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
\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
current = viewport.getAlignment().getSequenceAt(i);\r
jSize = current.getLength();\r
for (int j=0; j < jSize; j++)\r
- if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')\r
+ if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
{\r
current.deleteCharAt(j);\r
j--;\r
protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setGlobalColourScheme( null );\r
- alignPanel.setColourScheme();\r
+ changeColour();\r
}\r
\r
\r
public void clustalColour_actionPerformed(ActionEvent e)\r
{\r
- // alignPanel.setColourScheme( new ClustalxColourScheme() );\r
+ viewport.setGlobalColourScheme(new ClustalxColourScheme( ));\r
+ conservationMenuItem.setSelected(false);\r
+ abovePIDThreshold.setSelected(false);\r
+ changeColour();\r
}\r
\r
public void zappoColour_actionPerformed(ActionEvent e)\r
{\r
viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
- alignPanel.setColourScheme( );\r
+ changeColour();\r
}\r
\r
public void taylorColour_actionPerformed(ActionEvent e)\r
{\r
viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
- alignPanel.setColourScheme( );\r
+ changeColour();\r
}\r
\r
\r
public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
{\r
viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
- alignPanel.setColourScheme( );\r
+ changeColour();\r
}\r
\r
public void helixColour_actionPerformed(ActionEvent e)\r
{\r
viewport.setGlobalColourScheme( new HelixColourScheme() );\r
- alignPanel.setColourScheme();\r
+ changeColour();\r
}\r
\r
\r
public void strandColour_actionPerformed(ActionEvent e)\r
{\r
viewport.setGlobalColourScheme(new StrandColourScheme() );\r
- alignPanel.setColourScheme( );\r
+ changeColour();\r
}\r
\r
\r
public void turnColour_actionPerformed(ActionEvent e)\r
{\r
viewport.setGlobalColourScheme(new TurnColourScheme() );\r
- alignPanel.setColourScheme( );\r
+ changeColour();\r
}\r
\r
\r
public void buriedColour_actionPerformed(ActionEvent e)\r
{\r
viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
- alignPanel.setColourScheme( );\r
+ changeColour();\r
}\r
\r
+ void changeColour()\r
+ {\r
+ if(abovePIDThreshold.isSelected())\r
+ abovePIDThreshold_actionPerformed(null);\r
+ else if(conservationMenuItem.isSelected())\r
+ conservationMenuItem_actionPerformed(null);\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ alignPanel.seqPanel.seqCanvas.paintFlag = true;\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ void addConservationOrPIDColour()\r
{\r
- viewport.setConservationSelected(conservationMenuItem.isSelected());\r
- conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );\r
- alignPanel.setColourScheme();\r
+ int x=0, y=0, threshold = 70;\r
+\r
+ if(sliderFrame!=null)\r
+ try\r
+ {\r
+ x = sliderFrame.getX();\r
+ y = sliderFrame.getY();\r
+ SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();\r
+ threshold = sp.getValue();\r
+ sliderFrame.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ { ex.printStackTrace(); }\r
+\r
+ ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
+\r
+ ConservationColourScheme ccs = null;\r
+ if (oldCs instanceof ConservationColourScheme)\r
+ ccs = (ConservationColourScheme) oldCs;\r
+\r
+ if(conservationMenuItem.isSelected())\r
+ {\r
+ Alignment al = (Alignment)viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3, al.getSequences(), 0,\r
+ al.getWidth() );\r
+\r
+ c.calculate();\r
+ c.verdict(false, 100);\r
+\r
+ if(ccs!=null)\r
+ ccs = new ConservationColourScheme(c, ccs.cs);\r
+ else\r
+ ccs = new ConservationColourScheme(c, oldCs);\r
+\r
+ viewport.setGlobalColourScheme( ccs );\r
+\r
+ }\r
+ else if(oldCs instanceof ConservationColourScheme)\r
+ {\r
+ oldCs = ccs.cs;\r
+ viewport.setGlobalColourScheme( oldCs );\r
+ }\r
+\r
+\r
+ if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )\r
+ {\r
+ sliderFrame = new JInternalFrame();\r
+ sliderFrame.setMaximizable(false);\r
+ sliderFrame.setResizable(false);\r
+\r
+ SliderPanel sp = null;\r
+ if (conservationMenuItem.isSelected())\r
+ {\r
+ if(threshold > 50)\r
+ threshold = 30;\r
+ sp = new SliderPanel(alignPanel, threshold, true,ccs);\r
+ Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment (Global colour)", 400, 90);\r
+ threshold = 0;\r
+ }\r
+ else if (abovePIDThreshold.isSelected())\r
+ {\r
+ sp = new SliderPanel(alignPanel, threshold, false, oldCs);\r
+ sp.cs = oldCs;\r
+ Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);\r
+ }\r
+\r
+ sliderFrame.setContentPane(sp);\r
+ if(x!=0 && y!=0)\r
+ sliderFrame.setLocation(x,y);\r
+\r
+ }\r
+ else\r
+ threshold = 0;\r
+\r
+\r
+ if (oldCs instanceof ResidueColourScheme)\r
+ {\r
+ ResidueColourScheme rcs = (ResidueColourScheme) oldCs;\r
+ rcs.setThreshold(threshold);\r
+ }\r
+ else if (oldCs instanceof ScoreColourScheme)\r
+ {\r
+ ScoreColourScheme scs = (ScoreColourScheme) oldCs;\r
+ scs.setThreshold(threshold);\r
+ }\r
+\r
+ alignPanel.seqPanel.seqCanvas.paintFlag = true;\r
+ alignPanel.repaint();\r
+\r
}\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
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if(abovePIDThreshold.isSelected())\r
+ abovePIDThreshold.setSelected(false);\r
\r
+ viewport.setConservationSelected(conservationMenuItem.isSelected());\r
\r
- public void abovePIDColour_actionPerformed(ActionEvent e)\r
+ addConservationOrPIDColour();\r
+ }\r
+\r
+ JInternalFrame sliderFrame;\r
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme(new PIDColourScheme());\r
- alignPanel.setColourScheme( );\r
+ if(conservationMenuItem.isSelected())\r
+ conservationMenuItem.setSelected(false);\r
+\r
+ addConservationOrPIDColour();\r
}\r
\r
\r
+\r
public void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
JInternalFrame frame = new JInternalFrame();\r
- UserDefinedColours chooser = new UserDefinedColours( frame, viewport );\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
- viewport.setGlobalColourScheme(new PIDColourScheme() );\r
+ viewport.setGlobalColourScheme( new PIDColourScheme() );\r
alignPanel.setColourScheme( );\r
}\r
\r
\r
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(sp);\r
+ Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
+ frame.setMaximizable(false);\r
+ frame.setResizable(false);\r
\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff