import jalview.structure.*;\r
import jalview.datamodel.PDBEntry;\r
import jalview.io.*;\r
+import jalview.schemes.*;\r
\r
import org.jmol.api.*;\r
import org.jmol.adapter.smarter.SmarterJmolAdapter;\r
PDBEntry pdbentry;\r
SequenceI[] sequence;\r
StructureSelectionManager ssm;\r
+ JSplitPane splitPane;\r
RenderPanel renderPanel;\r
AlignmentPanel ap;\r
String fileLoadingError;\r
+ boolean colourBySequence = true;\r
+\r
+ public AppJMol(String file, String id,\r
+ SequenceI[] seq,\r
+ AlignmentPanel ap,\r
+ String loadStatus,\r
+ Rectangle bounds)\r
+ {\r
+ pdbentry = new PDBEntry();\r
+ pdbentry.setFile(file);\r
+ pdbentry.setId(id);\r
+ this.sequence = seq;\r
+ this.ap = ap;\r
+ this.setBounds(bounds);\r
+\r
+ colourBySequence = false;\r
+ seqColour.setSelected(false);\r
+\r
+ jalview.gui.Desktop.addInternalFrame(this, "Loading File",\r
+ bounds.width,bounds.height);\r
+\r
+ initJmol(loadStatus);\r
+\r
+ this.addInternalFrameListener(new InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosing(InternalFrameEvent internalFrameEvent)\r
+ {\r
+ closeViewer();\r
+ }\r
+ });\r
+ }\r
\r
public AppJMol(PDBEntry pdbentry, SequenceI[] seq, AlignmentPanel ap)\r
{\r
String alreadyMapped = StructureSelectionManager\r
.getStructureSelectionManager()\r
.alreadyMappedToFile(pdbentry.getId());\r
+\r
if (alreadyMapped != null)\r
{\r
int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
this.pdbentry = pdbentry;\r
this.sequence = seq;\r
\r
- renderPanel = new RenderPanel();\r
- this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);\r
-\r
jalview.gui.Desktop.addInternalFrame(this, "Loading File", 400, 400);\r
\r
if (pdbentry.getFile() != null)\r
{\r
- initJmol();\r
+ initJmol("load \""+pdbentry.getFile()+"\"");\r
}\r
else\r
{\r
});\r
}\r
\r
- void initJmol()\r
+ void initJmol(String command)\r
{\r
+ renderPanel = new RenderPanel();\r
+\r
+ this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);\r
+\r
StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +\r
pdbentry.getId());\r
\r
viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,\r
new SmarterJmolAdapter());\r
\r
+\r
viewer.setAppletContext("", null, null, "");\r
\r
viewer.setJmolStatusListener(this);\r
\r
- scriptWindow = new ScriptWindow(viewer);\r
-\r
jmolpopup = JmolPopup.newJmolPopup(viewer);\r
\r
- viewer.openFile(pdbentry.getFile());\r
-\r
+ viewer.evalStringQuiet(command);\r
}\r
\r
\r
String query = "pdb:" + pdbentry.getId();\r
pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")\r
.getAbsolutePath());\r
- initJmol();\r
+ initJmol("load "+pdbentry.getFile());\r
}\r
catch (Exception ex)\r
{\r
}\r
}\r
\r
+\r
+ public void seqColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ colourBySequence = seqColour.isSelected();\r
+ colourBySequence(ap);\r
+ }\r
+\r
+ public void chainColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ colourBySequence = false;\r
+ seqColour.setSelected(false);\r
+ viewer.evalStringQuiet("select *;color chain");\r
+ }\r
+\r
+ public void chargeColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ colourBySequence = false;\r
+ seqColour.setSelected(false);\r
+ viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"\r
+ +"select LYS,ARG;color blue;select CYS;color yellow");\r
+ }\r
+\r
+ public void zappoColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ setJalviewColourScheme(new ZappoColourScheme());\r
+ }\r
+\r
+ public void taylorColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ setJalviewColourScheme(new TaylorColourScheme());\r
+ }\r
+\r
+ public void hydroColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ setJalviewColourScheme(new HydrophobicColourScheme());\r
+ }\r
+\r
+ public void helixColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ setJalviewColourScheme(new HelixColourScheme());\r
+ }\r
+\r
+ public void strandColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ setJalviewColourScheme(new StrandColourScheme());\r
+ }\r
+\r
+ public void turnColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ setJalviewColourScheme(new TurnColourScheme());\r
+ }\r
+\r
+ public void buriedColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ setJalviewColourScheme(new BuriedColourScheme());\r
+ }\r
+\r
+ public void setJalviewColourScheme(ColourSchemeI cs)\r
+ {\r
+ colourBySequence = false;\r
+ seqColour.setSelected(false);\r
+\r
+ if(cs==null)\r
+ return;\r
+\r
+ String res;\r
+ int index;\r
+ Color col;\r
+\r
+ Enumeration en = ResidueProperties.aa3Hash.keys();\r
+ StringBuffer command = new StringBuffer("select *;color white;");\r
+ while(en.hasMoreElements())\r
+ {\r
+ res = en.nextElement().toString();\r
+ index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();\r
+ if(index>20)\r
+ continue;\r
+\r
+ col = cs.findColour(ResidueProperties.aa[index].charAt(0));\r
+\r
+ command.append("select "+res+";color["\r
+ + col.getRed() + ","\r
+ + col.getGreen() + ","\r
+ + col.getBlue() + "];");\r
+ }\r
+\r
+ viewer.evalStringQuiet(command.toString());\r
+ }\r
+\r
+ public void userColour_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ new UserDefinedColours(this, null);\r
+ }\r
+\r
+ public void backGround_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ java.awt.Color col = JColorChooser.showDialog(this,\r
+ "Select Background Colour",\r
+ null);\r
+\r
+ if (col != null)\r
+ {\r
+ viewer.evalStringQuiet("background ["\r
+ + col.getRed() + ","\r
+ + col.getGreen() + ","\r
+ + col.getBlue() + "];");\r
+ }\r
+ }\r
+\r
+\r
//////////////////////////////////\r
///StructureListener\r
public String getPdbFile()\r
FeatureRenderer fr;\r
public void colourBySequence(AlignmentPanel ap)\r
{\r
+ if(!colourBySequence)\r
+ return;\r
+\r
+\r
StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());\r
\r
if (mapping.length < 1)\r
\r
lastPos = pos;\r
\r
+ Color col = sr.getResidueBoxColour(sequence[s], r);\r
+\r
+ if (showFeatures)\r
+ col = fr.findFeatureColour(col, sequence[s], r);\r
+\r
+ if (command.toString().endsWith(":" + mapping[m].getChain()+\r
+ ";color["\r
+ + col.getRed() + ","\r
+ + col.getGreen() + ","\r
+ + col.getBlue() + "]"))\r
+ {\r
+ command = condenseCommand(command, pos);\r
+ continue;\r
+ }\r
+\r
command.append(";select " + pos);\r
\r
if (!mapping[m].getChain().equals(" "))\r
command.append(":" + mapping[m].getChain());\r
}\r
\r
- Color col = sr.getResidueBoxColour(sequence[s], r);\r
-\r
- if (showFeatures)\r
- col = fr.findFeatureColour(col, sequence[s], r);\r
-\r
- command.append("; color ["\r
- + col.getRed() + ","\r
- + col.getGreen() + ","\r
- + col.getBlue() + "]");\r
+ command.append(";color["\r
+ + col.getRed() + ","\r
+ + col.getGreen() + ","\r
+ + col.getBlue() + "]");\r
\r
}\r
+ break;\r
}\r
}\r
}\r
viewer.evalStringQuiet(command.toString());\r
}\r
\r
+ StringBuffer condenseCommand(StringBuffer command, int pos)\r
+ {\r
+ StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7));\r
+\r
+ command.delete(0, sb.length());\r
+\r
+ String start;\r
+\r
+ if (command.indexOf("-") > -1)\r
+ {\r
+ start = command.substring(0,command.indexOf("-"));\r
+ }\r
+ else\r
+ {\r
+ start = command.substring(0, command.indexOf(":"));\r
+ }\r
+\r
+ sb.append(start+"-"+pos+command.substring(command.indexOf(":")));\r
+\r
+ return sb;\r
+ }\r
+\r
/////////////////////////////////\r
//JmolStatusListener\r
\r
\r
public void showConsole(boolean showConsole)\r
{\r
- final String title = "Jmol Script Window for: "+this.getTitle();\r
if (scriptWindow == null)\r
- return;\r
- if (showConsole)\r
+ scriptWindow = new ScriptWindow(this);\r
+\r
+ if(showConsole)\r
{\r
- javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ if(splitPane==null)\r
{\r
- public void run()\r
- {\r
- jalview.gui.Desktop.addInternalFrame(scriptWindow,\r
- title,\r
- 400,\r
- 300);\r
- }\r
- });\r
+ splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);\r
+ splitPane.setTopComponent(renderPanel);\r
+ splitPane.setBottomComponent(scriptWindow);\r
+ this.getContentPane().add(splitPane, BorderLayout.CENTER);\r
+ }\r
\r
+ splitPane.setDividerLocation(getHeight()-200);\r
+ splitPane.validate();\r
}\r
else\r
- scriptWindow.setVisible(false);\r
+ {\r
+ if (splitPane != null)\r
+ splitPane.setVisible(false);\r
+\r
+ splitPane = null;\r
+\r
+ this.getContentPane().add(renderPanel, BorderLayout.CENTER);\r
+ }\r
+\r
+ validate();\r
}\r
\r
public float functionXY(String functionName, int x, int y)\r
git://source.jalview.org / jalview.git / blobdiff