         SwingUtils.showErrorDialog(fp, "Workflow name can't be left empty", "Error saving workflow");
         return;
       }
-      final String fn = StringUtils.appendOnce(text, ".workflow");
+      final String fn = StringUtils.appendOnce(text, workflowExt);
       if (saveDir.equals(fpWorkflowsDir) && defaultWorkflows.stream().anyMatch(path -> path.getFileName().toString().equalsIgnoreCase(fn))) {
         SwingUtils.showInfoDialog(this,
             "Name can't be the same as one of default ones",