getViewAsString can ignore sequenceGroup

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 325a676..2ce8f06 100755 (executable)
--- 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);\r
 \r
         if (reply == JOptionPane.YES_OPTION)\r
-          omitHidden = viewport.getSelectionAsString();\r
+          omitHidden = viewport.getViewAsString(false);\r
       }\r
 \r
       String output = new FormatAdapter().formatSequences(\r
           format,\r
           viewport.alignment.getSequencesArray(),\r
-          null);\r
-          //viewport.getSelectionAsNewSequence(),\r
-          //omitHidden) ;\r
-\r
+          omitHidden);\r
 \r
       if (output == null)\r
       {\r
@@ -400,12 +397,6 @@ public class AlignFrame
    */\r
   protected void outputText_actionPerformed(ActionEvent e)\r
   {\r
-    CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
-    Desktop.addInternalFrame(cap,\r
-                             "Alignment output - " + e.getActionCommand(), 600,\r
-                             500);\r
-\r
-\r
     String [] omitHidden = null;\r
 \r
     if(viewport.hasHiddenColumns)\r
@@ -417,12 +408,20 @@ public class AlignFrame
       JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);\r
 \r
       if(reply==JOptionPane.YES_OPTION)\r
-       omitHidden = viewport.getSelectionAsString();\r
+      {\r
+        omitHidden = viewport.getViewAsString(false);\r
+      }\r
     }\r
 \r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+    Desktop.addInternalFrame(cap,\r
+                             "Alignment output - " + e.getActionCommand(), 600,\r
+                             500);\r
+\r
+\r
     cap.setText(new FormatAdapter().formatSequences(\r
         e.getActionCommand(),\r
-        viewport.getSelectionAsNewSequence(),\r
+        viewport.alignment.getSequencesArray(),\r
         omitHidden));\r
   }\r
 \r
@@ -690,7 +689,7 @@ public class AlignFrame
 \r
     if (viewport.hasHiddenColumns)\r
     {\r
-      omitHidden = viewport.getSelectionAsString();\r
+      omitHidden = viewport.getViewAsString(true);\r
     }\r
 \r
     String output = new FormatAdapter().formatSequences(\r
@@ -849,7 +848,7 @@ public class AlignFrame
            for(int i=0; i<hc.size(); i++)\r
            {\r
              int [] region = (int[]) hc.elementAt(i);\r
-             af.viewport.hideColumns(region[0], region[1]);\r
+             af.viewport.hideColumns(region[0], region[1]+1);\r
            }\r
          }\r
 \r
@@ -2614,11 +2613,10 @@ public class AlignFrame
 \r
 \r
 \r
-\r
 public void showTranslation_actionPerformed(ActionEvent e)\r
 {\r
   SequenceI [] selection = viewport.getSelectionAsNewSequence();\r
-  String [] seqstring = viewport.getSelectionAsString();\r
+  String [] seqstring = viewport.getViewAsString(true);\r
 \r
   int s, sSize = selection.length;\r
   SequenceI [] newSeq = new SequenceI[sSize];\r

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index a101fcf..3742259 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1201,20 +1201,20 @@ public class AlignViewport
 \r
 \r
     /**\r
-     * This method returns the visible selected area as text, as\r
+     * This method returns the visible alignment as text, as\r
      * seen on the GUI, ie if columns are hidden they will not\r
      * be returned in the result.\r
      * Use this for calculating trees, PCA, redundancy etc on views\r
      * which contain hidden columns.\r
      * @return String[]\r
      */\r
-    public String [] getSelectionAsString()\r
+    public String [] getViewAsString(boolean selectedRegionOnly)\r
     {\r
       String [] selection = null;\r
       SequenceI [] seqs= null;\r
       int i, iSize;\r
       int start = 0, end = 0;\r
-      if(selectionGroup!=null)\r
+      if(selectedRegionOnly && selectionGroup!=null)\r
       {\r
         iSize = selectionGroup.getSize(false);\r
         seqs = selectionGroup.getSequencesInOrder(alignment);\r
@@ -1277,8 +1277,6 @@ public class AlignViewport
         {\r
           selection[i] = seqs[i].getSequence(start, end);\r
         }\r
-\r
-    //    System.out.println(seqs[i].getName()+"\t"+ selection[i]);\r
       }\r
 \r
       return selection;\r

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 371528a..ffc5a76 100755 (executable)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -59,7 +59,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
 \r
         boolean sameLength = true;\r
 \r
-        seqstrings = av.getSelectionAsString();\r
+        seqstrings = av.getViewAsString(true);\r
 \r
         if (av.getSelectionGroup() == null)\r
         {\r

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index ba961ee..ba3c9ac 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -54,7 +54,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         sequences = new Vector();\r
 \r
         SequenceI [] seqs;\r
-        String []  seqStrings = av.getSelectionAsString();\r
+        String []  seqStrings = av.getViewAsString(true);\r
 \r
         if(av.getSelectionGroup()==null)\r
         {\r

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ddb194e..6fbd0ee 100755 (executable)
--- 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)\r
     {\r
       System.out.println("PROMPT USER HERE");\r
-      omitHidden = ap.av.getSelectionAsString();\r
+      omitHidden = ap.av.getViewAsString(true);\r
     }\r
 \r
     cap.setText(new FormatAdapter().formatSequences(\r

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index b248294..3d1bfb7 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -147,7 +147,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 \r
         if (ap.av.hasHiddenColumns)\r
         {\r
-          omitHidden = ap.av.getSelectionAsString();\r
+          omitHidden = ap.av.getViewAsString(sg!=null);\r
         }\r
 \r
 \r

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 190f15c..f636257 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -163,7 +163,7 @@ public class TreePanel extends GTreePanel
           String [] seqStrings = null;\r
           if (av.hasHiddenColumns)\r
           {\r
-            seqStrings = av.getSelectionAsString();\r
+            seqStrings = av.getViewAsString(true);\r
           }\r
 \r
           if(av.getSelectionGroup()==null)\r