JAL-629 Enable output to STDOUT when specifying output filename as '-'. Must check...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 49bd4e9..711d224 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;
@@ -157,7 +158,6 @@ import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
-import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -1251,8 +1251,16 @@ 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))
@@ -1263,6 +1271,7 @@ 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);
 
@@ -1298,7 +1307,7 @@ 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)
         {
@@ -1310,7 +1319,9 @@ 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)
           {
@@ -1319,13 +1330,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
 
           out.print(output);
+          out.flush();
           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() }));
+          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)
         {
@@ -1456,9 +1479,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
-    try {
+    try
+    {
       htmlSVG.exportHTML(null);
-    } catch (ImageOutputException x) {
+    } catch (ImageOutputException x)
+    {
       // report problem to console and raise dialog
     }
   }
@@ -1467,51 +1492,64 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void bioJSMenuItem_actionPerformed(ActionEvent e)
   {
     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
-    try {
-    bjs.exportHTML(null);
-  } catch (ImageOutputException x) {
-    // report problem to console and raise dialog
-  }
+    try
+    {
+      bjs.exportHTML(null);
+    } catch (ImageOutputException x)
+    {
+      // report problem to console and raise dialog
+    }
   }
 
   public void createImageMap(File file, String image)
   {
-    try {
-    alignPanel.makePNGImageMap(file, image);
-    } catch (ImageOutputException x) {
+    try
+    {
+      alignPanel.makePNGImageMap(file, image);
+    } catch (ImageOutputException x)
+    {
       // report problem to console and raise dialog
     }
   }
 
   @Override
-  public void createPNG_actionPerformed(ActionEvent e) {
-    try{
+  public void createPNG_actionPerformed(ActionEvent e)
+  {
+    try
+    {
       createPNG(null);
     } catch (ImageOutputException ioex)
     {
       // raise dialog, and report via console
     }
   }
+
   @Override
-  public void createEPS_actionPerformed(ActionEvent e) {
-    try{
+  public void createEPS_actionPerformed(ActionEvent e)
+  {
+    try
+    {
       createEPS(null);
     } catch (ImageOutputException ioex)
     {
       // raise dialog, and report via console
     }
-    
+
   }
+
   @Override
-  public void createSVG_actionPerformed(ActionEvent e) {
-    try{
+  public void createSVG_actionPerformed(ActionEvent e)
+  {
+    try
+    {
       createSVG(null);
     } catch (ImageOutputException ioex)
     {
       // raise dialog, and report via console
     }
-    
+
   }
+
   /**
    * Creates a PNG image of the alignment and writes it to the given file. If
    * the file is null, the user is prompted to choose a file.
@@ -1523,7 +1561,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing());
   }
 
-  public void createPNG(File f, String renderer, BitmapImageSizing userBis) throws ImageOutputException
+  public void createPNG(File f, String renderer, BitmapImageSizing userBis)
+          throws ImageOutputException
   {
     alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis);
   }
@@ -1534,7 +1573,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
-  public void createEPS(File f)  throws ImageOutputException
+  public void createEPS(File f) throws ImageOutputException
   {
     createEPS(f, null);
   }
@@ -1550,7 +1589,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
-  public void createSVG(File f)  throws ImageOutputException
+  public void createSVG(File f) throws ImageOutputException
   {
     createSVG(f, null);
   }
@@ -2341,12 +2380,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             // annotation was duplicated earlier
             alignment.addAnnotation(sequences[i].getAnnotation()[a]);
             // take care of contact matrix too
-            ContactMatrixI cm=sequences[i].getContactMatrixFor(sequences[i].getAnnotation()[a]);
-            if (cm!=null)
+            ContactMatrixI cm = sequences[i]
+                    .getContactMatrixFor(sequences[i].getAnnotation()[a]);
+            if (cm != null)
             {
-              alignment.addContactListFor(sequences[i].getAnnotation()[a], cm);
+              alignment.addContactListFor(sequences[i].getAnnotation()[a],
+                      cm);
             }
-            
+
             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
                     a);
           }
@@ -4239,8 +4280,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return tp;
   }
 
-  public void showContactMapTree(AlignmentAnnotation aa,
-          ContactMatrixI cm)
+  public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm)
   {
     int x = 4, y = 5;
     int w = 400, h = 500;
@@ -4249,8 +4289,8 @@ 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))
                       : "");