From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 24 Nov 2016 16:43:06 +0000 (+0000)
Subject: Distinguish text-only output formats and others (.jar/.jvp)
X-Git-Tag: Release_2_10_3b1~407
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=781218e12641a89d5dd99906369d5b9807c1d203;p=jalview.git

Distinguish text-only output formats and others (.jar/.jvp)
---

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 1b66e9c..fbdf241 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -217,7 +217,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
       e.printStackTrace();
     }
 
-    for (String ff : FileFormat.getWritableFormats())
+    for (String ff : FileFormat.getWritableFormats(true))
     {
       MenuItem item = new MenuItem(ff);
 
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index e1b01a8..fcdf9d2 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -3241,7 +3241,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     inputText.addActionListener(this);
     Menu outputTextboxMenu = new Menu(
             MessageManager.getString("label.out_to_textbox"));
-    for (String ff : FileFormat.getWritableFormats())
+    for (String ff : FileFormat.getWritableFormats(true))
     {
       MenuItem item = new MenuItem(ff);
 
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 4d9dc4d..9f65708 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -258,7 +258,7 @@ public class PopupMenu extends JPopupMenu
     colours.add(purinePyrimidineColour);
     colours.add(RNAInteractionColour);
 
-    for (String ff : FileFormat.getWritableFormats())
+    for (String ff : FileFormat.getWritableFormats(true))
     {
       JMenuItem item = new JMenuItem(ff);
 
diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index a43bc22..d0ce86e 100644
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -218,7 +218,7 @@ public enum FileFormat implements FileFormatI
     }
 
   },
-  Pileup("PileUp", "pileup", false, true)
+  Pileup("PileUp", "pileup", true, true)
   {
     @Override
     public AlignmentFileI getAlignmentFile(String inFile,
@@ -329,7 +329,7 @@ public enum FileFormat implements FileFormatI
     }
 
   },
-  Features("GFF or Jalview features", "gff2,gff3", false, false)
+  Features("GFF or Jalview features", "gff2,gff3", true, false)
   {
     @Override
     public AlignmentFileI getAlignmentFile(String inFile,
@@ -351,7 +351,7 @@ public enum FileFormat implements FileFormatI
       return new FeaturesFile();
     }
   },
-  PDB("PDB", "", false, false)
+  PDB("PDB", "pdb,ent", true, false)
   {
 
     @Override
@@ -414,7 +414,7 @@ public enum FileFormat implements FileFormatI
       return new JmolParser(); // todo or null?
     }
   },
-  MMCif("mmCIF", "cif", false, false)
+  MMCif("mmCIF", "cif", true, false)
   {
 
     @Override
@@ -445,7 +445,7 @@ public enum FileFormat implements FileFormatI
       return new JmolParser(); // todo or null?
     }
   },
-  Jalview("Jalview", "jar,jvp", true, false)
+  Jalview("Jalview", "jar,jvp", true, true)
   {
 
     @Override
@@ -467,6 +467,12 @@ public enum FileFormat implements FileFormatI
     {
       return null;
     }
+
+    @Override
+    public boolean isTextFormat()
+    {
+      return false;
+    }
   };
 
   /**
@@ -496,12 +502,12 @@ public enum FileFormat implements FileFormatI
    * 
    * @return
    */
-  public static List<String> getWritableFormats()
+  public static List<String> getWritableFormats(boolean textOnly)
   {
     List<String> l = new ArrayList<String>();
     for (FileFormatI ff : values())
     {
-      if (ff.isWritable())
+      if (ff.isWritable() && (!textOnly || ff.isTextFormat()))
       {
         l.add(ff.toString());
       }
@@ -596,4 +602,10 @@ public enum FileFormat implements FileFormatI
   {
     return getAlignmentFile((AlignmentI) null);
   }
+
+  @Override
+  public boolean isTextFormat()
+  {
+    return true;
+  }
 }
diff --git a/src/jalview/io/FileFormatI.java b/src/jalview/io/FileFormatI.java
index 082d9f1..319df9f 100644
--- a/src/jalview/io/FileFormatI.java
+++ b/src/jalview/io/FileFormatI.java
@@ -10,6 +10,7 @@ public interface FileFormatI
   AlignmentFileI getAlignmentFile(String inFile, DataSourceType sourceType)
           throws IOException;
 
+  // TODO can we get rid of one of these methods?
   AlignmentFileI getAlignmentFile(FileParse source) throws IOException;
 
   AlignmentFileI getAlignmentFile(AlignmentI al);
@@ -26,7 +27,30 @@ public interface FileFormatI
    */
   String getExtensions();
 
+  /**
+   * Answers true if the format is one that Jalview can read. This implies that
+   * the format provides implementations for getAlignmentFile(FileParse) and
+   * getAlignmentFile(String, DataSourceType) which parse the data source for
+   * sequence data.
+   * 
+   * @return
+   */
   boolean isReadable();
 
+  /**
+   * Answers true if the format is one that Jalview can write. This implies that
+   * the object returned by getAlignmentFile provides an implementation of the
+   * print() method.
+   * 
+   * @return
+   */
   boolean isWritable();
+
+  /**
+   * Answers true if the format is one that Jalview can output as text, e.g. to
+   * a text box
+   * 
+   * @return
+   */
+  boolean isTextFormat();
 }
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 73d1b3c..44c4192 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -245,7 +245,7 @@ public class GAlignFrame extends JInternalFrame
       setJMenuBar(alignFrameMenuBar);
 
       // dynamically fill save as menu with available formats
-      for (String ff : FileFormat.getWritableFormats())
+      for (String ff : FileFormat.getWritableFormats(true))
       {
         JMenuItem item = new JMenuItem(ff);