To uppercase only visible

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 9429671..82477ea 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -239,13 +239,35 @@ public class APopupMenu
       {\r
         for (int g = 0; g < sg.getSize(true); g++)\r
         {\r
-          if (source == toggleCase)\r
-           ((SequenceI) sg.getSequences(true).elementAt(g))\r
-          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
-          else\r
-            ((SequenceI) sg.getSequences(true).elementAt(g))\r
-                .changeCase(source == toUpper, sg.getStartRes(),\r
-                                           sg.getEndRes() + 1);\r
+          int start = sg.getStartRes();\r
+          int end = sg.getEndRes() + 1;\r
+\r
+          do\r
+          {\r
+            if (ap.av.hasHiddenColumns)\r
+            {\r
+              end = ap.av.colSel.getHiddenBoundaryRight(start);\r
+              if (start == end)\r
+                end = sg.getEndRes() + 1;\r
+              if (end > sg.getEndRes())\r
+                end = sg.getEndRes() + 1;\r
+            }\r
+\r
+            if (source == toggleCase)\r
+              ( (SequenceI) sg.getSequences(true).elementAt(g))\r
+                  .toggleCase(start, end);\r
+            else\r
+              ( (SequenceI) sg.getSequences(true).elementAt(g))\r
+                  .changeCase(source == toUpper, start, end);\r
+\r
+            if (ap.av.hasHiddenColumns)\r
+            {\r
+              start = ap.av.colSel.adjustForHiddenColumns(end);\r
+              start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
+            }\r
+\r
+          }\r
+        while (end < sg.getEndRes());\r
         }\r
         ap.seqPanel.seqCanvas.repaint();\r
       }\r

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