import jalview.datamodel.*;\r
import jalview.analysis.*;\r
import jalview.io.*;\r
+import jalview.ws.*;\r
import MCview.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
import javax.swing.*;\r
import javax.swing.event.*;\r
import java.util.*;\r
+import jalview.datamodel.SequenceI;\r
\r
public class AlignFrame extends GAlignFrame\r
{\r
public AlignFrame(AlignmentI al)\r
{\r
super();\r
+\r
viewport = new AlignViewport(al,true,true,true,false);\r
alignPanel = new AlignmentPanel(this, viewport);\r
getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
fontNameMenuItem.setText(viewport.getFont().getName());\r
fontSizeMenuItem.setText(viewport.getFont().getSize()+"");\r
+\r
+ clustalColour.setSelected(true);\r
+ clustalColour_actionPerformed(null);\r
}\r
\r
protected void saveAs_actionPerformed(ActionEvent e)\r
frame.setResizable(false);\r
}\r
\r
+ protected void deleteGroups_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.alignment.deleteAllGroups();\r
+ viewport.getSelection().clear();\r
+\r
+ alignPanel.RefreshPanels();\r
+ }\r
+\r
+\r
\r
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
\r
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ viewport.setRubberbandGroup(null);\r
viewport.getSelection().clear();\r
PaintRefresher.Refresh(null);\r
}\r
JOptionPane op = new JOptionPane();\r
JInternalFrame frame = op.createInternalFrame(this, "Find");\r
Finder finder = new Finder(viewport, alignPanel, frame);\r
+ frame.setClosable(true);\r
frame.setContentPane(finder);\r
- frame.setSize(300,110);\r
+ frame.setSize(340,110);\r
frame.setVisible(true);\r
}\r
\r
protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
- alignPanel.RefreshPanels();\r
+ alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
}\r
\r
\r
alignPanel.RefreshPanels();\r
}\r
\r
+ public void secondaryStructure_actionPerformed(ActionEvent evt)\r
+ {\r
+ alignPanel.setSecondaryStructureVisible(secondaryStructure.isSelected());\r
+ }\r
\r
public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
{\r
\r
public void overviewMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ if (alignPanel.overviewPanel != null)\r
+ return;\r
\r
JInternalFrame frame = new JInternalFrame();\r
OverviewPanel overview = alignPanel.getOverviewPanel();\r
\r
public void clustalColour_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme(new ClustalxColourScheme( ));\r
+ viewport.setGlobalColourScheme(\r
+ new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
+ abovePIDThreshold.setSelected(false);\r
changeColour();\r
}\r
\r
changeColour();\r
}\r
\r
+ public void nucleotideColour_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setGlobalColourScheme( new NucleotideColourScheme() );\r
+ changeColour();\r
+ }\r
+\r
+\r
void changeColour()\r
{\r
if(abovePIDThreshold.isSelected())\r
- {\r
abovePIDThreshold_actionPerformed(null);\r
- alignPanel.setColourScheme( );\r
- }\r
else if(conservationMenuItem.isSelected())\r
conservationMenuItem_actionPerformed(null);\r
- else\r
- alignPanel.setColourScheme( );\r
\r
+ alignPanel.RefreshPanels();\r
}\r
\r
+\r
protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
{\r
- viewport.setConservationSelected(conservationMenuItem.isSelected());\r
+ if(abovePIDThreshold.isSelected())\r
+ {\r
+ abovePIDThreshold.setSelected(false);\r
+ Desktop.hidePIDSlider();\r
+ }\r
\r
- alignPanel.setColourScheme();\r
- ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
+ viewport.setConservationSelected(conservationMenuItem.isSelected());\r
\r
- if(conservationMenuItem.isSelected())\r
- {\r
- if(sliderPanel!=null)\r
- {\r
- sliderPanel.cs = oldCs;\r
- }\r
+ ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
\r
- else\r
- {\r
- sliderPanel = new SliderPanel(alignPanel, 30, true,\r
- viewport.getGlobalColourScheme());\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(sliderPanel);\r
- Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,\r
- 90);\r
- frame.setMaximizable(false);\r
- frame.setResizable(false);\r
- frame.addInternalFrameListener(new javax.swing.event.\r
- InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(javax.swing.event.InternalFrameEvent\r
- evt)\r
- {\r
- sliderPanel = null;\r
- };\r
- });\r
- }\r
- }\r
- else\r
- {\r
- if(oldCs instanceof ConservationColourScheme)\r
- {\r
- ConservationColourScheme ccs = (ConservationColourScheme)oldCs;\r
- viewport.setGlobalColourScheme( ccs.cs );\r
- }\r
- alignPanel.setColourScheme();\r
- }\r
+ ConservationColourScheme ccs = null;\r
+ if (oldCs instanceof ConservationColourScheme)\r
+ ccs = (ConservationColourScheme) oldCs;\r
\r
- }\r
+ if (conservationMenuItem.isSelected())\r
+ {\r
+ Alignment al = (Alignment) viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth());\r
\r
- SliderPanel sliderPanel;\r
- public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
- {\r
- ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
- int threshold = 0;\r
+ c.calculate();\r
+ c.verdict(false, 100);\r
\r
- if(abovePIDThreshold.isSelected())\r
- {\r
- if(sliderPanel!=null)\r
- sliderPanel.cs = oldCs;\r
+ if (ccs != null)\r
+ ccs = new ConservationColourScheme(c, ccs.cs);\r
+ else\r
+ ccs = new ConservationColourScheme(c, oldCs);\r
\r
- else\r
- {\r
- sliderPanel = new SliderPanel(alignPanel, 70, false, oldCs);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(sliderPanel);\r
- Desktop.addInternalFrame(frame, "Percentage Identity Threshold", 400,\r
- 90);\r
- frame.setMaximizable(false);\r
- frame.setResizable(false);\r
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
- {\r
- sliderPanel = null;\r
- };\r
- });\r
\r
- }\r
+ int threshold = Desktop.setConservationSliderSource(alignPanel, ccs, "Background");\r
\r
- threshold = sliderPanel.getValue();\r
- }\r
+ ccs.inc = threshold;\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
+ if (ccs.cs instanceof ResidueColourScheme)\r
+ ((ResidueColourScheme) ccs.cs).setThreshold(0);\r
+ else if (ccs.cs instanceof ScoreColourScheme)\r
+ ((ScoreColourScheme)ccs.cs).setThreshold(0);\r
+\r
+ viewport.setGlobalColourScheme(ccs);\r
+\r
+\r
+ }\r
+ else if (oldCs instanceof ConservationColourScheme)\r
+ {\r
+ /// ie, if we remove ConservationColourScheme from backgroundColour\r
+ oldCs = ccs.cs;\r
+ viewport.setGlobalColourScheme(oldCs);\r
+ Desktop.hideConservationSlider();\r
+ }\r
+\r
+ if(e!=null)\r
+ alignPanel.RefreshPanels();\r
+ }\r
+\r
+\r
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ {\r
+ if(conservationMenuItem.isSelected())\r
+ conservationMenuItem.setSelected(false);\r
+\r
+ ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
+ int threshold = 0;\r
+ if (oldCs instanceof ConservationColourScheme)\r
+ {\r
+ ConservationColourScheme ccs = (ConservationColourScheme) oldCs;\r
+ oldCs = ccs.cs;\r
+ }\r
+\r
+ if(abovePIDThreshold.isSelected())\r
+ {\r
+ threshold = Desktop.setPIDSliderSource(alignPanel, oldCs, "Background");\r
+ Desktop.hideConservationSlider();\r
+ }\r
+ else\r
+ Desktop.hidePIDSlider();\r
\r
- alignPanel.setColourScheme();\r
+ if (oldCs instanceof ResidueColourScheme)\r
+ ((ResidueColourScheme) oldCs).setThreshold(threshold);\r
+ else if (oldCs instanceof ScoreColourScheme)\r
+ ((ScoreColourScheme)oldCs).setThreshold(threshold);\r
\r
+ viewport.setGlobalColourScheme(oldCs);\r
+ if(e!=null)\r
+ alignPanel.RefreshPanels();\r
}\r
\r
\r
public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
{\r
viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) );\r
- alignPanel.setColourScheme();\r
+ changeColour();\r
}\r
\r
\r
\r
- protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );\r
- Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);\r
- }\r
-\r
-\r
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
{\r
addHistoryItem("sort");\r
\r
\r
\r
+\r
public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
{\r
- JOptionPane.showInternalMessageDialog(this, "Jalview is currently being reengineered"\r
- +"\nwithin the Barton Group, Dundee University."\r
- +"\nThis will be available as a web service 2005",\r
- "Web service", JOptionPane.INFORMATION_MESSAGE);\r
+ JInternalFrame frame = new JInternalFrame();\r
+ ClustalThread ct = new ClustalThread(frame);\r
+ Thread t = new Thread(ct);\r
+ t.start();\r
+ frame.setContentPane(ct);\r
+ Desktop.addInternalFrame(frame, title, 300, 80);\r
+\r
+ }\r
+\r
+ class ClustalThread extends JPanel implements Runnable\r
+ {\r
+ Image [] image;\r
+ int imageIndex = 0;\r
+ boolean webServiceRunning = false;\r
+ JInternalFrame frame;\r
+ public ClustalThread(JInternalFrame frame)\r
+ {\r
+ this.frame = frame;\r
+ image = new Image[9];\r
+ for(int i=0; i<9; i++)\r
+ {\r
+ java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");\r
+ if (url != null)\r
+ {\r
+ image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
+ MediaTracker mt = new MediaTracker(this);\r
+ mt.addImage(image[i], i);\r
+ try{mt.waitForID(i);}\r
+ catch(Exception ex){}\r
+ }\r
+ }\r
+ DNATwirler twirler = new DNATwirler();\r
+ twirler.start();\r
+ webServiceRunning = true;\r
+ }\r
+\r
+ class DNATwirler extends Thread\r
+ {\r
+ public void run()\r
+ {\r
+ while(webServiceRunning)\r
+ {\r
+ try{\r
+ Thread.sleep(100);\r
+ imageIndex++;\r
+ imageIndex %=9;\r
+ repaint();\r
+ }\r
+ catch(Exception ex){}\r
+ }\r
+ }\r
+ }\r
+\r
+ // JBPNote\r
+ // Should check to see if the server settings are valid\r
+ // Need visual-delay indication here.\r
+ public void run()\r
+ {\r
+ jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
+ Vector sv = viewport.getAlignment().getSequences();\r
+ SequenceI[] seqs = new SequenceI[sv.size()];\r
+\r
+ int i = 0;\r
+ do\r
+ {\r
+ seqs[i] = (SequenceI) sv.elementAt(i);\r
+ }\r
+ while (++i < sv.size());\r
+\r
+ SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
+\r
+ if (alignment != null)\r
+ {\r
+ AlignFrame af = new AlignFrame(new Alignment(alignment));\r
+ Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
+ 700, 500); // JBPNote - is there a new window geom. property ?\r
+ }\r
+ else\r
+ JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ webServiceRunning = false;\r
+ try{\r
+ frame.setClosed(true);\r
+ }catch(Exception ex){}\r
+ }\r
+\r
+ public void paintComponent(Graphics g)\r
+ {\r
+ g.setColor(Color.white);\r
+ g.fillRect(0,0,getWidth(), getHeight());\r
+ if(image!=null)\r
+ {\r
+ g.drawImage(image[imageIndex],10,10,this);\r
+ }\r
+ g.setFont(new Font("Arial", Font.BOLD, 12));\r
+ g.setColor(Color.black);\r
+ g.drawString("Clustal Alignment Web Service running", 30,30);\r
+ }\r
+\r
+\r
}\r
\r
+\r
public void pdbTest_actionPerformed(ActionEvent e)\r
{\r
- String reply = JOptionPane.showInternalInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE);\r
+ String reply =\r
+ JOptionPane.showInternalInputDialog(this, "Enter pdb code",\r
+ "PDB test viewer", JOptionPane.QUESTION_MESSAGE);\r
\r
String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";\r
if (reply.length()>1)\r
git://source.jalview.org / jalview.git / blobdiff