JAL-4285 Better checkFiles processing. Better dialog.

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index d1e4536..70eeb95 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1467,4 +1467,4 @@ label.all_known_alignment_files = All known alignment files
 label.command_line_arguments = Command Line Arguments
 warning.using_old_command_line_arguments = It looks like you are using old command line arguments.  These are now deprecated and will be removed in a future release of Jalview.\nFind out about the new command line arguments at\n
 warning.using_mixed_command_line_arguments = Jalview cannot use both old (-arg) and new (--arg) command line arguments.  Please check your command line arguments.\ne.g. {0} and {1}
-warning.the_following_errors = The following errors and warnings occurred whilst processing files.
+warning.the_following_errors = The following errors and warnings occurred whilst processing files:

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index 999c8cd..a0b9292 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -1441,5 +1441,4 @@ label.all_known_alignment_files = Todos los archivos de alineaci
 label.command_line_arguments = Argumentos de línea de comando
 warning.using_old_command_line_arguments = Parece que estás utilizando argumentos antiguos de línea de comando. Estos ahora están en desuso y se eliminarán en una versión futura de Jalview.\nObtenga más información sobre los nuevos argumentos de la línea de comando en\n
 warning.using_mixed_command_line_arguments = Jalview no puede utilizar argumentos de línea de comando antiguos (-arg) y nuevos (--arg). Verifique los argumentos de su línea de comando.\ne.g. {0} y {1}
-warning.the_following_errors = Se produjeron los siguientes errores y advertencias al procesar archivos.
-
+warning.the_following_errors = Se produjeron los siguientes errores y advertencias al procesar archivos:

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 8312b29..ba72831 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -143,8 +143,9 @@ public class Commands
     }
 
     // report errors
-    Console.debug("All errors from command line argument commands:\n"
-            + errorsToString());
+    Console.warn(
+            "The following errors and warnings occurred whilst processing files:\n"
+                    + errorsToString());
     // gui errors reported in Jalview
 
     if (argParser.getBoolean(Arg.QUIT))
@@ -178,7 +179,7 @@ public class Commands
       return true;
     }
 
-    boolean isError = false;
+    Boolean isError = Boolean.valueOf(false);
 
     // set wrap scope here so it can be applied after structures are opened
     boolean wrap = false;
@@ -692,14 +693,10 @@ public class Commands
                 AppJmol jmol = (AppJmol) sview;
                 try
                 {
-                  whatNext wn = this.checksBeforeWritingToFile(avm, subVals,
-                          false, structureImageFilename, "structure image");
-                  if (wn == whatNext.ERROR)
-                  {
-                    isError = true;
-                    continue;
-                  }
-                  else if (wn == whatNext.CONTINUE)
+                  boolean success = this.checksBeforeWritingToFile(avm,
+                          subVals, false, structureImageFilename,
+                          "structure image", isError);
+                  if (!success)
                   {
                     continue;
                   }
@@ -794,7 +791,7 @@ public class Commands
       return false;
     }
 
-    boolean isError = false;
+    Boolean isError = Boolean.valueOf(false);
     if (avm.containsArg(Arg.IMAGE))
     {
       for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
@@ -836,14 +833,9 @@ public class Commands
 
         Console.info("Writing " + file);
 
-        whatNext wn = this.checksBeforeWritingToFile(avm, subVal, false,
-                fileName, "image");
-        if (wn == whatNext.ERROR)
-        {
-          isError = true;
-          continue;
-        }
-        else if (wn == whatNext.CONTINUE)
+        boolean success = checksBeforeWritingToFile(avm, subVal, false,
+                fileName, "image", isError);
+        if (!success)
         {
           continue;
         }
@@ -921,7 +913,7 @@ public class Commands
       return false;
     }
 
-    boolean isError = false;
+    Boolean isError = Boolean.valueOf(false);
 
     if (avm.containsArg(Arg.OUTPUT))
     {
@@ -988,14 +980,9 @@ public class Commands
           }
         }
 
-        whatNext wn = this.checksBeforeWritingToFile(avm, subVals, true,
-                fileName, ff.getName());
-        if (wn == whatNext.ERROR)
-        {
-          isError = true;
-          continue;
-        }
-        else if (wn == whatNext.CONTINUE)
+        boolean success = checksBeforeWritingToFile(avm, subVals, true,
+                fileName, ff.getName(), isError);
+        if (!success)
         {
           continue;
         }
@@ -1113,14 +1100,9 @@ public class Commands
     errors.add(errorMessage);
   }
 
-  private enum whatNext
-  {
-    OKAY, CONTINUE, ERROR;
-  }
-
-  private whatNext checksBeforeWritingToFile(ArgValuesMap avm,
+  private boolean checksBeforeWritingToFile(ArgValuesMap avm,
           SubVals subVal, boolean includeBackups, String filename,
-          String adjective)
+          String adjective, Boolean isError)
   {
     File file = new File(filename);
 
@@ -1145,7 +1127,7 @@ public class Commands
               + Arg.OVERWRITE.argString()
               + (includeBackups ? " or " + Arg.BACKUPS.argString() : "")
               + " set");
-      return whatNext.CONTINUE;
+      return false;
     }
 
     boolean mkdirs = ArgParser.getFromSubValArgOrPref(avm, Arg.MKDIRS,
@@ -1158,10 +1140,11 @@ public class Commands
               + "' does not exist for " + adjective + " file '" + filename
               + "'."
               + (mkdirs ? "" : "  Try using " + Arg.MKDIRS.argString()));
-      return whatNext.ERROR;
+      isError = true;
+      return false;
     }
 
-    return whatNext.OKAY;
+    return true;
   }
 
   public List<String> getErrors()
@@ -1174,8 +1157,9 @@ public class Commands
     StringBuilder sb = new StringBuilder();
     for (String error : errors)
     {
+      if (sb.length() > 0)
+        sb.append("\n");
       sb.append("- " + error);
-      sb.append("\n");
     }
     return sb.toString();
   }

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index dbc1d88..2c07296 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -2060,13 +2060,13 @@ public class Jalview
     if (oldStyle)
     {
       String warning = MessageManager
-              .getString("warning.using_old_command_line_arguments")
-              + "https://www.jalview.org/help/html/features/commandline.html";
+              .getString("warning.using_old_command_line_arguments");
+      String url = "https://www.jalview.org/help/html/features/commandline.html";
       if (Desktop.instance != null)
       {
         String cont = MessageManager.getString("label.continue");
 
-        Desktop.instance.nonBlockingDialog(32, 2, title, warning, cont,
+        Desktop.instance.nonBlockingDialog(32, 2, title, warning, url, cont,
                 JvOptionPane.WARNING_MESSAGE, false, false);
       }
     }
@@ -2077,8 +2077,16 @@ public class Jalview
         String message = MessageManager
                 .getString("warning.the_following_errors");
         String ok = MessageManager.getString("action.ok");
-        Desktop.instance.nonBlockingDialog(60, 16, title,
-                message + "\n" + j.getCommands().errorsToString(), ok,
+        int shortest = 60;
+        List<String> errors = j.getCommands().getErrors();
+        for (int i = 0; i < errors.size(); i++)
+        {
+          shortest = Math.min(shortest, errors.get(i).length());
+        }
+        Desktop.instance.nonBlockingDialog(
+                Math.max(message.length(), Math.min(60, shortest)),
+                Math.min(errors.size(), 20), title, message,
+                j.getCommands().errorsToString(), ok,
                 JvOptionPane.WARNING_MESSAGE, true, true);
       }
     }

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index f0753bc..ee24c25 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
+import java.awt.Component;
 import java.awt.Dimension;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
@@ -3744,24 +3745,26 @@ public class Desktop extends jalview.jbgui.GDesktop
   public void nonBlockingDialog(String title, String message, String button,
           int type, boolean scrollable, boolean modal)
   {
-    nonBlockingDialog(32, 2, title, message, button, type, scrollable,
+    nonBlockingDialog(32, 2, title, message, null, button, type, scrollable,
             modal);
   }
 
   public void nonBlockingDialog(int width, int height, String title,
-          String message, String button, int type, boolean scrollable,
-          boolean modal)
+          String message, String boxtext, String button, int type,
+          boolean scrollable, boolean modal)
   {
     if (type < 0)
     {
       type = JvOptionPane.WARNING_MESSAGE;
     }
+    JLabel jl = new JLabel(message);
+
     JTextArea jta = new JTextArea(height, width);
     // jta.setLineWrap(true);
     jta.setEditable(false);
     jta.setWrapStyleWord(true);
     jta.setAutoscrolls(true);
-    jta.setText(message);
+    jta.setText(boxtext);
 
     JScrollPane jsp = scrollable
             ? new JScrollPane(jta, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
@@ -3769,10 +3772,33 @@ public class Desktop extends jalview.jbgui.GDesktop
             : null;
 
     JvOptionPane jvp = JvOptionPane.newOptionDialog(this);
+
+    JPanel jp = new JPanel();
+    jp.setLayout(new BoxLayout(jp, BoxLayout.Y_AXIS));
+
+    if (message != null)
+    {
+      jl.setAlignmentX(Component.LEFT_ALIGNMENT);
+      jp.add(jl);
+    }
+    if (boxtext != null)
+    {
+      if (scrollable)
+      {
+        jsp.setAlignmentX(Component.LEFT_ALIGNMENT);
+        jp.add(jsp);
+      }
+      else
+      {
+        jta.setAlignmentX(Component.LEFT_ALIGNMENT);
+        jp.add(jta);
+      }
+    }
+
     jvp.setResponseHandler(JOptionPane.YES_OPTION, () -> {
     });
-    jvp.showDialogOnTopAsync(this, scrollable ? jsp : jta, title,
-            JOptionPane.YES_OPTION, type, null, new Object[]
+    jvp.showDialogOnTopAsync(this, jp, title, JOptionPane.YES_OPTION, type,
+            null, new Object[]
             { button }, button, modal, null, false);
   }