/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
import java.awt.*;
import java.awt.event.*;
+import jalview.api.SequenceStructureBinding;
import jalview.datamodel.*;
import jalview.structure.*;
import jalview.io.*;
import org.jmol.api.*;
-import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.popup.*;
+import org.jmol.viewer.JmolConstants;
+
import jalview.schemes.*;
-public class AppletJmol extends EmbmenuFrame implements StructureListener,
- JmolStatusListener, KeyListener, ActionListener, ItemListener
+public class AppletJmol extends EmbmenuFrame implements
+// StructureListener,
+ KeyListener, ActionListener, ItemListener, SequenceStructureBinding
{
Menu fileMenu = new Menu("File");
MenuItem jmolHelp = new MenuItem("Jmol Help");
- JmolViewer viewer;
-
- JmolPopup jmolpopup;
-
Panel scriptWindow;
TextField inputLine;
TextArea history;
- SequenceI[] sequence;
-
- String[] chains;
-
- StructureSelectionManager ssm;
-
RenderPanel renderPanel;
AlignmentPanel ap;
boolean loadedInline;
- PDBEntry pdbentry;
+ // boolean colourBySequence = true;
- boolean colourBySequence = true;
+ FeatureRenderer fr = null;
- Vector atomsPicked = new Vector();
+ AppletJmolBinding jmb;
/**
* datasource protocol for access to PDBEntry
*/
String protocol = null;
-
+ /**
+ * Load a bunch of pdb entries associated with sequences in the alignment and display them - aligning them if necessary.
+ * @param pdbentries each pdb file (at least one needed)
+ * @param boundseqs each set of sequences for each pdb file (must match number of pdb files)
+ * @param boundchains the target pdb chain corresponding with each sequence associated with each pdb file (may be null at any level)
+ * @param align true/false
+ * @param ap associated alignment
+ * @param protocol how to get pdb data
+ */
+ public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs, String[][] boundchains, boolean align, AlignmentPanel ap, String protocol)
+ {
+ throw new Error("Not yet implemented.");
+ }
public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
AlignmentPanel ap, String protocol)
{
this.ap = ap;
- this.sequence = seq;
- this.chains = chains;
- this.pdbentry = pdbentry;
- this.protocol = protocol;
+ jmb = new AppletJmolBinding(this, new PDBEntry[]
+ { pdbentry }, new SequenceI[][]{seq}, new String[][]{ chains }, protocol);
+ jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
if (protocol.equals(AppletFormatAdapter.PASTE))
coloursMenu.add(user);
helpMenu.add(jmolHelp);
+ this.setLayout(new BorderLayout());
setMenuBar(menuBar);
renderPanel = new RenderPanel();
embedMenuIfNeeded(renderPanel);
this.add(renderPanel, BorderLayout.CENTER);
- viewer = JmolViewer.allocateViewer(renderPanel,
- new SmarterJmolAdapter());
-
- viewer.setAppletContext("jalview", ap.av.applet.getDocumentBase(),
- ap.av.applet.getCodeBase(), null);
-
- viewer.setJmolStatusListener(this);
-
- jmolpopup = JmolPopup.newJmolPopup(viewer);
+ scriptWindow = new Panel();
+ scriptWindow.setVisible(false);
+ // this.add(scriptWindow, BorderLayout.SOUTH);
+
+ try
+ {
+ jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()+"_jmol_",
+ ap.av.applet.getDocumentBase(), ap.av.applet.getCodeBase(),
+ "-applet", scriptWindow, null);
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
+ + ap.av.applet.getDocumentBase()
+ + "\nCodebase="
+ + ap.av.applet.getCodeBase());
+ e.printStackTrace();
+ dispose();
+ return;
+ }
+ jmb.newJmolPopup(true, "Jmol", true);
this.addWindowListener(new WindowAdapter()
{
closeViewer();
}
});
-
+ if (pdbentry.getProperty()==null)
+ {
+ pdbentry.setProperty(new Hashtable());
+ pdbentry.getProperty().put("protocol", protocol);
+ }
if (pdbentry.getFile() != null)
{
// import structure data from pdbentry.getFile based on given protocol
if (protocol.equals(AppletFormatAdapter.PASTE))
{
+ // TODO: JAL-623 : correctly record file contents for matching up later
+ // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
loadInline(pdbentry.getFile());
}
else if (protocol.equals(AppletFormatAdapter.FILE)
|| protocol.equals(AppletFormatAdapter.URL))
{
- viewer.openFile(pdbentry.getFile());
+ jmb.viewer.openFile(pdbentry.getFile());
}
else
{
throw new Exception(
"Invalid datasource. Could not obtain Reader.");
}
- viewer.openReader(pdbentry.getFile(), pdbentry.getId(), freader);
+ jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
+ freader);
} catch (Exception e)
{
// give up!
}
}
- jalview.bin.JalviewLite.addFrame(this, "Jmol", 400, 400);
+ jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
}
public void loadInline(String string)
{
loadedInline = true;
- viewer.openStringInline(string);
+ jmb.loadInline(string);
}
void setChainMenuItems(Vector chains)
void centerViewer()
{
- StringBuffer cmd = new StringBuffer();
+ Vector toshow = new Vector();
+ String lbl;
+ int mlength, p, mnum;
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
{
CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
if (item.getState())
- cmd.append(":" + item.getLabel() + " or ");
+ {
+ toshow.addElement(item.getLabel());
+ }
}
}
-
- if (cmd.length() > 0)
- cmd.setLength(cmd.length() - 4);
-
- viewer
- .evalString("select *;restrict " + cmd + ";cartoon;center "
- + cmd);
+ jmb.centerViewer(toshow);
}
void closeViewer()
{
- viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
- viewer.evalStringQuiet("zap");
- viewer.setJmolStatusListener(null);
- viewer = null;
-
- // We'll need to find out what other
- // listeners need to be shut down in Jmol
- StructureSelectionManager.getStructureSelectionManager()
- .removeStructureViewerListener(this, pdbentry.getId());
-
+ jmb.closeViewer();
+ jmb = null;
this.setVisible(false);
}
Frame frame = new Frame();
frame.add(cap);
+ StringBuffer sb = new StringBuffer();
+ try {
+ for (int s = 0; s < jmb.pdbentry.length; s++)
+ {
+ sb.append(StructureSelectionManager.getStructureSelectionManager()
+ .printMapping(jmb.pdbentry[s].getFile()));
+ sb.append("\n");
+ }
+ cap.setText(sb.toString());
+ }
+ catch (OutOfMemoryError ex)
+ {
+ frame.dispose();
+ System.err.println("Out of memory when trying to create dialog box with sequence-structure mapping.");
+ return;
+ }
jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
550, 600);
- cap.setText(StructureSelectionManager.getStructureSelectionManager()
- .printMapping(pdbentry.getFile()));
}
else if (evt.getSource() == charge)
{
- colourBySequence = false;
- seqColour.setState(false);
- viewer
- .evalStringQuiet("select *;color white;select ASP,GLU;color red;"
- + "select LYS,ARG;color blue;select CYS;color yellow");
+ setEnabled(charge);
+ jmb.colourByCharge();
}
else if (evt.getSource() == chain)
{
- colourBySequence = false;
- seqColour.setState(false);
- viewer.evalStringQuiet("select *;color chain");
+ setEnabled(chain);
+ jmb.colourByChain();
}
else if (evt.getSource() == zappo)
{
- setJalviewColourScheme(new ZappoColourScheme());
+ setEnabled(zappo);
+ jmb.setJalviewColourScheme(new ZappoColourScheme());
}
else if (evt.getSource() == taylor)
{
- setJalviewColourScheme(new TaylorColourScheme());
+ setEnabled(taylor);
+ jmb.setJalviewColourScheme(new TaylorColourScheme());
}
else if (evt.getSource() == hydro)
{
- setJalviewColourScheme(new HydrophobicColourScheme());
+ setEnabled(hydro);
+ jmb.setJalviewColourScheme(new HydrophobicColourScheme());
}
else if (evt.getSource() == helix)
{
- setJalviewColourScheme(new HelixColourScheme());
+ setEnabled(helix);
+ jmb.setJalviewColourScheme(new HelixColourScheme());
}
else if (evt.getSource() == strand)
{
- setJalviewColourScheme(new StrandColourScheme());
+ setEnabled(strand);
+ jmb.setJalviewColourScheme(new StrandColourScheme());
}
else if (evt.getSource() == turn)
{
- setJalviewColourScheme(new TurnColourScheme());
+ setEnabled(turn);
+ jmb.setJalviewColourScheme(new TurnColourScheme());
}
else if (evt.getSource() == buried)
{
- setJalviewColourScheme(new BuriedColourScheme());
+ setEnabled(buried);
+ jmb.setJalviewColourScheme(new BuriedColourScheme());
}
else if (evt.getSource() == user)
{
+ setEnabled(user);
new UserDefinedColours(this);
}
else if (evt.getSource() == jmolHelp)
if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
}
+
centerViewer();
allChainsSelected = false;
}
}
- public void setJalviewColourScheme(ColourSchemeI cs)
+ /**
+ * tick or untick the seqColour menu entry depending upon if it was selected
+ * or not.
+ *
+ * @param itm
+ */
+ private void setEnabled(MenuItem itm)
{
- colourBySequence = false;
- seqColour.setState(false);
-
- if (cs == null)
- return;
-
- String res;
- int index;
- Color col;
-
- Enumeration en = ResidueProperties.aa3Hash.keys();
- StringBuffer command = new StringBuffer("select *;color white;");
- while (en.hasMoreElements())
- {
- res = en.nextElement().toString();
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
- if (index > 20)
- continue;
-
- col = cs.findColour(ResidueProperties.aa[index].charAt(0));
-
- command.append("select " + res + ";color[" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
- }
-
- viewer.evalStringQuiet(command.toString());
+ seqColour.setState(itm == seqColour);
+ jmb.setColourBySequence(itm == seqColour);
}
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == seqColour)
{
- lastCommand = null;
- colourBySequence = seqColour.getState();
- colourBySequence(ap);
+ setEnabled(seqColour);
+ jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
}
else if (!allChainsSelected)
centerViewer();
{
if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
{
- viewer.evalString(inputLine.getText());
+ jmb.eval(inputLine.getText());
history.append("\n$ " + inputLine.getText());
inputLine.setText("");
}
{
}
- // ////////////////////////////////
- // /StructureListener
- public String getPdbFile()
- {
- return "???";
- }
-
- String lastMessage;
-
- public void mouseOverStructure(int atomIndex, String strInfo)
- {
- int pdbResNum;
-
- int chainSeparator = strInfo.indexOf(":");
-
- if (chainSeparator == -1)
- chainSeparator = strInfo.indexOf(".");
-
- pdbResNum = Integer.parseInt(strInfo.substring(
- strInfo.indexOf("]") + 1, chainSeparator));
-
- String chainId;
-
- if (strInfo.indexOf(":") > -1)
- chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo
- .indexOf("."));
- else
- {
- chainId = " ";
- }
-
- if (lastMessage == null || !lastMessage.equals(strInfo))
- ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
-
- lastMessage = strInfo;
- }
-
- StringBuffer resetLastRes = new StringBuffer();
-
- StringBuffer eval = new StringBuffer();
-
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- if (!pdbfile.equals(pdbentry.getFile()))
- return;
-
- if (resetLastRes.length() > 0)
- {
- viewer.evalStringQuiet(resetLastRes.toString());
- }
-
- eval.setLength(0);
- eval.append("select " + pdbResNum);
-
- resetLastRes.setLength(0);
- resetLastRes.append("select " + pdbResNum);
-
- eval.append(":");
- resetLastRes.append(":");
- if (!chain.equals(" "))
- {
- eval.append(chain);
- resetLastRes.append(chain);
- }
-
- eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
-
- resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
- + " and not hetero; spacefill 0;");
-
- eval.append("spacefill 200;select none");
-
- viewer.evalStringQuiet(eval.toString());
-
- }
-
public void updateColours(Object source)
{
- colourBySequence((AlignmentPanel) source);
+ AlignmentPanel ap = (AlignmentPanel) source;
+ jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
}
- // End StructureListener
- // //////////////////////////
-
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- if (!pdbfile.equals(pdbentry.getFile()))
- return null;
-
- return new Color(viewer.getAtomArgb(atomIndex));
- }
-
- String lastCommand;
-
- FeatureRenderer fr = null;
-
- public void colourBySequence(AlignmentPanel sourceap)
+ public void updateTitleAndMenus()
{
- this.ap = sourceap;
-
- if (!colourBySequence)
- return;
-
- StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
-
- if (mapping.length < 1)
- return;
-
- SequenceRenderer sr = new SequenceRenderer(ap.av);
-
- boolean showFeatures = false;
-
- if (ap.av.showSequenceFeatures)
- {
- showFeatures = true;
- if (fr == null)
- {
- fr = new jalview.appletgui.FeatureRenderer(ap.av);
- }
-
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
- }
-
- StringBuffer command = new StringBuffer();
-
- int lastPos = -1;
- for (int s = 0; s < sequence.length; s++)
+ if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
{
- for (int sp, m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[s]
- && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
- {
- SequenceI asp = ap.av.alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // no mapping to gaps in sequence
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(sequence[s], r);
-
- if (showFeatures)
- col = fr.findFeatureColour(col, sequence[s], r);
-
- if (command.toString().endsWith(
- ":" + mapping[m].getChain() + ";color[" + col.getRed()
- + "," + col.getGreen() + "," + col.getBlue()
- + "]"))
- {
- command = condenseCommand(command.toString(), pos);
- continue;
- }
-
- command.append(";select " + pos);
-
- if (!mapping[m].getChain().equals(" "))
- {
- command.append(":" + mapping[m].getChain());
- }
-
- command.append(";color[" + col.getRed() + "," + col.getGreen()
- + "," + col.getBlue() + "]");
- }
- break;
- }
- }
- }
-
- if (lastCommand == null || !lastCommand.equals(command.toString()))
- {
- viewer.evalStringQuiet(command.toString());
- }
- lastCommand = command.toString();
- }
-
- StringBuffer condenseCommand(String command, int pos)
- {
-
- StringBuffer sb = new StringBuffer(command.substring(0, command
- .lastIndexOf("select") + 7));
-
- command = command.substring(sb.length());
-
- String start;
-
- if (command.indexOf("-") > -1)
- {
- start = command.substring(0, command.indexOf("-"));
- }
- else
- {
- start = command.substring(0, command.indexOf(":"));
- }
-
- sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-
- return sb;
- }
-
- // ///////////////////////////////
- // JmolStatusListener
-
- public String eval(String strEval)
- {
- // System.out.println(strEval);
- // "# 'eval' is implemented only for the applet.";
- return null;
- }
-
- public void createImage(String file, String type, int quality)
- {
- }
-
- public void setCallbackFunction(String callbackType,
- String callbackFunction)
- {
- }
-
- public void notifyFileLoaded(String fullPathName, String fileName,
- String modelName, Object clientFile, String errorMsg)
- {
- if (errorMsg != null)
- {
- fileLoadingError = errorMsg;
repaint();
return;
}
+ setChainMenuItems(jmb.chainNames);
+ jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
- fileLoadingError = null;
-
- if (fileName != null)
- {
- // FILE LOADED OK
- jmolpopup.updateComputedMenus();
- viewer
- .evalStringQuiet("select backbone;restrict;cartoon;wireframe off;spacefill off");
-
- ssm = StructureSelectionManager.getStructureSelectionManager();
- MCview.PDBfile pdb;
- if (loadedInline)
- {
- pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(),
- AppletFormatAdapter.PASTE);
- pdbentry.setFile("INLINE" + pdb.id);
- }
- else
- {
- // TODO: Jmol can in principle retrieve from CLASSLOADER but this needs
- // to be tested. See mantis bug
- // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
-
- pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(),
- AppletFormatAdapter.URL);
-
- }
-
- pdbentry.setId(pdb.id);
-
- ssm.addStructureViewerListener(this);
-
- Vector chains = new Vector();
- for (int i = 0; i < pdb.chains.size(); i++)
- {
- chains.addElement(((MCview.PDBChain) pdb.chains.elementAt(i)).id);
- }
- setChainMenuItems(chains);
-
- colourBySequence(ap);
-
- StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
- + pdbentry.getId());
-
- if (pdbentry.getProperty() != null)
- {
- if (pdbentry.getProperty().get("method") != null)
- {
- title.append(" Method: ");
- title.append(pdbentry.getProperty().get("method"));
- }
- if (pdbentry.getProperty().get("chains") != null)
- {
- title.append(" Chain:");
- title.append(pdbentry.getProperty().get("chains"));
- }
- }
-
- this.setTitle(title.toString());
-
- }
- else
- return;
- }
-
- public void notifyFrameChanged(int frameNo)
- {
- boolean isAnimationRunning = (frameNo <= -2);
- }
-
- public void notifyScriptStart(String statusMessage, String additionalInfo)
- {
- }
-
- public void sendConsoleEcho(String strEcho)
- {
- if (scriptWindow == null)
- showConsole(true);
-
- history.append("\n" + strEcho);
- }
-
- public void sendConsoleMessage(String strStatus)
- {
- if (history != null && strStatus != null
- && !strStatus.equals("Script completed"))
- {
- history.append("\n" + strStatus);
- }
- }
-
- public void notifyScriptTermination(String strStatus, int msWalltime)
- {
- }
-
- public void handlePopupMenu(int x, int y)
- {
- jmolpopup.show(x, y);
- }
-
- public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
- {
- notifyAtomPicked(iatom, strMeasure);
- }
-
- public void notifyNewDefaultModeMeasurement(int count, String strInfo)
- {
- }
-
- public void notifyAtomPicked(int atomIndex, String strInfo)
- {
-
- int chainSeparator = strInfo.indexOf(":");
-
- if (chainSeparator == -1)
- chainSeparator = strInfo.indexOf(".");
-
- String picked = strInfo.substring(strInfo.indexOf("]") + 1,
- chainSeparator);
-
- if (strInfo.indexOf(":") > -1)
- picked += strInfo.substring(strInfo.indexOf(":") + 1, strInfo
- .indexOf("."));
-
- picked += ".CA";
-
- if (!atomsPicked.contains(picked))
- {
- viewer.evalString("select " + picked + ";label %n %r:%c");
- atomsPicked.addElement(picked);
- }
- else
- {
- viewer.evalString("select " + picked + ";label off");
- atomsPicked.removeElement(picked);
- }
- }
-
- public void notifyAtomHovered(int atomIndex, String strInfo)
- {
- mouseOverStructure(atomIndex, strInfo);
- }
-
- public void sendSyncScript(String script, String appletName)
- {
+ setTitle(jmb.getViewerTitle());
}
public void showUrl(String url)
{
}
}
-
+ Panel splitPane=null;
public void showConsole(boolean showConsole)
{
- if (scriptWindow == null)
- {
- scriptWindow = new Panel(new BorderLayout());
- inputLine = new TextField();
- history = new TextArea(5, 40);
- scriptWindow.add(history, BorderLayout.CENTER);
- scriptWindow.add(inputLine, BorderLayout.SOUTH);
- add(scriptWindow, BorderLayout.SOUTH);
+ if (showConsole)
+ {
+ remove(renderPanel);
+ splitPane = new Panel();
+
+ splitPane.setLayout(new java.awt.GridLayout(2,1));
+ splitPane.add(renderPanel);
+ splitPane.add(scriptWindow);
+ scriptWindow.setVisible(true);
+ this.add(splitPane, BorderLayout.CENTER);
+ splitPane.setVisible(true);
+ splitPane.validate();
+ } else {
scriptWindow.setVisible(false);
- history.setEditable(false);
- inputLine.addKeyListener(this);
+ remove(splitPane);
+ add(renderPanel, BorderLayout.CENTER);
+ splitPane=null;
}
-
- scriptWindow.setVisible(!scriptWindow.isVisible());
validate();
}
- public float functionXY(String functionName, int x, int y)
+ public float[][] functionXY(String functionName, int x, int y)
{
- return 0;
+ return null;
}
// /End JmolStatusListener
currentSize = this.getSize();
rectClip = g.getClipBounds();
- if (viewer == null)
+ if (jmb.viewer == null)
{
g.setColor(Color.black);
g.fillRect(0, 0, currentSize.width, currentSize.height);
}
else
{
- viewer.renderScreenImage(g, currentSize, rectClip);
+ jmb.viewer.renderScreenImage(g, currentSize, rectClip);
}
}
}
+ /*
+ * @Override public Color getColour(int atomIndex, int pdbResNum, String
+ * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain,
+ * pdbId); }
+ *
+ * @Override public String[] getPdbFile() { return jmb.getPdbFile(); }
+ *
+ * @Override public void highlightAtom(int atomIndex, int pdbResNum, String
+ * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain,
+ * pdbId);
+ *
+ * }
+ *
+ * @Override public void mouseOverStructure(int atomIndex, String strInfo) {
+ * jmb.mouseOverStructure(atomIndex, strInfo);
+ *
+ * }
+ */
+ public void setJalviewColourScheme(UserColourScheme ucs)
+ {
+ jmb.setJalviewColourScheme(ucs);
+ }
}
git://source.jalview.org / jalview.git / blobdiff