import java.awt.event.*;\r
import java.awt.print.*;\r
import javax.swing.*;\r
+import javax.swing.event.*;\r
import java.util.*;\r
\r
public class AlignFrame extends GAlignFrame\r
\r
protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
{\r
- HTMLOutput htmlOutput = new HTMLOutput(viewport.getAlignment(), alignPanel.seqPanel.getColourScheme());\r
+ HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
htmlOutput = null;\r
}\r
\r
}\r
\r
\r
-\r
public void groupsMenuItem_actionPerformed(ActionEvent e)\r
{\r
GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
frame.setResizable(false);\r
}\r
\r
- public void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGroupEdit( groupEditingMenuItem.isSelected() );\r
- }\r
\r
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
PaintRefresher.Refresh(null);\r
}\r
\r
- public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete selection");\r
-\r
- for (int i=0;i < viewport.getSelection().size(); i++)\r
- viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));\r
-\r
- viewport.getSelection().clear();\r
- viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- public void moveSelectedMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- copySelectedMenuItem_actionPerformed(null);\r
- deleteSelectedMenuItem_actionPerformed(null);\r
- alignPanel.repaint();\r
- }\r
-\r
- public void copySelectedMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if(viewport.getSelection().size()==0)\r
- return;\r
-\r
- SequenceI[] s = new Sequence[viewport.getSelection().size()];\r
- for (int i=0; i < viewport.getSelection().size(); i++) {\r
- s[i] = new Sequence(viewport.getSelection().sequenceAt(i));\r
- }\r
- AlignFrame af = new AlignFrame(new Alignment(s));\r
- int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
- if(newHeight>500)\r
- newHeight=500;\r
- Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);\r
- }\r
\r
public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
{\r
\r
protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
- updateResidueView();\r
+ viewport.setColourText( colourTextMenuItem.isSelected() );\r
+ alignPanel.RefreshPanels();\r
}\r
\r
void SetFont()\r
\r
protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
{\r
- updateResidueView();\r
+ viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
+ alignPanel.RefreshPanels();\r
}\r
\r
\r
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
{\r
- updateResidueView();\r
+ viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
+ alignPanel.RefreshPanels();\r
}\r
\r
public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
- updateResidueView();\r
+ viewport.setShowText( viewTextMenuItem.isSelected() );\r
+ alignPanel.RefreshPanels();\r
}\r
\r
\r
}\r
\r
\r
- void updateResidueView()\r
- {\r
- if (viewport.getSelection().size() == 0)\r
- {\r
- for (int i = 0; i < viewport.alignment.getGroups().size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);\r
- sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );\r
- sg.setDisplayText( viewTextMenuItem.isSelected() );\r
- sg.setColourText( colourTextMenuItem.isSelected() );\r
- }\r
- }\r
- else\r
- {\r
- SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));\r
- if (alignPanel.seqPanel.isNewSelection(sg))\r
- {\r
- sg = viewport.getAlignment().addGroup();\r
- for (int i = 0; i < viewport.getSelection().size(); i++)\r
- {\r
- viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (\r
- Sequence) viewport.sel.sequenceAt(i)),\r
- (Sequence) viewport.sel.sequenceAt(\r
- i));\r
- viewport.alignment.addToGroup(sg,\r
- (Sequence) viewport.sel.sequenceAt(i));\r
- }\r
- }\r
-\r
- sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());\r
- sg.setDisplayText(viewTextMenuItem.isSelected());\r
- sg.setColourText(colourTextMenuItem.isSelected());\r
- }\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
-\r
public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
{\r
alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
\r
protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme(null, false);\r
+ viewport.setGlobalColourScheme( null );\r
+ alignPanel.setColourScheme();\r
}\r
\r
\r
public void clustalColour_actionPerformed(ActionEvent e)\r
{\r
- // alignPanel.setColourScheme( new ClustalxColourScheme() );\r
+ viewport.setGlobalColourScheme(new ClustalxColourScheme( ));\r
+ alignPanel.setColourScheme( );\r
}\r
\r
public void zappoColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new ZappoColourScheme(), conservationMenuItem.isSelected() );\r
+ viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
+ alignPanel.setColourScheme( );\r
}\r
\r
public void taylorColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new TaylorColourScheme(),conservationMenuItem.isSelected() );\r
+ viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
+ alignPanel.setColourScheme( );\r
}\r
\r
\r
public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new HydrophobicColourScheme(),conservationMenuItem.isSelected() );\r
+ viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
+ alignPanel.setColourScheme( );\r
}\r
\r
public void helixColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new HelixColourScheme(),conservationMenuItem.isSelected() );\r
+ viewport.setGlobalColourScheme( new HelixColourScheme() );\r
+ alignPanel.setColourScheme();\r
}\r
\r
\r
public void strandColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new StrandColourScheme() ,conservationMenuItem.isSelected() );\r
+ viewport.setGlobalColourScheme(new StrandColourScheme() );\r
+ alignPanel.setColourScheme( );\r
}\r
\r
\r
public void turnColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new TurnColourScheme() ,conservationMenuItem.isSelected() );\r
+ viewport.setGlobalColourScheme(new TurnColourScheme() );\r
+ alignPanel.setColourScheme( );\r
}\r
\r
\r
public void buriedColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new BuriedColourScheme() ,conservationMenuItem.isSelected() );\r
+ viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
+ alignPanel.setColourScheme( );\r
}\r
\r
\r
protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme ( alignPanel.seqPanel.getColourScheme(),conservationMenuItem.isSelected() );\r
- conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );\r
- }\r
-\r
-\r
+ viewport.setConservationSelected(conservationMenuItem.isSelected());\r
+ alignPanel.setColourScheme();\r
\r
- public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(cip);\r
- Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);\r
- frame.setMaximizable(false);\r
- }\r
+ if(conservationMenuItem.isSelected())\r
+ {\r
+ SliderPanel sp = new SliderPanel(alignPanel, 30, true, viewport.getGlobalColourScheme());\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(sp);\r
+ Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400, 90);\r
+ frame.setMaximizable(false);\r
+ }\r
+ }\r
\r
\r
- public void abovePIDColour_actionPerformed(ActionEvent e)\r
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new PIDColourScheme() ,conservationMenuItem.isSelected() );\r
+ if(abovePIDThreshold.isSelected())\r
+ {\r
+ SliderPanel sp = new SliderPanel(alignPanel, 70, false,\r
+ viewport.getGlobalColourScheme());\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(sp);\r
+ Desktop.addInternalFrame(frame, "Percentage Identity Threshold", 400, 90);\r
+ frame.setMaximizable(false);\r
+ }\r
}\r
\r
\r
public void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
JInternalFrame frame = new JInternalFrame();\r
- UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );\r
+ UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
frame.setContentPane(chooser);\r
Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
frame.setResizable(false);\r
\r
public void PIDColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new PIDColourScheme(),conservationMenuItem.isSelected() );\r
+ viewport.setGlobalColourScheme( new PIDColourScheme() );\r
+ alignPanel.setColourScheme( );\r
}\r
\r
\r
public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) ,conservationMenuItem.isSelected() );\r
+ viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) );\r
+ alignPanel.setColourScheme();\r
}\r
\r
\r
\r
protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
{\r
- ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );\r
+ ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );\r
Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff