From ef6555067c63693c06f0b6335a1c9f5761d712c6 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 21 Jul 2006 09:27:20 +0000
Subject: [PATCH] getViewAsString can ignore sequenceGroup

---
 src/jalview/gui/AlignFrame.java         |   32 +++++++++++++++----------------
 src/jalview/gui/AlignViewport.java      |    8 +++-----
 src/jalview/gui/PCAPanel.java           |    2 +-
 src/jalview/gui/PairwiseAlignPanel.java |    2 +-
 src/jalview/gui/PopupMenu.java          |    2 +-
 src/jalview/gui/RedundancyPanel.java    |    2 +-
 src/jalview/gui/TreePanel.java          |    2 +-
 7 files changed, 23 insertions(+), 27 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 325a676..2ce8f06 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -359,16 +359,13 @@ public class AlignFrame
             JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
 
         if (reply == JOptionPane.YES_OPTION)
-          omitHidden = viewport.getSelectionAsString();
+          omitHidden = viewport.getViewAsString(false);
       }
 
       String output = new FormatAdapter().formatSequences(
           format,
           viewport.alignment.getSequencesArray(),
-          null);
-          //viewport.getSelectionAsNewSequence(),
-          //omitHidden) ;
-
+          omitHidden);
 
       if (output == null)
       {
@@ -400,12 +397,6 @@ 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)
@@ -417,12 +408,20 @@ public class AlignFrame
       JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
 
       if(reply==JOptionPane.YES_OPTION)
-       omitHidden = viewport.getSelectionAsString();
+      {
+        omitHidden = viewport.getViewAsString(false);
+      }
     }
 
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    Desktop.addInternalFrame(cap,
+                             "Alignment output - " + e.getActionCommand(), 600,
+                             500);
+
+
     cap.setText(new FormatAdapter().formatSequences(
         e.getActionCommand(),
-        viewport.getSelectionAsNewSequence(),
+        viewport.alignment.getSequencesArray(),
         omitHidden));
   }
 
@@ -690,7 +689,7 @@ public class AlignFrame
 
     if (viewport.hasHiddenColumns)
     {
-      omitHidden = viewport.getSelectionAsString();
+      omitHidden = viewport.getViewAsString(true);
     }
 
     String output = new FormatAdapter().formatSequences(
@@ -849,7 +848,7 @@ public class AlignFrame
            for(int i=0; i<hc.size(); i++)
            {
              int [] region = (int[]) hc.elementAt(i);
-             af.viewport.hideColumns(region[0], region[1]);
+             af.viewport.hideColumns(region[0], region[1]+1);
            }
          }
 
@@ -2614,11 +2613,10 @@ public class AlignFrame
 
 
 
-
 public void showTranslation_actionPerformed(ActionEvent e)
 {
   SequenceI [] selection = viewport.getSelectionAsNewSequence();
-  String [] seqstring = viewport.getSelectionAsString();
+  String [] seqstring = viewport.getViewAsString(true);
 
   int s, sSize = selection.length;
   SequenceI [] newSeq = new SequenceI[sSize];
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index a101fcf..3742259 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1201,20 +1201,20 @@ public class AlignViewport
 
 
     /**
-     * This method returns the visible selected area as text, as
+     * This method returns the visible alignment as text, as
      * seen on the GUI, ie if columns are hidden they will not
      * be returned in the result.
      * Use this for calculating trees, PCA, redundancy etc on views
      * which contain hidden columns.
      * @return String[]
      */
-    public String [] getSelectionAsString()
+    public String [] getViewAsString(boolean selectedRegionOnly)
     {
       String [] selection = null;
       SequenceI [] seqs= null;
       int i, iSize;
       int start = 0, end = 0;
-      if(selectionGroup!=null)
+      if(selectedRegionOnly && selectionGroup!=null)
       {
         iSize = selectionGroup.getSize(false);
         seqs = selectionGroup.getSequencesInOrder(alignment);
@@ -1277,8 +1277,6 @@ public class AlignViewport
         {
           selection[i] = seqs[i].getSequence(start, end);
         }
-
-    //    System.out.println(seqs[i].getName()+"\t"+ selection[i]);
       }
 
       return selection;
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 371528a..ffc5a76 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -59,7 +59,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
 
         boolean sameLength = true;
 
-        seqstrings = av.getSelectionAsString();
+        seqstrings = av.getViewAsString(true);
 
         if (av.getSelectionGroup() == null)
         {
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index ba961ee..ba3c9ac 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -54,7 +54,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         sequences = new Vector();
 
         SequenceI [] seqs;
-        String []  seqStrings = av.getSelectionAsString();
+        String []  seqStrings = av.getViewAsString(true);
 
         if(av.getSelectionGroup()==null)
         {
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ddb194e..6fbd0ee 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1183,7 +1183,7 @@ public class PopupMenu extends JPopupMenu
     if(ap.av.hasHiddenColumns)
     {
       System.out.println("PROMPT USER HERE");
-      omitHidden = ap.av.getSelectionAsString();
+      omitHidden = ap.av.getViewAsString(true);
     }
 
     cap.setText(new FormatAdapter().formatSequences(
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index b248294..3d1bfb7 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -147,7 +147,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
         if (ap.av.hasHiddenColumns)
         {
-          omitHidden = ap.av.getSelectionAsString();
+          omitHidden = ap.av.getViewAsString(sg!=null);
         }
 
 
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 190f15c..f636257 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -163,7 +163,7 @@ public class TreePanel extends GTreePanel
           String [] seqStrings = null;
           if (av.hasHiddenColumns)
           {
-            seqStrings = av.getSelectionAsString();
+            seqStrings = av.getViewAsString(true);
           }
 
           if(av.getSelectionGroup()==null)
-- 
1.7.10.2