import java.awt.event.ComponentListener;
import java.io.File;
import java.net.URL;
-import java.security.AccessControlException;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
+import java.util.StringTokenizer;
import java.util.Vector;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
implements JmolStatusListener, JmolSelectionListener,
ComponentListener
{
+ private String lastMessage;
+
boolean allChainsSelected = false;
/*
String lastCommand;
- String lastMessage;
-
boolean loadedInline;
StringBuffer resetLastRes = new StringBuffer();
// remove listeners for all structures in viewer
getSsm().removeStructureViewerListener(this, this.getStructureFiles());
if (viewer != null)
+ {
viewer.dispose();
+ }
lastCommand = null;
viewer = null;
releaseUIResources();
}
Thread colourby = null;
+
/**
* Sends a set of colour commands to the structure viewer
*
colourby.interrupt();
colourby = null;
}
- colourby = new Thread(new Runnable()
+ Thread colourby = new Thread(new Runnable()
{
@Override
public void run()
}
});
colourby.start();
+ this.colourby = colourby;
}
/**
*/
private int _modelFileNameMap[];
- // ////////////////////////////////
- // /StructureListener
- // @Override
- public synchronized String[] getPdbFilex()
- {
- if (viewer == null)
- {
- return new String[0];
- }
- if (modelFileNames == null)
- {
- List<String> mset = new ArrayList<>();
- _modelFileNameMap = new int[viewer.ms.mc];
- String m = viewer.ms.getModelFileName(0);
- if (m != null)
- {
- String filePath = m;
- try
- {
- filePath = new File(m).getAbsolutePath();
- } catch (AccessControlException x)
- {
- // usually not allowed to do this in applet
- System.err.println(
- "jmolBinding: Using local file string from Jmol: " + m);
- }
- if (filePath.indexOf("/file:") != -1)
- {
- // applet path with docroot - discard as format won't match pdbfile
- filePath = m;
- }
- mset.add(filePath);
- _modelFileNameMap[0] = 0; // filename index for first model is always 0.
- }
- int j = 1;
- for (int i = 1; i < viewer.ms.mc; i++)
- {
- m = viewer.ms.getModelFileName(i);
- String filePath = m;
- if (m != null)
- {
- try
- {
- filePath = new File(m).getAbsolutePath();
- } catch (AccessControlException x)
- {
- // usually not allowed to do this in applet, so keep raw handle
- // System.err.println("jmolBinding: Using local file string from
- // Jmol: "+m);
- }
- }
-
- /*
- * add this model unless it is read from a structure file we have
- * already seen (example: 2MJW is an NMR structure with 10 models)
- */
- if (!mset.contains(filePath))
- {
- mset.add(filePath);
- _modelFileNameMap[j] = i; // record the model index for the filename
- j++;
- }
- }
- modelFileNames = mset.toArray(new String[mset.size()]);
- }
- return modelFileNames;
- }
-
@Override
public synchronized String[] getStructureFiles()
{
viewer.openStringInline(string);
}
- public void mouseOverStructure(int atomIndex, String strInfo)
+ protected void mouseOverStructure(int atomIndex, final String strInfo)
{
int pdbResNum;
int alocsep = strInfo.indexOf("^");
try
{
// recover PDB filename for the model hovered over.
- int mnumber = new Integer(mdlId).intValue() - 1;
+ int mnumber = Integer.valueOf(mdlId).intValue() - 1;
if (_modelFileNameMap != null)
{
int _mp = _modelFileNameMap.length - 1;
} catch (Exception e)
{
}
- ;
}
- if (lastMessage == null || !lastMessage.equals(strInfo))
+
+ /*
+ * highlight position on alignment(s); if some text is returned,
+ * show this as a second line on the structure hover tooltip
+ */
+ String label = getSsm().mouseOverStructure(pdbResNum, chainId,
+ pdbfilename);
+ if (label != null)
{
- getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename);
+ // change comma to pipe separator (newline token for Jmol)
+ label = label.replace(',', '|');
+ StringTokenizer toks = new StringTokenizer(strInfo, " ");
+ StringBuilder sb = new StringBuilder();
+ sb.append("select ").append(String.valueOf(pdbResNum)).append(":")
+ .append(chainId).append("/1");
+ sb.append(";set hoverLabel \"").append(toks.nextToken()).append(" ")
+ .append(toks.nextToken());
+ sb.append("|").append(label).append("\"");
+ evalStateCommand(sb.toString());
}
-
- lastMessage = strInfo;
}
public void notifyAtomHovered(int atomIndex, String strInfo, String data)
{
+ if (strInfo.equals(lastMessage))
+ {
+ return;
+ }
+ lastMessage = strInfo;
if (data != null)
{
System.err.println("Ignoring additional hover info: " + data
// see JAL-623 - need method of matching pasted data up
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- pdbfile, DataSourceType.PASTE,
- getIProgressIndicator());
+ pdbfile, DataSourceType.PASTE, getIProgressIndicator());
getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
matches = true;
foundEntry = true;
public void showHelp()
{
- showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp");
+ showUrl("http://wiki.jmol.org"
+ // BH 2018 "http://jmol.sourceforge.net/docs/JmolUserGuide/"
+ , "jmolHelp");
}
/**
*/
public abstract void showConsole(boolean show);
-
public static Viewer getJmolData(JmolParser jmolParser)
{
return (Viewer) JmolViewer.allocateViewer(null, null, null, null, null,
String commandOptions, final Container consolePanel,
String buttonsToShow)
{
-
+
System.err.println("Allocating Jmol Viewer: " + commandOptions);
-
+
if (commandOptions == null)
{
commandOptions = "";
htmlName + ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
- viewer.setJmolStatusListener(this); // extends JmolCallbackListener
+ viewer.setJmolStatusListener(this);
+
+ // BH how about extending Jmol's status listener?
- try {
+ try
+ {
console = createJmolConsole(consolePanel, buttonsToShow);
- } catch (Throwable e) {
- System.err.println("Could not create Jmol application console. " + e.getMessage());
+ } catch (Throwable e)
+ {
+ System.err.println("Could not create Jmol application console. "
+ + e.getMessage());
e.printStackTrace();
}
if (consolePanel != null)
protected abstract JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow);
- // BH 2018 -- Jmol console is not working due to problems with styled documents.
-
+ // BH 2018 -- Jmol console is not working due to problems with styled
+ // documents.
protected org.jmol.api.JmolAppConsoleInterface console = null;
public void setBackgroundColour(java.awt.Color col)
{
jmolHistory(false);
- jmolScript("background [" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
+ jmolScript("background [" + col.getRed() + "," + col.getGreen() + ","
+ + col.getBlue() + "];");
jmolHistory(true);
}
private String jmolScript(String script)
{
-
+
System.err.println(">>Jmol>> " + script);
-
+
String s = viewer.scriptWait(script);
-
+
System.err.println("<<Jmol<< " + s);
-
+
return s;
}
git://source.jalview.org / jalview.git / blobdiff