import javax.swing.*;\r
import javax.swing.event.*;\r
import java.util.*;\r
-import java.awt.datatransfer.*;\r
+import java.awt.datatransfer.*;\r
\r
\r
public class AlignFrame extends GAlignFrame\r
{\r
final AlignmentPanel alignPanel;\r
final AlignViewport viewport;\r
+ public static final int NEW_WINDOW_WIDTH = 700;\r
+ public static final int NEW_WINDOW_HEIGHT = 500;\r
+\r
public AlignFrame(AlignmentI al)\r
{\r
+ try{\r
+ String ip = java.net.InetAddress.getLocalHost().getHostAddress();\r
+ if( !ip.startsWith("10."))\r
+ alignMenu.setVisible(false);\r
+ }\r
+ catch(java.net.UnknownHostException e){}\r
viewport = new AlignViewport(al,true,true,false);\r
\r
String fontName = jalview.bin.Cache.getProperty("FONT_NAME");\r
if(fontName!=null && fontStyle!=null && fontSize!=null)\r
viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
\r
-\r
- alignPanel = new AlignmentPanel(this, viewport);\r
- getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
-\r
// add conservation graph to alignment\r
viewport.updateConservation();\r
viewport.updateConsensus();\r
\r
+\r
+ alignPanel = new AlignmentPanel(this, viewport);\r
+\r
alignPanel.annotationPanel.adjustPanelHeight();\r
alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
\r
+ getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
+\r
\r
addInternalFrameListener(new InternalFrameAdapter()\r
{\r
else if(e.getActionCommand().equals("PFAM"))\r
suffix = new String[]{"pfam"};\r
\r
+\r
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
, suffix, e.getActionCommand()+" file");\r
chooser.setFileView(new JalviewFileView());\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, 500);\r
+ Desktop.addInternalFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
}\r
else\r
{\r
}\r
\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
\r
public void findMenuItem_actionPerformed(ActionEvent e)\r
{\r
- JInternalFrame frame = new JInternalFrame();\r
- Finder finder = new Finder(viewport, alignPanel, frame);\r
- frame.setContentPane(finder);\r
- Desktop.addInternalFrame(frame, "Find", 340,110);\r
+ JInternalFrame frame = new JInternalFrame();\r
+ Finder finder = new Finder(viewport, alignPanel, frame);\r
+ frame.setContentPane(finder);\r
+ Desktop.addInternalFrame(frame, "Find", 340,110, false);\r
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
\r
}\r
\r
\r
public void font_actionPerformed(ActionEvent e)\r
{\r
- // JOptionPane op = new JOptionPane();\r
JInternalFrame frame = new JInternalFrame();\r
FontChooser fc = new FontChooser( alignPanel, frame );\r
frame.setContentPane(fc);\r
{\r
viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
+ scaleAbove.setVisible( wrapMenuItem.isSelected() );\r
+ scaleLeft.setVisible( wrapMenuItem.isSelected() );\r
+ scaleRight.setVisible( wrapMenuItem.isSelected() );\r
+ alignPanel.RefreshPanels();\r
+ }\r
+\r
+ protected void scaleAbove_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
+ alignPanel.repaint();\r
}\r
\r
+ protected void scaleLeft_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ protected void scaleRight_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleRightWrapped(scaleRight.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+\r
\r
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
{\r
\r
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())\r
+ {\r
+ annotationPanelMenuItem.setSelected(false);\r
+ return;\r
+ }\r
+ viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );\r
alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );\r
}\r
\r
sg.sequences, sg.getStartRes(),\r
sg.getEndRes());\r
c.calculate();\r
- c.verdict(false, 100);\r
+ c.verdict(false, viewport.ConsPercGaps);\r
ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
-\r
sg.cs = ccs;\r
}\r
\r
}\r
\r
\r
- if ( viewport.getAbovePIDThreshold())\r
+ if ( viewport.getAbovePIDThreshold() )\r
{\r
- int threshold = 0;\r
- threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\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
+ // 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
Conservation c = new Conservation("All",\r
ResidueProperties.propHash, 3,\r
al.getSequences(), 0,\r
- al.getWidth());\r
+ al.getWidth()-1);\r
\r
c.calculate();\r
- c.verdict(false, 100);\r
+ c.verdict(false, viewport.ConsPercGaps);\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
alignPanel.RefreshPanels();\r
}\r
\r
+ protected void modifyPID_actionPerformed(ActionEvent e)\r
+ {\r
+ if(viewport.getAbovePIDThreshold())\r
+ Desktop.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background");\r
+ }\r
+\r
+ protected void modifyConservation_actionPerformed(ActionEvent e)\r
+ {\r
+ if(viewport.getConservationSelected())\r
+ Desktop.setConservationSliderSource(alignPanel, viewport.globalColourScheme, "Background");\r
+ }\r
+\r
\r
protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
{\r
JInternalFrame frame = new JInternalFrame();\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
- frame.setIconifiable(false);\r
- frame.setMaximizable(false);\r
+ Desktop.addInternalFrame(frame,"User defined colours", 450,540, false );\r
}\r
\r
public void PIDColour_actionPerformed(ActionEvent e)\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
- AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\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
+ Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);\r
\r
}\r
\r
return;\r
}\r
\r
- TreePanel tp=null;\r
- if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)\r
- {\r
- tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,\r
+ final TreePanel tp;\r
+ if (viewport.getSelectionGroup() != null &&\r
+ viewport.getSelectionGroup().getSize() > 3)\r
+ {\r
+ tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
+ pwType,\r
0, viewport.alignment.getWidth());\r
- }\r
- else\r
- {\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- type, pwType, 0, viewport.alignment.getWidth());\r
- }\r
+ }\r
+ else\r
+ {\r
+ tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
+ type, pwType, 0, viewport.alignment.getWidth());\r
+ }\r
+\r
+ addTreeMenuItem(tp, title);\r
\r
Desktop.addInternalFrame(tp, title, 600, 500);\r
}\r
\r
+ void addTreeMenuItem(final TreePanel treePanel, String title)\r
+ {\r
+ final JMenuItem item = new JMenuItem(title);\r
+ sortByTreeMenu.add(item);\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem("sort");\r
+ AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
+ alignPanel.RefreshPanels();\r
+ }\r
+ });\r
+\r
+ treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ sortByTreeMenu.remove(item);\r
+ };\r
+ });\r
\r
+ }\r
\r
\r
public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
{\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
+ WebserviceInfo info = new WebserviceInfo("Clustal web service",\r
+ "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+\r
+ " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."\r
+ +" Nucleic Acids Research, submitted, June 1994.",\r
+ 450, 150);\r
\r
+ ClustalThread thread = new ClustalThread(info);\r
+ thread.start();\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
+ class ClustalThread extends Thread\r
{\r
- this.frame = frame;\r
- image = new Image[9];\r
- for(int i=0; i<9; i++)\r
+ WebserviceInfo info;\r
+ public ClustalThread(WebserviceInfo info)\r
+ {this.info = info; }\r
+\r
+ public void run()\r
{\r
- java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");\r
- if (url != null)\r
+ info.setStatus(WebserviceInfo.STATE_RUNNING);\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
- 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
+ seqs[i] = (SequenceI) sv.elementAt(i);\r
}\r
- }\r
- DNATwirler twirler = new DNATwirler();\r
- twirler.start();\r
- webServiceRunning = true;\r
- }\r
+ while (++i < sv.size());\r
\r
- class DNATwirler extends Thread\r
- {\r
- public void run()\r
- {\r
- while(webServiceRunning)\r
+ SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
+ if (alignment != null)\r
+ {\r
+ AlignFrame af = new AlignFrame(new Alignment(alignment));\r
+ Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),\r
+ NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
+ af.clustalColour_actionPerformed(null);\r
+ af.clustalColour.setSelected(true);\r
+ info.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
+ }\r
+ else\r
{\r
- try{\r
- Thread.sleep(100);\r
- imageIndex++;\r
- imageIndex %=9;\r
- repaint();\r
- }\r
- catch(Exception ex){}\r
+ info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ info.appendProgressText("Problem obtaining clustal alignment");\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
protected void jpred_actionPerformed(ActionEvent e)\r
{\r
\r
- JInternalFrame frame = new JInternalFrame();\r
if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)\r
{\r
// JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
SequenceGroup seqs = viewport.getSelectionGroup();\r
if (seqs.getSize() == 1 || !viewport.alignment.isAligned())\r
{\r
- JPredClient ct = new JPredClient( (SequenceI)\r
- seqs.getSequenceAt(0));\r
+ JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));\r
}\r
else\r
{\r
tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
fin, "FromFile", choice);\r
Desktop.addInternalFrame(tp, title, 600, 500);\r
+ addTreeMenuItem(tp, title);\r
}\r
}\r
catch (Exception ex)\r
git://source.jalview.org / jalview.git / blobdiff