import jalview.datamodel.*;\r
import jalview.analysis.*;\r
import jalview.io.*;\r
-import MCview.*;\r
+import jalview.ws.*;\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 java.awt.datatransfer.*;\r
+\r
\r
public class AlignFrame extends GAlignFrame\r
{\r
getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
fontNameMenuItem.setText(viewport.getFont().getName());\r
fontSizeMenuItem.setText(viewport.getFont().getSize()+"");\r
+\r
+ addInternalFrameListener(new InternalFrameAdapter()\r
+ {\r
+ public void internalFrameActivated(InternalFrameEvent evt)\r
+ {\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ { alignPanel.requestFocus(); }\r
+ });\r
+\r
+ }\r
+ });\r
+\r
}\r
\r
protected void saveAs_actionPerformed(ActionEvent e)\r
{\r
- JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
+ JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
chooser.setToolTipText("Save");\r
int value = chooser.showSaveDialog(this);\r
if(value == JFileChooser.APPROVE_OPTION)\r
{\r
String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.LAST_DIRECTORY = choice;\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
try{\r
java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );\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
+ protected void createJPG_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;\r
+ int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();\r
+\r
+\r
+ if(!viewport.getWrapAlignment())\r
+ {\r
+ height = viewport.alignment.getHeight() * viewport.charHeight;\r
+ width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;\r
+ }\r
+\r
+ alignPanel.makeJPG( width, height);\r
+ }\r
+\r
+\r
public void printMenuItem_actionPerformed(ActionEvent e)\r
{\r
//Putting in a thread avoids Swing painting problems\r
}catch(Exception ex){}\r
}\r
\r
- ArrayList historyList = new ArrayList();\r
- ArrayList redoList = new ArrayList();\r
+ Stack historyList = new Stack();\r
+ Stack redoList = new Stack();\r
\r
void updateEditMenuBar()\r
{\r
alignPanel.RefreshPanels();\r
}\r
\r
+ public void moveSelectedSequences(boolean up)\r
+ {\r
+ SequenceGroup sg = viewport.getRubberbandGroup();\r
+ if (sg == null)\r
+ return;\r
+\r
+ if (up)\r
+ {\r
+ for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
+ {\r
+ SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+ if (!sg.sequences.contains(seq))\r
+ continue;\r
+\r
+ SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
+ if (sg.sequences.contains(temp))\r
+ continue;\r
+\r
+ viewport.alignment.getSequences().setElementAt(temp, i);\r
+ viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
+ {\r
+ SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+ if (!sg.sequences.contains(seq))\r
+ continue;\r
+\r
+ SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
+ if (sg.sequences.contains(temp))\r
+ continue;\r
+\r
+ viewport.alignment.getSequences().setElementAt(temp, i);\r
+ viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
+ }\r
+ }\r
+\r
+ alignPanel.RefreshPanels();\r
+ }\r
+\r
+\r
+\r
+ protected void copy_actionPerformed(ActionEvent e)\r
+ {\r
+ if(viewport.getRubberbandGroup()==null)\r
+ return;\r
+\r
+ SequenceGroup sg = viewport.getRubberbandGroup();\r
+\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ StringBuffer buffer= new StringBuffer();\r
+\r
+ for(int i=0; i<sg.getSize(); i++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
+ +seq.findPosition( sg.getEndRes() )+ "\t"\r
+ +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
+ }\r
+ c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
+\r
+ }\r
+\r
+\r
+ protected void pasteNew_actionPerformed(ActionEvent e)\r
+ {\r
+ paste(true);\r
+ }\r
+\r
+ protected void pasteThis_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem("Paste");\r
+ paste(false);\r
+ }\r
+\r
+ void paste(boolean newAlignment)\r
+ {\r
+ try{\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ Transferable contents = c.getContents(this);\r
+ if (contents == null)\r
+ return;\r
+\r
+ String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
+ StringTokenizer st = new StringTokenizer(str);\r
+ ArrayList seqs = new ArrayList();\r
+ while (st.hasMoreElements())\r
+ {\r
+ String name = st.nextToken();\r
+ int start = Integer.parseInt(st.nextToken());\r
+ int end = Integer.parseInt(st.nextToken());\r
+ Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
+\r
+ if(!newAlignment)\r
+ viewport.alignment.addSequence(sequence);\r
+ else\r
+ seqs.add(sequence);\r
+ }\r
+\r
+ if(newAlignment)\r
+ {\r
+ SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
+ seqs.toArray(newSeqs);\r
+ AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
+ int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
+ if (newHeight > 500)\r
+ newHeight = 500;\r
+ Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
+ }\r
+ else\r
+ {\r
+ viewport.setEndSeq(viewport.alignment.getHeight());\r
+ viewport.alignment.getWidth();\r
+ alignPanel.RefreshPanels();\r
+ }\r
+\r
+ }catch(Exception ex){}// could be anything being pasted in here\r
+\r
+ }\r
+\r
+\r
+ protected void cut_actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed(null);\r
+ delete_actionPerformed(null);\r
+ }\r
+\r
+ protected void delete_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem("Delete");\r
+ if (viewport.getRubberbandGroup() == null)\r
+ return;\r
+\r
+ SequenceGroup sg = viewport.getRubberbandGroup();\r
+ for (int i=0;i < sg.sequences.size(); i++)\r
+ viewport.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
+\r
+ viewport.alignment.deleteGroup(sg);\r
+ viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
+ if(viewport.getAlignment().getHeight()<1)\r
+ try\r
+ {\r
+ this.setClosed(true);\r
+ }catch(Exception ex){}\r
+ alignPanel.RefreshPanels();\r
+\r
+ }\r
+\r
+\r
\r
protected void redoMenuItem_actionPerformed(ActionEvent e)\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
+ protected void deleteGroups_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGroupEdit( groupEditingMenuItem.isSelected() );\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
Selection sel = viewport.getSelection();\r
\r
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ viewport.setRubberbandGroup(null);\r
viewport.getSelection().clear();\r
PaintRefresher.Refresh(null);\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
\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 renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
+ alignPanel.RefreshPanels();\r
+ }\r
+\r
+ public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
+ {\r
+ viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
+ if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
+ {\r
+ AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
+ ((Alignment)viewport.alignment).featuresAdded = true;\r
+ }\r
+ alignPanel.RefreshPanels();\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
protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme(null, false);\r
+ changeColour( null );\r
}\r
\r
\r
public void clustalColour_actionPerformed(ActionEvent e)\r
{\r
- // alignPanel.setColourScheme( new ClustalxColourScheme() );\r
+ abovePIDThreshold.setSelected(false);\r
+ changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
}\r
\r
public void zappoColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new ZappoColourScheme(), conservationMenuItem.isSelected() );\r
+ changeColour(new ZappoColourScheme());\r
}\r
\r
public void taylorColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new TaylorColourScheme(),conservationMenuItem.isSelected() );\r
+ changeColour(new TaylorColourScheme());\r
}\r
\r
\r
public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new HydrophobicColourScheme(),conservationMenuItem.isSelected() );\r
+ changeColour( new HydrophobicColourScheme() );\r
}\r
\r
public void helixColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new HelixColourScheme(),conservationMenuItem.isSelected() );\r
+ changeColour(new HelixColourScheme() );\r
}\r
\r
\r
public void strandColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new StrandColourScheme() ,conservationMenuItem.isSelected() );\r
+ changeColour(new StrandColourScheme());\r
}\r
\r
\r
public void turnColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new TurnColourScheme() ,conservationMenuItem.isSelected() );\r
+ changeColour(new TurnColourScheme());\r
}\r
\r
\r
public void buriedColour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new BuriedColourScheme() ,conservationMenuItem.isSelected() );\r
+ changeColour(new BuriedColourScheme() );\r
}\r
\r
+ public void nucleotideColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new NucleotideColourScheme());\r
+ }\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+\r
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme ( alignPanel.seqPanel.getColourScheme(),conservationMenuItem.isSelected() );\r
- conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );\r
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
}\r
\r
\r
\r
- public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
+ void changeColour(ColourSchemeI cs)\r
+ {\r
+\r
+ if(viewport.getColourAppliesToAllGroups())\r
+ {\r
+ Vector groups = viewport.alignment.getGroups();\r
+ for(int i=0; i<groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
+ sg.cs = cs;\r
+\r
+ if(abovePIDThreshold.isSelected())\r
+ abovePIDThreshold_actionPerformed(null);\r
+ else if( viewport.getConservationSelected() )\r
+ {\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, sg.getStartRes(),\r
+ sg.getEndRes());\r
+ c.calculate();\r
+ c.verdict(false, 100);\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
+\r
+ sg.cs = ccs;\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+\r
+ if ( viewport.getAbovePIDThreshold())\r
+ {\r
+ int threshold = 0;\r
+ threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
+ Desktop.hideConservationSlider();\r
+\r
+ if (cs instanceof ResidueColourScheme)\r
+ ( (ResidueColourScheme) cs).setThreshold(threshold);\r
+ else if (cs instanceof ScoreColourScheme)\r
+ ( (ScoreColourScheme) cs).setThreshold(threshold);\r
+\r
+ viewport.setGlobalColourScheme(cs);\r
+\r
+ }\r
+ else\r
+ if (cs instanceof ResidueColourScheme)\r
+ ( (ResidueColourScheme) cs).setThreshold(0);\r
+ else if (cs instanceof ScoreColourScheme)\r
+ ( (ScoreColourScheme) cs).setThreshold(0);\r
+\r
+\r
+\r
+\r
+if ( viewport.getConservationSelected() )\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
+ ConservationColourScheme ccs = null;\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
+ c.calculate();\r
+ c.verdict(false, 100);\r
+\r
+ ccs = new ConservationColourScheme(c, cs);\r
+\r
+ int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
+ "Background");\r
\r
+ ccs.inc = threshold;\r
+\r
+ viewport.setGlobalColourScheme(ccs);\r
+\r
+ }\r
+ else\r
+ viewport.setGlobalColourScheme( cs );\r
+\r
+ alignPanel.RefreshPanels();\r
+ }\r
\r
- public void abovePIDColour_actionPerformed(ActionEvent e)\r
+\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new PIDColourScheme() ,conservationMenuItem.isSelected() );\r
+ viewport.setConservationSelected(conservationMenuItem.isSelected());\r
+\r
+ viewport.setAbovePIDThreshold(false);\r
+ abovePIDThreshold.setSelected(false);\r
+ Desktop.hidePIDSlider();\r
+ if(!viewport.getConservationSelected())\r
+ Desktop.hideConservationSlider();\r
+\r
+ ColourSchemeI cs = viewport.getGlobalColourScheme();\r
+ if(cs instanceof ConservationColourScheme )\r
+ changeColour( ((ConservationColourScheme)cs).cs );\r
+ else\r
+ changeColour( cs );\r
+ }\r
+\r
+\r
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
+\r
+ conservationMenuItem.setSelected(false);\r
+ viewport.setConservationSelected(false);\r
+ Desktop.hideConservationSlider();\r
+\r
+ if(!viewport.getAbovePIDThreshold())\r
+ Desktop.hidePIDSlider();\r
+\r
+\r
+ ColourSchemeI cs = viewport.getGlobalColourScheme();\r
+ if(cs instanceof ConservationColourScheme )\r
+ changeColour( ((ConservationColourScheme)cs).cs );\r
+ else\r
+ changeColour( cs );\r
+\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
+ changeColour( new PIDColourScheme() );\r
}\r
\r
\r
public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) ,conservationMenuItem.isSelected() );\r
+ changeColour(new Blosum62ColourScheme(viewport) );\r
}\r
\r
\r
\r
- protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );\r
- Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);\r
- }\r
-\r
-\r
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
{\r
addHistoryItem("sort");\r
public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
{\r
addHistoryItem("sort");\r
- AlignmentSorter.sortGroups(viewport.getAlignment());\r
+ AlignmentSorter.sortByGroup(viewport.getAlignment());\r
AlignmentSorter.sortGroups(viewport.getAlignment());\r
alignPanel.RefreshPanels();\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
Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
}catch(java.lang.OutOfMemoryError ex)\r
{\r
- JOptionPane.showMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
+ JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
"Out of memory", JOptionPane.WARNING_MESSAGE);\r
}\r
\r
\r
void NewTreePanel(String type, String pwType, String title)\r
{\r
- JInternalFrame frame = new javax.swing.JInternalFrame();\r
+ //are the sequences aligned?\r
+ if(!viewport.alignment.isAligned())\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
+ "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
+ return;\r
+ }\r
+\r
TreePanel tp=null;\r
if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
{\r
tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
- viewport.getStartRes(), viewport.getEndRes());\r
+ 0, viewport.alignment.getWidth());\r
}\r
else\r
{\r
tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- type, pwType, viewport.getStartRes(),\r
- viewport.getEndRes());\r
+ type, pwType, 0, viewport.alignment.getWidth());\r
}\r
\r
- frame.setContentPane(tp);\r
- Desktop.addInternalFrame(frame, title, 600, 500);\r
+ Desktop.addInternalFrame(tp, title, 600, 500);\r
}\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
- public void pdbTest_actionPerformed(ActionEvent e)\r
+ class ClustalThread extends JPanel implements Runnable\r
{\r
- String reply = JOptionPane.showInputDialog(this, "Enter pdb code", "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
+ 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("/images/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
- 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
+ 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
+ af.clustalColour.setSelected(true);\r
+ af.clustalColour_actionPerformed(null);\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
git://source.jalview.org / jalview.git / blobdiff