From 0a9efc350cacfca8bbc1c317b9fdfbbc0ba511c6 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 19 Jul 2006 15:20:10 +0000
Subject: [PATCH] Save output use whole alignment

---
 src/jalview/gui/AlignFrame.java |   45 +++++++++++++++++++++++++++------------
 1 file changed, 31 insertions(+), 14 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 0edc578..d6143bf 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -352,15 +352,16 @@ public class AlignFrame
 
       if (viewport.hasHiddenColumns)
       {
-        System.out.println("PROMPT USER HERE");
-        omitHidden = viewport.getSelectionAsString();
+     //  System.out.println("PROMPT USER HERE");
+     //   omitHidden = viewport.getSelectionAsString();
       }
 
       String output = new FormatAdapter().formatSequences(
           format,
-          viewport.getSelectionAsNewSequence(),
-          omitHidden) ;
-
+          viewport.alignment.getSequencesArray(),
+          null);
+          //viewport.getSelectionAsNewSequence(),
+          //omitHidden) ;
 
 
       if (output == null)
@@ -394,14 +395,17 @@ public class AlignFrame
   protected void outputText_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    Desktop.addInternalFrame(cap,
+                             "Alignment output - " + e.getActionCommand(), 600,
+                             500);
 
 
     String [] omitHidden = null;
 
     if(viewport.hasHiddenColumns)
     {
-      System.out.println("PROMPT USER HERE");
-      omitHidden = viewport.getSelectionAsString();
+   //   System.out.println("PROMPT USER HERE");
+   //   omitHidden = viewport.getSelectionAsString();
     }
 
     cap.setText(new FormatAdapter().formatSequences(
@@ -670,13 +674,21 @@ public class AlignFrame
     }
 
     SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+    String[] omitHidden = null;
+
+    if (viewport.hasHiddenColumns)
+    {
+      omitHidden = viewport.getSelectionAsString();
+    }
 
-    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+    String output = new FormatAdapter().formatSequences(
+        "Fasta",
+        seqs,
+        omitHidden);
 
-    FastaFile ff = new FastaFile();
-    ff.addJVSuffix( viewport.showJVSuffix );
 
-    c.setContents(new StringSelection(ff.print(seqs)), Desktop.instance);
+    Toolkit.getDefaultToolkit().getSystemClipboard()
+        .setContents(new StringSelection(output), Desktop.instance);
 
     Vector hiddenColumns = null;
     if(viewport.hasHiddenColumns && viewport.getSelectionGroup()!=null)
@@ -692,6 +704,7 @@ public class AlignFrame
                           region[1]-hiddenOffset});
       }
     }
+
     Desktop.jalviewClipboard = new Object[]{ seqs,
         viewport.alignment.getDataset(),
         hiddenColumns};
@@ -2555,7 +2568,10 @@ public class AlignFrame
 
 public void showTranslation_actionPerformed(ActionEvent e)
 {
-  int s, sSize = viewport.alignment.getHeight();
+  SequenceI [] selection = viewport.getSelectionAsNewSequence();
+  String [] seqstring = viewport.getSelectionAsString();
+
+  int s, sSize = selection.length;
   SequenceI [] newSeq = new SequenceI[sSize];
 
   int res, resSize;
@@ -2564,7 +2580,7 @@ public void showTranslation_actionPerformed(ActionEvent e)
   for(s=0; s<sSize; s++)
   {
     protein = new StringBuffer();
-    seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());
+    seq = AlignSeq.extractGaps("-. ", seqstring[s]);
     resSize = seq.length();
     resSize -= resSize%3;
 
@@ -2580,7 +2596,8 @@ public void showTranslation_actionPerformed(ActionEvent e)
       else
         protein.append( aa );
     }
-    newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());
+    newSeq[s] = new Sequence(selection[s].getName(),
+                             protein.toString());
   }
 
 
-- 
1.7.10.2