Merge branch 'feature/JAL-244_Automatically_adjust_left_margin_to_avoid_cropping_anno...

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3e24e67..217175e 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -49,6 +49,7 @@ import java.beans.PropertyChangeEvent;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.net.URL;
 import java.util.ArrayList;
@@ -623,12 +624,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         // if (viewport.cursorMode)
         // {
         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
-        // //System.out.println("A");
+        // //jalview.bin.Console.outPrintln("A");
         // }
         // break;
         /*
          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
-         * System.out.println("closing bracket"); } break;
+         * jalview.bin.Console.outPrintln("closing bracket"); } break;
          */
         case KeyEvent.VK_DELETE:
         case KeyEvent.VK_BACK_SPACE:
@@ -829,7 +830,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               @Override
               public void propertyChange(PropertyChangeEvent evt)
               {
-                // // System.out.println("Discoverer property change.");
+                // // jalview.bin.Console.outPrintln("Discoverer property
+                // change.");
                 // if (evt.getPropertyName().equals("services"))
                 {
                   SwingUtilities.invokeLater(new Runnable()
@@ -838,7 +840,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     @Override
                     public void run()
                     {
-                      System.err.println(
+                      jalview.bin.Console.errPrintln(
                               "Rebuild WS Menu for service change");
                       BuildWebServiceMenu();
                     }
@@ -853,7 +855,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
-        // System.out.println("deregistering discoverer listener");
+        // jalview.bin.Console.outPrintln("deregistering discoverer listener");
         Desktop.instance.removeJalviewPropertyChangeListener("services",
                 thisListener);
         closeMenuItem_actionPerformed(true);
@@ -1250,8 +1252,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public void saveAlignment(String file, FileFormatI format)
   {
+    saveAlignment(file, format, false);
+  }
+
+  public void saveAlignment(String file, FileFormatI format, boolean stdout)
+  {
     lastSaveSuccessful = true;
-    lastFilenameSaved = file;
+    if (!stdout)
+    {
+      lastFilenameSaved = file;
+    }
     lastFormatSaved = format;
 
     if (FileFormat.Jalview.equals(format))
@@ -1262,6 +1272,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         shortName = shortName
                 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
       }
+      // TODO deal with stdout=true
       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
               shortName);
 
@@ -1297,7 +1308,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       else
       {
         // create backupfiles object and get new temp filename destination
-        boolean doBackup = BackupFiles.getEnabled();
+        boolean doBackup = BackupFiles.getEnabled() && !stdout;
         BackupFiles backupfiles = null;
         if (doBackup)
         {
@@ -1309,7 +1320,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           String tempFilePath = doBackup ? backupfiles.getTempFilePath()
                   : file;
           Console.trace("ALIGNFRAME setting PrintWriter");
-          PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
+          PrintWriter out = stdout
+                  ? new PrintWriter(new OutputStreamWriter(System.out))
+                  : new PrintWriter(new FileWriter(tempFilePath));
 
           if (backupfiles != null)
           {
@@ -1318,13 +1331,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
 
           out.print(output);
-          Console.trace("ALIGNFRAME about to close file");
-          out.close();
-          Console.trace("ALIGNFRAME closed file");
-          AlignFrame.this.setTitle(file);
-          statusBar.setText(MessageManager.formatMessage(
-                  "label.successfully_saved_to_file_in_format", new Object[]
-                  { fileName, format.getName() }));
+          out.flush();
+          if (!stdout)
+          {
+            Console.trace("ALIGNFRAME about to close file");
+            out.close();
+            Console.trace("ALIGNFRAME closed file");
+          }
+          AlignFrame.this.setTitle(stdout ? "STDOUT" : file);
+          if (stdout)
+          {
+            statusBar.setText(MessageManager.formatMessage(
+                    "label.successfully_printed_to_stdout_in_format",
+                    new Object[]
+                    { format.getName() }));
+          }
+          else
+          {
+            statusBar.setText(MessageManager.formatMessage(
+                    "label.successfully_saved_to_file_in_format",
+                    new Object[]
+                    { fileName, format.getName() }));
+          }
           lastSaveSuccessful = true;
         } catch (IOException e)
         {
@@ -2471,7 +2499,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     } catch (Exception ex)
     {
       ex.printStackTrace();
-      System.out.println("Exception whilst pasting: " + ex);
+      jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex);
       // could be anything being pasted in here
     }
 
@@ -2519,7 +2547,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     } catch (Exception ex)
     {
       ex.printStackTrace();
-      System.out.println("Exception whilst pasting: " + ex);
+      jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex);
       // could be anything being pasted in here
     } catch (OutOfMemoryError oom)
     {
@@ -3155,16 +3183,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void wrapMenuItem_actionPerformed(ActionEvent e)
   {
-    setWrapFormat(wrapMenuItem.isSelected());
+    setWrapFormat(wrapMenuItem.isSelected(), false);
   }
 
-  public void setWrapFormat(boolean b)
+  public void setWrapFormat(boolean b, boolean setMenuItem)
   {
     scaleAbove.setVisible(b);
     scaleLeft.setVisible(b);
     scaleRight.setVisible(b);
     viewport.setWrapAlignment(b);
     alignPanel.updateLayout();
+    if (setMenuItem)
+    {
+      wrapMenuItem.setSelected(b);
+    }
   }
 
   @Override
@@ -4270,8 +4302,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       NewickFile fin = new NewickFile(
               new FileParse(cm.getNewick(), DataSourceType.PASTE));
-      String title = aa.label + " "
-              + cm.getTreeMethod() + " tree" + (aa.sequenceRef != null
+      String title = aa.label + " " + cm.getTreeMethod() + " tree"
+              + (aa.sequenceRef != null
                       ? (" for " + aa.sequenceRef.getDisplayId(false))
                       : "");
 
@@ -4324,7 +4356,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       try
       {
-        System.err.println("Waiting for building menu to finish.");
+        jalview.bin.Console
+                .errPrintln("Waiting for building menu to finish.");
         Thread.sleep(10);
       } catch (Exception e)
       {
@@ -4340,7 +4373,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         final List<JMenuItem> legacyItems = new ArrayList<>();
         try
         {
-          // System.err.println("Building ws menu again "
+          // jalview.bin.Console.errPrintln("Building ws menu again "
           // + Thread.currentThread());
           // TODO: add support for context dependent disabling of services based
           // on
@@ -4878,7 +4911,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                     Desktop.instance);
                     if (pe != null)
                     {
-                      System.err.println("Associated file : "
+                      jalview.bin.Console.errPrintln("Associated file : "
                               + (fm[0].toString()) + " with "
                               + toassoc.getDisplayId(true));
                       assocfiles++;
@@ -5911,7 +5944,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               viewport.getAlignment()));
     } catch (Exception ex)
     {
-      System.err.println(ex.getMessage());
+      jalview.bin.Console.errPrintln(ex.getMessage());
       return;
     }
   }
@@ -5933,7 +5966,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         console.runScript();
       } catch (Exception ex)
       {
-        System.err.println((ex.toString()));
+        jalview.bin.Console.errPrintln((ex.toString()));
         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                 MessageManager.getString("label.couldnt_run_groovy_script"),
                 MessageManager.getString("label.groovy_support_failed"),
@@ -5942,7 +5975,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      System.err.println("Can't run Groovy script as console not found");
+      jalview.bin.Console
+              .errPrintln("Can't run Groovy script as console not found");
     }
   }