Keyboard editing added to applet

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 189a36d..7a0052f 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -250,6 +250,13 @@ public class AlignFrame extends Frame implements ActionListener,
 \r
   public void keyPressed(KeyEvent evt)\r
   {\r
+    if (viewport.cursorMode\r
+        && evt.getKeyCode() >= KeyEvent.VK_0\r
+        && evt.getKeyCode() <= KeyEvent.VK_9)\r
+    {\r
+      alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
+    }\r
+\r
     switch (evt.getKeyCode())\r
     {\r
       case 27: // escape key\r
@@ -262,6 +269,10 @@ public class AlignFrame extends Frame implements ActionListener,
         }\r
         break;\r
       case KeyEvent.VK_C:\r
+        if (viewport.cursorMode)\r
+        {\r
+          alignPanel.seqPanel.setCursorColumn();\r
+        }\r
         if (evt.isControlDown() || evt.isMetaDown())\r
         {\r
           copy_actionPerformed();\r
@@ -280,21 +291,110 @@ public class AlignFrame extends Frame implements ActionListener,
         }\r
         break;\r
       case KeyEvent.VK_DOWN:\r
-        moveSelectedSequences(false);\r
+        if(viewport.cursorMode)\r
+        {\r
+          alignPanel.seqPanel.moveCursor(0,1);\r
+        }\r
+        else\r
+          moveSelectedSequences(false);\r
         break;\r
+\r
       case KeyEvent.VK_UP:\r
-        moveSelectedSequences(true);\r
+        if (viewport.cursorMode)\r
+        {\r
+          alignPanel.seqPanel.moveCursor(0,-1);\r
+        }\r
+        else\r
+          moveSelectedSequences(true);\r
+        break;\r
+\r
+      case KeyEvent.VK_LEFT:\r
+        if(viewport.cursorMode)\r
+        {\r
+          alignPanel.seqPanel.moveCursor(-1,0);\r
+        }\r
+        break;\r
+\r
+      case KeyEvent.VK_RIGHT:\r
+        if (viewport.cursorMode)\r
+        {\r
+          alignPanel.seqPanel.moveCursor(1,0);\r
+        }\r
+        break;\r
+      case KeyEvent.VK_SPACE:\r
+        if(viewport.cursorMode)\r
+        {\r
+          alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());\r
+        }\r
+        break;\r
+\r
+      case KeyEvent.VK_DELETE:\r
+        if(viewport.cursorMode)\r
+        {\r
+          alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());\r
+        }\r
+        break;\r
+\r
+      case KeyEvent.VK_BACK_SPACE:\r
+        if(!viewport.cursorMode)\r
+        {\r
+          cut_actionPerformed();\r
+          alignPanel.seqPanel.seqCanvas.repaint();\r
+        }\r
+        break;\r
+\r
+      case KeyEvent.VK_S:\r
+        if(viewport.cursorMode)\r
+        {\r
+          alignPanel.seqPanel.setCursorRow();\r
+        }\r
+        break;\r
+      case KeyEvent.VK_P:\r
+        if(viewport.cursorMode)\r
+        {\r
+          alignPanel.seqPanel.setCursorPosition();\r
+        }\r
+        break;\r
+\r
+      case KeyEvent.VK_ENTER:\r
+      case KeyEvent.VK_COMMA:\r
+        if(viewport.cursorMode)\r
+        {\r
+          alignPanel.seqPanel.setCursorRowAndColumn();\r
+        }\r
         break;\r
+\r
+      case KeyEvent.VK_Q:\r
+        if(viewport.cursorMode)\r
+        {\r
+          alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
+        }\r
+        break;\r
+      case KeyEvent.VK_M:\r
+        if(viewport.cursorMode)\r
+        {\r
+          alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
+        }\r
+        break;\r
+\r
+     case KeyEvent.VK_F2:\r
+       viewport.cursorMode = ! viewport.cursorMode;\r
+       statusBar.setText("Keyboard editing mode is "+\r
+           (viewport.cursorMode ? "on" : "off"));\r
+       if(viewport.cursorMode)\r
+       {\r
+         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
+         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
+       }\r
+       alignPanel.seqPanel.seqCanvas.repaint();\r
+       break;\r
+\r
       case KeyEvent.VK_F:\r
         if (evt.isControlDown())\r
         {\r
           findMenuItem_actionPerformed();\r
         }\r
         break;\r
-      case KeyEvent.VK_BACK_SPACE:\r
-      case KeyEvent.VK_DELETE:\r
-        cut_actionPerformed();\r
-        break;\r
     }\r
   }\r
   public void keyReleased(KeyEvent evt)\r
@@ -335,6 +435,8 @@ public void itemStateChanged(ItemEvent evt)
             abovePIDThreshold_actionPerformed();\r
           else if(evt.getSource()==applyToAllGroups)\r
             applyToAllGroups_actionPerformed();\r
+      else if(evt.getSource()==autoCalculate)\r
+          viewport.autocalculateConsensus = autoCalculate.getState();\r
   }\r
  public void actionPerformed(ActionEvent evt)\r
  {\r
@@ -1003,8 +1105,13 @@ public void itemStateChanged(ItemEvent evt)
 \r
   public void alignmentChanged()\r
   {\r
-    viewport.updateConsensus();\r
-    viewport.updateConservation ();\r
+    viewport.alignment.padGaps();\r
+    if(viewport.autocalculateConsensus)\r
+    {\r
+      viewport.updateConsensus();\r
+      viewport.updateConservation();\r
+    }\r
+\r
     resetAllColourSchemes();\r
     if(alignPanel.overviewPanel!=null)\r
       alignPanel.overviewPanel.updateOverviewImage();\r
@@ -1749,6 +1856,8 @@ public void itemStateChanged(ItemEvent evt)
     protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
     MenuItem modifyPID = new MenuItem();\r
     MenuItem modifyConservation = new MenuItem();\r
+    protected CheckboxMenuItem autoCalculate\r
+        = new CheckboxMenuItem("Autocalculate Consensus", true);\r
     protected Menu sortByTreeMenu = new Menu();\r
     Menu sort = new Menu();\r
     Menu calculate = new Menu();\r
@@ -1926,6 +2035,7 @@ public void itemStateChanged(ItemEvent evt)
         sortByTreeMenu.setLabel("By Tree Order");\r
         sort.setLabel("Sort");\r
         calculate.setLabel("Calculate Tree");\r
+        autoCalculate.addItemListener(this);\r
         inputText.setLabel("Input from textbox");\r
         inputText.addActionListener(this);\r
 \r
@@ -2021,6 +2131,7 @@ public void itemStateChanged(ItemEvent evt)
         calculateMenu.addSeparator();\r
         calculateMenu.add(pairwiseAlignmentMenuItem);\r
         calculateMenu.add(PCAMenuItem);\r
+        calculateMenu.add(autoCalculate);\r
         this.add(statusBar, BorderLayout.SOUTH);\r
         pasteMenu.add(pasteNew);\r
         pasteMenu.add(pasteThis);\r