From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 22 Aug 2006 14:29:10 +0000 (+0000)
Subject: To uppercase only visible
X-Git-Tag: Release_2_1~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=16019224bf7ab31b3b19e6e27aa55b4d75de6f8b;p=jalview.git

To uppercase only visible
---

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 9429671..82477ea 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -239,13 +239,35 @@ public class APopupMenu
       {
         for (int g = 0; g < sg.getSize(true); g++)
         {
-          if (source == toggleCase)
-           ((SequenceI) sg.getSequences(true).elementAt(g))
-          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
-          else
-            ((SequenceI) sg.getSequences(true).elementAt(g))
-                .changeCase(source == toUpper, sg.getStartRes(),
-                                           sg.getEndRes() + 1);
+          int start = sg.getStartRes();
+          int end = sg.getEndRes() + 1;
+
+          do
+          {
+            if (ap.av.hasHiddenColumns)
+            {
+              end = ap.av.colSel.getHiddenBoundaryRight(start);
+              if (start == end)
+                end = sg.getEndRes() + 1;
+              if (end > sg.getEndRes())
+                end = sg.getEndRes() + 1;
+            }
+
+            if (source == toggleCase)
+              ( (SequenceI) sg.getSequences(true).elementAt(g))
+                  .toggleCase(start, end);
+            else
+              ( (SequenceI) sg.getSequences(true).elementAt(g))
+                  .changeCase(source == toUpper, start, end);
+
+            if (ap.av.hasHiddenColumns)
+            {
+              start = ap.av.colSel.adjustForHiddenColumns(end);
+              start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+            }
+
+          }
+        while (end < sg.getEndRes());
         }
         ap.seqPanel.seqCanvas.repaint();
       }
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 3481a31..69e83f5 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1160,45 +1160,58 @@ public class PopupMenu extends JPopupMenu
 
   public void upperCase_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg==null)
-      return;
-
-    for(int g=0; g<sg.getSize(true); g++)
-    {
-    ( (SequenceI)sg.getSequences(true).elementAt(g))
-        .changeCase(true, sg.getStartRes(), sg.getEndRes()+1);
-    }
-    ap.repaint();
+    changeCase(e.getSource());
   }
 
   public void lowerCase_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg==null)
-      return;
-
-    for(int g=0; g<sg.getSize(true); g++)
-    {
-       ( (SequenceI)sg.getSequences(true).elementAt(g))
-           .changeCase(false, sg.getStartRes(), sg.getEndRes()+1);
-    }
-    ap.repaint();
+    changeCase(e.getSource());
   }
 
   public void toggle_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg == null)
-      return;
+    changeCase(e.getSource());
+  }
 
-    for (int g = 0; g < sg.getSize(true); g++)
+  void changeCase(Object source)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if (sg != null)
     {
-      ( (SequenceI)sg.getSequences(true).elementAt(g))
-          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
-    }
+      for (int g = 0; g < sg.getSize(true); g++)
+      {
+        int start = sg.getStartRes();
+        int end = sg.getEndRes() + 1;
+
+        do
+        {
+          if (ap.av.hasHiddenColumns)
+          {
+            end = ap.av.colSel.getHiddenBoundaryRight(start);
+            if (start == end)
+              end = sg.getEndRes() + 1;
+            if (end > sg.getEndRes())
+              end = sg.getEndRes() + 1;
+          }
+
+          if (source == toggle)
+            ( (SequenceI) sg.getSequences(true).elementAt(g))
+                .toggleCase(start, end);
+          else
+            ( (SequenceI) sg.getSequences(true).elementAt(g))
+                .changeCase(source == upperCase, start, end);
 
-    ap.repaint();
+          if (ap.av.hasHiddenColumns)
+          {
+            start = ap.av.colSel.adjustForHiddenColumns(end);
+            start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+          }
+
+        }
+        while (end < sg.getEndRes());
+      }
+      ap.repaint();
+    }
   }
 
   public void outputText_actionPerformed(ActionEvent e)