JAL-3628 More Cache.log.debug statements

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b7d8b3a..4810a96 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -20,6 +20,54 @@
  */
 package jalview.gui;
 
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.CrossRef;
@@ -91,6 +139,7 @@ import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
@@ -100,53 +149,6 @@ import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTargetDragEvent;
-import java.awt.dnd.DropTargetDropEvent;
-import java.awt.dnd.DropTargetEvent;
-import java.awt.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusAdapter;
-import java.awt.event.FocusEvent;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseEvent;
-import java.awt.print.PageFormat;
-import java.awt.print.PrinterJob;
-import java.beans.PropertyChangeEvent;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.PrintWriter;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
-import javax.swing.JLayeredPane;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
-
 /**
  * DOCUMENT ME!
  * 
@@ -1197,39 +1199,65 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       else
       {
         // create backupfiles object and get new temp filename destination
+        Cache.log.debug("ALIGNFRAME making backupfiles object for " + file);
         BackupFiles backupfiles = new BackupFiles(file);
 
         try
         {
+          Cache.log.debug("ALIGNFRAME setting PrintWriter");
           PrintWriter out = new PrintWriter(
                   new FileWriter(backupfiles.getTempFilePath()));
 
+          Cache.log.debug("ALIGNFRAME using temp file "
+                  + backupfiles.getTempFilePath());
+
           out.print(output);
+          Cache.log.debug("ALIGNFRAME about to close file");
           out.close();
+          Cache.log.debug("ALIGNFRAME closed file");
           this.setTitle(file);
           statusBar.setText(MessageManager.formatMessage(
                   "label.successfully_saved_to_file_in_format", new Object[]
                   { fileName, format.getName() }));
+        } catch (IOException e)
+        {
+          success = false;
+          Cache.log.error(
+                  "ALIGNFRAME Something happened writing the temp file");
+          Cache.log.error(e.getMessage());
+          Cache.log.debug(e.getStackTrace());
+
         } catch (Exception ex)
         {
           success = false;
-          ex.printStackTrace();
+          Cache.log.error(
+                  "ALIGNFRAME Something else happened writing the temp file");
+          Cache.log.error(ex.getMessage());
+          Cache.log.debug(ex.getStackTrace());
         }
 
         backupfiles.setWriteSuccess(success);
+        Cache.log.debug("ALIGNFRAME writing temp file was "
+                + (success ? "" : "not ") + "successful");
         // do the backup file roll and rename the temp file to actual file
+        Cache.log.debug("ALIGNFRAME about to rollBackupsAndRenameTempFile");
         success = backupfiles.rollBackupsAndRenameTempFile();
+        Cache.log.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
+                + (success ? "" : "un") + "successfully");
 
       }
     }
 
     if (!success)
     {
-      JvOptionPane.showInternalMessageDialog(this, MessageManager
-              .formatMessage("label.couldnt_save_file", new Object[]
-              { fileName }),
-              MessageManager.getString("label.error_saving_file"),
-              JvOptionPane.WARNING_MESSAGE);
+      if (!Platform.isHeadless())
+      {
+        JvOptionPane.showInternalMessageDialog(this, MessageManager
+                .formatMessage("label.couldnt_save_file", new Object[]
+                { fileName }),
+                MessageManager.getString("label.error_saving_file"),
+                JvOptionPane.WARNING_MESSAGE);
+      }
     }
 
     return success;
@@ -2736,8 +2764,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (viewport.getViewName() == null)
     {
-      viewport.setViewName(MessageManager
-              .getString("label.view_name_original"));
+      viewport.setViewName(
+              MessageManager.getString("label.view_name_original"));
     }
 
     /*
@@ -3366,8 +3394,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      * otherwise set the chosen colour scheme (or null for 'None')
      */
     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
-            viewport,
-            viewport.getAlignment(), viewport.getHiddenRepSequences());
+            viewport, viewport.getAlignment(),
+            viewport.getHiddenRepSequences());
     changeColour(cs);
   }
 
@@ -5694,6 +5722,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   private Rectangle lastFeatureSettingsBounds = null;
+
   @Override
   public void setFeatureSettingsGeometry(Rectangle bounds)
   {

diff --git a/src/jalview/io/BackupFiles.java b/src/jalview/io/BackupFiles.java
index 1a0f72d..d52dfbf 100644 (file)
--- a/src/jalview/io/BackupFiles.java
+++ b/src/jalview/io/BackupFiles.java
@@ -131,26 +131,37 @@ public class BackupFiles
       {
         String tempfilename = file.getName();
         File tempdir = file.getParentFile();
+        Cache.log.debug(
+                "BACKUPFILES [file!=null] attempting to create temp file "
+                        + tempfilename + " in dir " + tempdir);
         temp = File.createTempFile(tempfilename,
                 TEMP_FILE_EXT + newTempFileSuffix, tempdir);
       }
       else
       {
+        Cache.log.debug(
+                "BACKUPFILES [file==null] attempting to create default temp file "
+                        + DEFAULT_TEMP_FILE + " with extension "
+                        + TEMP_FILE_EXT);
         temp = File.createTempFile(DEFAULT_TEMP_FILE, TEMP_FILE_EXT);
       }
     } catch (IOException e)
     {
-      Cache.log.error(
-              "Could not create temp file to save into (IOException)");
+      Cache.log
+              .error("Could not create temp file to save to (IOException)");
+      Cache.log.error(e.getMessage());
+      Cache.log.debug(e.getStackTrace());
     } catch (Exception e)
     {
       Cache.log.error("Exception ctreating temp file for saving");
+      Cache.log.debug(e.getStackTrace());
     }
     this.setTempFile(temp);
   }
 
   public static void classInit()
   {
+    Cache.log.debug("BACKUPFILES classInit");
     setEnabled(Cache.getDefault(ENABLED, true));
     BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
             .getSavedBackupEntry();
@@ -201,6 +212,7 @@ public class BackupFiles
       Cache.log.error(
               "IOException when getting Canonical Path of temp file '"
                       + this.getTempFile().getName() + "'");
+      Cache.log.debug(e.getStackTrace());
     }
     return path;
   }
@@ -244,22 +256,27 @@ public class BackupFiles
       return true;
     }
 
+    Cache.log.debug("BACKUPFILES rollBackupFiles starting");
+
     String dir = "";
     File dirFile;
     try
     {
       dirFile = file.getParentFile();
       dir = dirFile.getCanonicalPath();
-      Cache.log.debug("BACKUPFILES: dir: " + dir);
+      Cache.log.debug("BACKUPFILES dir: " + dir);
     } catch (Exception e)
     {
       Cache.log.error(
               "Could not get canonical path for file '" + file + "'");
+      Cache.log.error(e.getMessage());
+      Cache.log.debug(e.getStackTrace());
       return false;
     }
     String filename = file.getName();
     String basename = filename;
 
+    Cache.log.debug("BACKUPFILES filename is " + filename);
     boolean ret = true;
     // Create/move backups up one
 
@@ -276,6 +293,8 @@ public class BackupFiles
     if (backupFiles.length == 0)
     {
       // No other backup files. Just need to move existing file to backupfile_1
+      Cache.log.debug(
+              "BACKUPFILES no existing backup files, setting index to 1");
       nextIndexNum = 1;
     }
     else
@@ -288,6 +307,7 @@ public class BackupFiles
       if (reverseOrder)
       {
         // backup style numbering
+        Cache.log.debug("BACKUPFILES rolling files in reverse order");
 
         int tempMax = noMax ? -1 : max;
         // noMax == true means no limits
@@ -319,6 +339,7 @@ public class BackupFiles
             // no "oldest" file to delete
             previousFile = backupfile_n;
             fileToBeDeleted = null;
+            Cache.log.debug("BACKUPFILES No oldest file to delete");
             continue;
           }
 
@@ -329,6 +350,10 @@ public class BackupFiles
             File replacementFile = backupfile_n;
             long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
             long replacementFileLMT = replacementFile.lastModified();
+            Cache.log.debug("BACKUPFILES fileToBeDeleted is "
+                    + fileToBeDeleted.getAbsolutePath());
+            Cache.log.debug("BACKUPFILES replacementFile is "
+                    + backupfile_n.getAbsolutePath());
 
             try
             {
@@ -352,6 +377,11 @@ public class BackupFiles
 
                 boolean delete = confirmNewerDeleteFile(fileToBeDeleted,
                         replacementFile, true);
+                Cache.log.debug("BACKUPFILES "
+                        + (delete ? "confirmed" : "not") + " deleting file "
+                        + fileToBeDeleted.getAbsolutePath()
+                        + " which is newer than "
+                        + replacementFile.getAbsolutePath());
 
                 if (delete)
                 {
@@ -360,11 +390,17 @@ public class BackupFiles
                 }
                 else
                 {
+                  Cache.log.debug("BACKUPFILES moving "
+                          + fileToBeDeleted.getAbsolutePath() + " to "
+                          + oldestTempFile.getAbsolutePath());
                   moveFileToFile(fileToBeDeleted, oldestTempFile);
                 }
               }
               else
               {
+                Cache.log.debug("BACKUPFILES going to move "
+                        + fileToBeDeleted.getAbsolutePath() + " to "
+                        + oldestTempFile.getAbsolutePath());
                 moveFileToFile(fileToBeDeleted, oldestTempFile);
                 addDeleteFile(oldestTempFile);
               }
@@ -489,7 +525,7 @@ public class BackupFiles
             if (delete)
             {
               addDeleteFile(fileToBeDeleted);
-              Cache.log.debug("BACKUPFILES addDeleteFile(fileToBeDelted): "
+              Cache.log.debug("BACKUPFILES addDeleteFile(fileToBeDeleted): "
                       + fileToBeDeleted);
             }
 
@@ -828,10 +864,15 @@ public class BackupFiles
     int pos = deleteFiles.indexOf(fileToBeDeleted);
     if (pos > -1)
     {
+      Cache.log.debug("BACKUPFILES not adding file "
+              + fileToBeDeleted.getAbsolutePath()
+              + " to the delete list (already at index" + pos + ")");
       return true;
     }
     else
     {
+      Cache.log.debug("BACKUPFILES adding file "
+              + fileToBeDeleted.getAbsolutePath() + " to the delete list");
       deleteFiles.add(fileToBeDeleted);
     }
     return ret;
@@ -845,19 +886,24 @@ public class BackupFiles
     try
     {
       // delete destination file - not usually necessary but Just In Case...
+      Cache.log.debug("BACKUPFILES deleting " + newFile.getAbsolutePath());
       newFile.delete();
+      Cache.log.debug("BACKUPFILES moving " + oldFile.getAbsolutePath()
+              + " to " + newFile.getAbsolutePath());
       Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING);
       ret = true;
+      Cache.log.debug("BACKUPFILES move seemse to have succeeded");
     } catch (IOException e)
     {
       Cache.log.warn("Could not move file '" + oldPath.toString() + "' to '"
               + newPath.toString() + "'");
-      Cache.log.error(e.getStackTrace());
+      Cache.log.error(e.getMessage());
+      Cache.log.debug(e.getStackTrace());
       ret = false;
     } catch (Exception e)
     {
       Cache.log.error(e.getMessage());
-      Cache.log.error(e.getStackTrace());
+      Cache.log.debug(e.getStackTrace());
       ret = false;
     }
     return ret;