c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
-\r
sg.cs = ccs;\r
}\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, viewport.ConsPercGaps);\r
\r
ccs = new ConservationColourScheme(c, cs);\r
\r
- // int threshold = Desktop.setConservationSliderSource(alignPanel, ccs, "Background");\r
-\r
- // ccs.inc = threshold;\r
-\r
viewport.setGlobalColourScheme(ccs);\r
\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
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, 320, 90);\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 angle = 0;\r
- boolean webServiceRunning = false;\r
- JInternalFrame frame;\r
- public ClustalThread(JInternalFrame frame)\r
+ class ClustalThread extends Thread\r
{\r
- this.frame = frame;\r
+ WebserviceInfo info;\r
+ public ClustalThread(WebserviceInfo info)\r
+ {this.info = info; }\r
\r
- java.net.URL url = getClass().getResource("/images/logo.gif");\r
- if (url != null)\r
+ public void run()\r
{\r
- image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
- MediaTracker mt = new MediaTracker(this);\r
- mt.addImage(image, 0);\r
- try\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
- mt.waitForID(0);\r
+ seqs[i] = (SequenceI) sv.elementAt(i);\r
}\r
- catch (Exception ex)\r
- {}\r
- }\r
+ while (++i < sv.size());\r
\r
- ImageSpinner spinner = new ImageSpinner();\r
- spinner.start();\r
- webServiceRunning = true;\r
- }\r
-\r
- class ImageSpinner 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(10);\r
- angle+=1;\r
- angle %=360;\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
- Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
- af.clustalColour_actionPerformed(null);\r
- af.clustalColour.setSelected(true);\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 g1)\r
- {\r
- Graphics2D g = (Graphics2D)g1;\r
- g.setColor(Color.white);\r
- g.fillRect(0,0,getWidth(), getHeight());\r
- if(image!=null)\r
- {\r
-\r
- g.rotate (Math.toRadians(angle), 28, 28);\r
-\r
- g.drawImage(image,10,10,this);\r
- g.rotate (-Math.toRadians(angle), 28, 28 );\r
- }\r
- g.setFont(new Font("Arial", Font.BOLD, 12));\r
- g.setColor(Color.black);\r
- g.drawString("Clustal Alignment Web Service running", 60,30);\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
git://source.jalview.org / jalview.git / blobdiff