Commands, history, consensus, refresh updated

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

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 7ceb570..fccc30f 100755 (executable)
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -27,6 +27,7 @@ import java.awt.*;
 \r
 import jalview.datamodel.*;\r
 import jalview.appletgui.PaintRefresher;\r
+import jalview.commands.*;\r
 \r
 public class RedundancyPanel extends SliderPanel implements Runnable, WindowListener\r
 {\r
@@ -187,70 +188,84 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
     }\r
 \r
     ap.idPanel.idCanvas.setHighlighted(redundantSeqs);\r
-\r
-    PaintRefresher.Refresh(null,ap.av.alignment);\r
+    PaintRefresher.Refresh(this,\r
+                           ap.av.getSequenceSetId(),\r
+                           true,\r
+                           true);\r
 \r
     }\r
   public void applyButton_actionPerformed()\r
-  {\r
-   // historyList.push(new HistoryItem("Remove redundancy",\r
-   //                     ap.av.alignment, HistoryItem.HIDE));\r
+  {        Vector del = new Vector();\r
 \r
-            if ((historyList.size() == 1) ||\r
-                    !ap.alignFrame.historyList.contains(historyList.firstElement()))\r
-            {\r
-      //          ap.alignFrame.addHistoryItem((HistoryItem) historyList.firstElement());\r
-     //           ap.alignFrame.updateEditMenuBar();\r
-            }\r
+        undoButton.setEnabled(true);\r
 \r
-            Vector del = new Vector();\r
+        float value = slider.getValue();\r
+        SequenceGroup sg = ap.av.getSelectionGroup();\r
 \r
-            undoButton.setEnabled(true);\r
+        for (int i = 0; i < redundancy.length; i++)\r
+        {\r
+          if (value <= redundancy[i])\r
+          {\r
+            del.addElement(originalSequences[i]);\r
+          }\r
+        }\r
 \r
-            float value = slider.getValue();\r
-            SequenceGroup sg = ap.av.getSelectionGroup();\r
+        // This has to be done before the restoreHistoryItem method of alignFrame will\r
+        // actually restore these sequences.\r
+        if (del.size() > 0)\r
+        {\r
+          SequenceI [] deleted = new SequenceI[del.size()];\r
 \r
-            for (int i = 0; i < redundancy.length; i++)\r
-            {\r
-              if (value <= redundancy[i])\r
-              {\r
-                SequenceI seq = originalSequences[i];\r
-                ap.av.alignment.deleteSequence(seq);\r
-                del.addElement(seq);\r
-                if (sg != null)\r
-                {\r
-                  sg.deleteSequence(seq, false);\r
-                }\r
-              }\r
-            }\r
+          int width = 0;\r
+          for (int i = 0; i < del.size(); i++)\r
+          {\r
+            deleted[i] = (SequenceI)del.elementAt(i);\r
+            if(deleted[i].getLength()>width)\r
+              width = deleted[i].getLength();\r
+          }\r
 \r
+          EditCommand cut = new EditCommand("Remove Redundancy",\r
+              EditCommand.CUT, deleted,0,width,ap.av.alignment);\r
 \r
-            // This has to be done before the restoreHistoryItem method of alignFrame will\r
-            // actually restore these sequences.\r
-            if (del.size() > 0)\r
+          for (int i = 0; i < del.size(); i++)\r
+          {\r
+            ap.av.alignment.deleteSequence( deleted[i] );\r
+            PaintRefresher.Refresh(this,\r
+                                   ap.av.getSequenceSetId(),\r
+                                   true,\r
+                                   true);\r
+            if (sg != null)\r
             {\r
-                for (int i = 0, j = del.size(); i < j; i++)\r
-                {\r
-                    SequenceI sq = (SequenceI) del.elementAt(i);\r
-                    sq.deleteChars(0, sq.getLength());\r
-                }\r
+              sg.deleteSequence(deleted[i], false);\r
             }\r
+          }\r
+\r
+          historyList.push(cut);\r
 \r
-        ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());\r
-        ap.alignFrame.updateEditMenuBar();\r
+          ap.alignFrame.addHistoryItem(cut);\r
+\r
+          ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());\r
+        }\r
 \r
   }\r
 \r
   public void undoButton_actionPerformed()\r
   {\r
-  //  HistoryItem hi = (HistoryItem) historyList.pop();\r
-  //  ap.alignFrame.restoreHistoryItem(hi);\r
+    CommandI command = (CommandI) historyList.pop();\r
+    command.undoCommand();\r
+\r
+    if (ap.av.historyList.contains(command))\r
+    {\r
+      ap.av.historyList.removeElement(command);\r
+      ap.alignFrame.updateEditMenuBar();\r
+    }\r
+\r
+    ap.repaint();\r
 \r
     if (historyList.size() == 0)\r
     {\r
       undoButton.setEnabled(false);\r
-    }\r
-    ap.alignFrame.updateEditMenuBar();\r
+      }\r
   }\r
 \r
   public void valueField_actionPerformed(ActionEvent e)\r