import jalview.datamodel.*;\r
import jalview.analysis.*;\r
import jalview.io.*;\r
-import java.awt.event.*;\r
+import jalview.ws.*;\r
+import MCview.*;\r
import java.awt.*;\r
+import java.awt.event.*;\r
+import java.awt.print.*;\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
- AlignmentPanel alignPanel;\r
- AlignViewport viewport;\r
+ final AlignmentPanel alignPanel;\r
+ final AlignViewport viewport;\r
public AlignFrame(AlignmentI al)\r
{\r
super();\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
- public void saveAsPostscriptMenuItem_actionPerformed(ActionEvent e)\r
+ public void printMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ //Putting in a thread avoids Swing painting problems\r
+ PrintThread thread = new PrintThread();\r
+ thread.start();\r
+ }\r
+\r
+ class PrintThread extends Thread\r
+ {\r
+ public void run()\r
+ {\r
+ PrinterJob printJob = PrinterJob.getPrinterJob();\r
+ PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
+ printJob.setPrintable(alignPanel, pf);\r
+ if (printJob.printDialog())\r
+ {\r
+ try\r
+ {\r
+ printJob.print();\r
+ }\r
+ catch (Exception PrintException)\r
+ {\r
+ PrintException.printStackTrace();\r
+ }\r
+ }\r
+ }\r
\r
}\r
\r
+\r
+\r
+\r
public void closeMenuItem_actionPerformed(ActionEvent e)\r
{\r
try{\r
}catch(Exception ex){}\r
}\r
\r
- public void groupsMenuItem_actionPerformed(ActionEvent e)\r
+ ArrayList historyList = new ArrayList();\r
+ ArrayList redoList = new ArrayList();\r
+\r
+ void updateEditMenuBar()\r
{\r
+ if(historyList.size()>0)\r
+ {\r
+ undoMenuItem.setEnabled(true);\r
+ Object [] history = (Object[])historyList.get(0);\r
+ undoMenuItem.setText("Undo "+history[0]);\r
+ }\r
+ else\r
+ {\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setText("Undo");\r
+ }\r
+\r
+ if(redoList.size()>0)\r
+ {\r
+ redoMenuItem.setEnabled(true);\r
+ Object [] history = (Object[])redoList.get(0);\r
+ redoMenuItem.setText("Redo "+history[0]);\r
+ }\r
+ else\r
+ {\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setText("Redo");\r
+ }\r
+ }\r
+\r
+ public void addHistoryItem(String type)\r
+ {\r
+ // must make sure we add new sequence objects her, not refs to the existing sequences\r
+ redoList.clear();\r
+ SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
+ for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
+ {\r
+ seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
+ viewport.getAlignment().getSequenceAt(i).getSequence());\r
+ }\r
+\r
+ historyList.add(0, new Object[]{type, seq} );\r
+ updateEditMenuBar();\r
+ }\r
+\r
+ protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ Object [] history = (Object[])historyList.remove(0);\r
+ // add the redo state before continuing!!\r
+ SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
+ for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
+ {\r
+ seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
+ viewport.getAlignment().getSequenceAt(i).\r
+ getSequence());\r
+ }\r
+ /////////\r
+\r
+ redoList.add(0, new Object[] {history[0], seq});\r
+\r
+ seq = (SequenceI[]) history[1];\r
+ viewport.setAlignment( new Alignment(seq) );\r
+ updateEditMenuBar();\r
+ alignPanel.RefreshPanels();\r
+ }\r
+\r
\r
+ protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ Object [] history = (Object[])redoList.remove(0);\r
+ SequenceI[] seq = (SequenceI[]) history[1];\r
+ viewport.setAlignment( new Alignment(seq) );\r
+ updateEditMenuBar();\r
+ alignPanel.RefreshPanels();\r
}\r
\r
- public void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
+\r
+ public void groupsMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(geditor);\r
+ Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
+ frame.setResizable(false);\r
+ }\r
\r
+ protected void deleteGroups_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.alignment.deleteAllGroups();\r
+ alignPanel.RefreshPanels();\r
}\r
\r
+\r
+\r
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
Selection sel = viewport.getSelection();\r
PaintRefresher.Refresh(null);\r
}\r
\r
- public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\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
-\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
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ addHistoryItem("delete columns");\r
ColumnSelection colSel = viewport.getColumnSelection();\r
if (colSel.size() > 0)\r
{\r
\r
public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ addHistoryItem("delete columns");\r
ColumnSelection colSel = viewport.getColumnSelection();\r
if (colSel.size() > 0)\r
{\r
\r
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ addHistoryItem("delete gapped columns");\r
viewport.getAlignment().removeGaps();\r
alignPanel.RefreshPanels();\r
}\r
\r
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ addHistoryItem("delete all gaps");\r
SequenceI current;\r
int jSize;\r
for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\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
\r
public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
{\r
- String thisChar = "-";\r
- String nextChar = ".";\r
- if(viewport.getGapCharacter().equals("-"))\r
+ char thisChar = '-';\r
+ char nextChar = '.';\r
+ if(viewport.getGapCharacter()=='-')\r
{\r
- thisChar = ".";\r
- nextChar = "-";\r
+ thisChar = '.';\r
+ nextChar = '-';\r
}\r
setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
viewport.setGapCharacter(thisChar);\r
+ alignPanel.RefreshPanels();\r
+ }\r
+\r
+ public void findMenuItem_actionPerformed(ActionEvent e)\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(340,110);\r
+ frame.setVisible(true);\r
}\r
\r
\r
+\r
public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
{\r
String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
\r
\r
- String selection = JOptionPane.showInputDialog(this,\r
+ String selection = JOptionPane.showInternalInputDialog(this,\r
"Select font",\r
"Font selection",\r
JOptionPane.QUESTION_MESSAGE,\r
\r
public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
{\r
- String selection = JOptionPane.showInputDialog(this,\r
+ String selection = JOptionPane.showInternalInputDialog(this,\r
"Select font size",\r
"Font size",\r
JOptionPane.QUESTION_MESSAGE,\r
\r
public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
{\r
- String selection = JOptionPane.showInputDialog(this,\r
+ String selection = JOptionPane.showInternalInputDialog(this,\r
"Select font style",\r
"Font style",\r
JOptionPane.QUESTION_MESSAGE,\r
\r
protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
- viewport.setColourText( colourTextMenuItem.isSelected() );\r
- alignPanel.RefreshPanels();\r
+ viewport.setColourText( colourTextMenuItem.isSelected() );\r
+ alignPanel.RefreshPanels();\r
}\r
\r
void SetFont()\r
\r
}\r
\r
+ protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
+ alignPanel.RefreshPanels();\r
+ }\r
+\r
+\r
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
}\r
\r
\r
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setRenderGaps(renderGapsMenuItem.isSelected());\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
alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\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
}catch(java.lang.OutOfMemoryError ex)\r
{\r
- JOptionPane.showMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!",\r
+ JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
+ +"\nTry reducing the font size.",\r
"Out of memory", JOptionPane.WARNING_MESSAGE);\r
}\r
\r
\r
}\r
\r
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setGlobalColourScheme( null );\r
+ changeColour();\r
+ }\r
+\r
\r
- public void clustalColour_actionPerformed(ActionEvent e)\r
+ public void Colour_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
- alignPanel.setColourScheme( new ZappoColourScheme() );\r
+ viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
+ changeColour();\r
}\r
\r
public void taylorColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new TaylorColourScheme() );\r
+ viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
+ changeColour();\r
}\r
\r
\r
public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new HydrophobicColourScheme() );\r
+ viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
+ changeColour();\r
}\r
\r
public void helixColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.seqPanel.setColourScheme( new HelixColourScheme() );\r
+ viewport.setGlobalColourScheme( new HelixColourScheme() );\r
+ changeColour();\r
}\r
\r
+\r
public void strandColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new StrandColourScheme() );\r
+ viewport.setGlobalColourScheme(new StrandColourScheme() );\r
+ changeColour();\r
}\r
\r
+\r
public void turnColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new TurnColourScheme() );\r
+ viewport.setGlobalColourScheme(new TurnColourScheme() );\r
+ changeColour();\r
}\r
\r
+\r
public void buriedColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new BuriedColourScheme() );\r
+ viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
+ changeColour();\r
}\r
\r
- public void conservationColour_actionPerformed(ActionEvent e)\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
+ abovePIDThreshold_actionPerformed(null);\r
+ else if(conservationMenuItem.isSelected())\r
+ conservationMenuItem_actionPerformed(null);\r
+\r
\r
+ alignPanel.RefreshPanels();\r
}\r
\r
- public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ void addConservationOrPIDColour()\r
+ {\r
+ int x=0, y=0, threshold = 70;\r
\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
- public void abovePIDColour_actionPerformed(ActionEvent e)\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
+\r
+ }\r
+\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new PIDColourScheme() );\r
+ if(abovePIDThreshold.isSelected())\r
+ abovePIDThreshold.setSelected(false);\r
+\r
+ viewport.setConservationSelected(conservationMenuItem.isSelected());\r
+\r
+ addConservationOrPIDColour();\r
}\r
\r
+ JInternalFrame sliderFrame;\r
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ {\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, 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() );\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) );\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
\r
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ addHistoryItem("sort");\r
AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
alignPanel.RefreshPanels();\r
}\r
\r
public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ addHistoryItem("sort");\r
AlignmentSorter.sortByID( viewport.getAlignment() );\r
alignPanel.RefreshPanels();\r
}\r
\r
public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
{\r
- AlignmentSorter.sortGroups(viewport.getAlignment());\r
+ addHistoryItem("sort");\r
+ AlignmentSorter.sortByGroup(viewport.getAlignment());\r
AlignmentSorter.sortGroups(viewport.getAlignment());\r
alignPanel.RefreshPanels();\r
}\r
\r
public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ addHistoryItem("sort");\r
if(viewport.getCurrentTree()==null)\r
return;\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
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
{\r
if(viewport.getSelection().size()<2)\r
- JOptionPane.showMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
+ JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
else\r
{\r
JInternalFrame frame = new JInternalFrame();\r
if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
|| viewport.getAlignment().getHeight()<4)\r
{\r
- JOptionPane.showMessageDialog(this, "Principal component analysis must take\n"\r
+ JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
+"at least 4 input sequences.",\r
"Sequence selection insufficient",\r
JOptionPane.WARNING_MESSAGE);\r
return;\r
}\r
\r
- PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(pcaPanel);\r
- Desktop.addInternalFrame(frame, "Principal component analysis", 400,400);\r
+ try{\r
+ PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(pcaPanel);\r
+ Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
+ }catch(java.lang.OutOfMemoryError ex)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
+ "Out of memory", JOptionPane.WARNING_MESSAGE);\r
+ }\r
+\r
+\r
}\r
\r
public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
\r
\r
\r
+\r
public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
{\r
- JOptionPane.showMessageDialog(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 =\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
+ url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;\r
+\r
+ try\r
+ {\r
+ PDBfile pdb = new PDBfile(url,\r
+ "URL");\r
+ Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);\r
+ seq.setPDBfile(pdb);\r
+ ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;\r
+ ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;\r
+ // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();\r
+\r
+ rotCanvas rc = new rotCanvas(pdb);\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(rc);\r
+ Desktop.addInternalFrame(frame, url, 400,400);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ }\r
+\r
+\r
+ public void doKeyPressed(KeyEvent evt)\r
+ {\r
+\r
+ System.out.println(evt.getKeyChar());\r
+ if(evt.isControlDown() && evt.getKeyChar()=='f')\r
+ findMenuItem_actionPerformed(null);\r
+\r
+ }\r
+\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff