To uppercase only visible

[jalview.git] / src / jalview / appletgui / APopupMenu.java

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