void changeCase(ActionEvent e

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index c673af1..d099944 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -21,11 +21,9 @@ package jalview.gui;
 import MCview.*;\r
 \r
 import jalview.analysis.*;\r
-\r
 import jalview.datamodel.*;\r
-\r
-\r
 import jalview.schemes.*;\r
+import jalview.commands.ChangeCaseCommand;\r
 \r
 import java.awt.*;\r
 import java.awt.event.*;\r
@@ -452,7 +450,7 @@ public class PopupMenu extends JPopupMenu
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        upperCase_actionPerformed(e);\r
+        changeCase(e);\r
       }\r
     });\r
     copy.setText("Copy");\r
@@ -468,7 +466,7 @@ public class PopupMenu extends JPopupMenu
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        lowerCase_actionPerformed(e);\r
+        changeCase(e);\r
       }\r
     });\r
     toggle.setText("Toggle Case");\r
@@ -476,7 +474,7 @@ public class PopupMenu extends JPopupMenu
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        toggle_actionPerformed(e);\r
+        changeCase(e);\r
       }\r
     });\r
     pdbMenu.setText("Associate Structure with Sequence");\r
@@ -523,12 +521,12 @@ public class PopupMenu extends JPopupMenu
     groupMenu.addSeparator();\r
     groupMenu.add(groupName);\r
     groupMenu.add(unGroupMenuItem);\r
-        groupMenu.add(colourMenu);\r
+    groupMenu.add(colourMenu);\r
     groupMenu.add(showBoxes);\r
-        groupMenu.add(showText);\r
-        groupMenu.add(showColourText);\r
+    groupMenu.add(showText);\r
+    groupMenu.add(showColourText);\r
     groupMenu.add(outline);\r
-        sequenceMenu.add(sequenceName);\r
+    sequenceMenu.add(sequenceName);\r
     sequenceMenu.add(pdbMenu);\r
     colourMenu.add(noColourmenuItem);\r
         colourMenu.add(clustalColour);\r
@@ -1176,58 +1174,74 @@ public class PopupMenu extends JPopupMenu
     ap.alignFrame.cut_actionPerformed(null);\r
   }\r
 \r
-  public void upperCase_actionPerformed(ActionEvent e)\r
-  {\r
-    changeCase(e.getSource());\r
-  }\r
-\r
-  public void lowerCase_actionPerformed(ActionEvent e)\r
-  {\r
-    changeCase(e.getSource());\r
-  }\r
-\r
-  public void toggle_actionPerformed(ActionEvent e)\r
-  {\r
-    changeCase(e.getSource());\r
-  }\r
-\r
-  void changeCase(Object source)\r
+  void changeCase(ActionEvent e)\r
   {\r
+    Object source = e.getSource();\r
     SequenceGroup sg = ap.av.getSelectionGroup();\r
+    Vector regions = new Vector();\r
     if (sg != null)\r
     {\r
-      for (int g = 0; g < sg.getSize(true); g++)\r
+      int start = sg.getStartRes();\r
+      int end = sg.getEndRes() + 1;\r
+\r
+      do\r
       {\r
-        int start = sg.getStartRes();\r
-        int end = sg.getEndRes() + 1;\r
+        if (ap.av.hasHiddenColumns)\r
+        {\r
+          if(start==0)\r
+            start = ap.av.colSel.adjustForHiddenColumns(start);\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
-        do\r
+        regions.addElement(new int[]\r
+                           {start, end});\r
+\r
+        if (ap.av.hasHiddenColumns)\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
+          start = ap.av.colSel.adjustForHiddenColumns(end);\r
+          start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
+        }\r
+      }\r
+      while (end < sg.getEndRes());\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
+      int[][] startEnd = new int[regions.size()][2];\r
+      for (int i = 0; i < regions.size(); i++)\r
+      {\r
+        startEnd[i] = (int[]) regions.elementAt(i);\r
+      }\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
+      String description;\r
+      int caseChange;\r
+\r
+      if(source==toggle)\r
+      {\r
+        description = "Toggle Case";\r
+        caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
       }\r
+      else if(source==upperCase)\r
+      {\r
+        description = "To Upper Case";\r
+        caseChange = ChangeCaseCommand.TO_UPPER;\r
+      }\r
+      else\r
+      {\r
+        description = "To Lower Case";\r
+        caseChange = ChangeCaseCommand.TO_LOWER;\r
+      }\r
+\r
+      ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
+          description, sg.getSequencesAsArray(true), startEnd, caseChange\r
+          );\r
+\r
+      ap.alignFrame.addHistoryItem(caseCommand);\r
+\r
+\r
       PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
     }\r
   }\r
@@ -1337,13 +1351,7 @@ public class PopupMenu extends JPopupMenu
       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();\r
       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
       int end = sg.findEndRes(sg.getSequenceAt(i));\r
-\r
-      features[i] = new SequenceFeature(\r
-          "",\r
-          "Search Results", null,\r
-          start,\r
-          end,\r
-          "Search Results");\r
+      features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");\r
     }\r
 \r
     if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r