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package jalview.ext.jmol; |
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import java.awt.Container; |
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import java.awt.event.ComponentEvent; |
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import java.awt.event.ComponentListener; |
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import java.io.File; |
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import java.net.URL; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.HashMap; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.StringTokenizer; |
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import java.util.Vector; |
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import javax.swing.SwingUtilities; |
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import org.jmol.adapter.smarter.SmarterJmolAdapter; |
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import org.jmol.api.JmolAppConsoleInterface; |
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import org.jmol.api.JmolSelectionListener; |
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import org.jmol.api.JmolStatusListener; |
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import org.jmol.api.JmolViewer; |
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import org.jmol.c.CBK; |
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import org.jmol.viewer.Viewer; |
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import jalview.api.AlignmentViewPanel; |
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import jalview.api.FeatureRenderer; |
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import jalview.api.FeatureSettingsModelI; |
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import jalview.api.SequenceRenderer; |
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import jalview.bin.Console; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.AppJmol; |
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import jalview.gui.IProgressIndicator; |
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import jalview.gui.StructureViewer.ViewerType; |
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import jalview.io.DataSourceType; |
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import jalview.io.StructureFile; |
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import jalview.structure.AtomSpec; |
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import jalview.structure.StructureCommand; |
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import jalview.structure.StructureCommandI; |
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import jalview.structure.StructureSelectionManager; |
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import jalview.structures.models.AAStructureBindingModel; |
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import jalview.ws.dbsources.Pdb; |
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import javajs.util.BS; |
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|
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| 54.1% |
Uncovered Elements: 222 (484) |
Complexity: 148 |
Complexity Density: 0.49 |
|
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public abstract class JalviewJmolBinding extends AAStructureBindingModel |
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implements JmolStatusListener, JmolSelectionListener, |
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ComponentListener |
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{ |
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private String lastMessage; |
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private boolean associateNewStructs = false; |
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private Vector<String> atomsPicked = new Vector<>(); |
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|
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private String lastCommand; |
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private boolean loadedInline; |
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|
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private StringBuffer resetLastRes = new StringBuffer(); |
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|
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public Viewer jmolViewer; |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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public JalviewJmolBinding(StructureSelectionManager ssm,... |
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PDBEntry[] pdbentry, SequenceI[][] sequenceIs, |
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DataSourceType protocol) |
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{ |
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super(ssm, pdbentry, sequenceIs, protocol); |
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setStructureCommands(new JmolCommands()); |
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} |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
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0 |
public JalviewJmolBinding(StructureSelectionManager ssm,... |
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SequenceI[][] seqs, Viewer theViewer) |
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{ |
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super(ssm, seqs); |
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|
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jmolViewer = theViewer; |
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jmolViewer.setJmolStatusListener(this); |
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jmolViewer.addSelectionListener(this); |
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setStructureCommands(new JmolCommands()); |
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} |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public String getViewerTitle()... |
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{ |
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return getViewerTitle("Jmol", true); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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40 |
private String jmolScript(String script)... |
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{ |
127 |
40 |
return jmolScript(script, false); |
128 |
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} |
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| 100% |
Uncovered Elements: 0 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
130 |
1061 |
private String jmolScript(String script, boolean useScriptWait)... |
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{ |
132 |
1061 |
Console.debug(">>Jmol>> " + script); |
133 |
1061 |
String s; |
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1061 |
if (useScriptWait) |
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{ |
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2 |
s = jmolViewer.scriptWait(script); |
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} |
138 |
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else |
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{ |
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1059 |
s = jmolViewer.evalStringQuiet(script); |
141 |
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} |
142 |
1061 |
Console.debug("<<Jmol<< " + s); |
143 |
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|
144 |
1061 |
return s; |
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} |
146 |
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| 84.6% |
Uncovered Elements: 2 (13) |
Complexity: 4 |
Complexity Density: 0.44 |
|
147 |
404 |
@Override... |
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public List<String> executeCommand(StructureCommandI command, |
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boolean getReply) |
150 |
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{ |
151 |
404 |
if (command == null) |
152 |
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{ |
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0 |
return null; |
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} |
155 |
404 |
String cmd = command.getCommand(); |
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404 |
jmolHistory(false); |
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404 |
if (lastCommand == null || !lastCommand.equals(cmd)) |
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{ |
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jmolScript(cmd + "\n", command.isWaitNeeded()); |
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} |
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404 |
jmolHistory(true); |
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404 |
lastCommand = cmd; |
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404 |
return null; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
public void createImage(String file, String type, int quality)... |
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{ |
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jalview.bin.Console.outPrintln("JMOL CREATE IMAGE"); |
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} |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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4 |
@Override... |
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public String createImage(String fileName, String type, |
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Object textOrBytes, int quality) |
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{ |
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jalview.bin.Console.outPrintln("JMOL CREATE IMAGE"); |
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4 |
return null; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
179 |
0 |
@Override... |
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public String eval(String strEval) |
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{ |
182 |
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183 |
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184 |
0 |
return null; |
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} |
186 |
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189 |
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190 |
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191 |
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192 |
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193 |
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| 100% |
Uncovered Elements: 0 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
194 |
51 |
@Override... |
195 |
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public Map<String, String> getHetatmNames() |
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{ |
197 |
51 |
HashMap<String, String> hetlist = new HashMap(); |
198 |
103 |
for (int mc = 0; mc < jmolViewer.ms.mc; mc++) |
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{ |
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52 |
Map<String, String> hets = jmolViewer.ms.getHeteroList(mc); |
201 |
52 |
if (hets != null) |
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{ |
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12 |
hetlist.putAll(hets); |
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} |
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} |
206 |
51 |
return hetlist; |
207 |
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} |
208 |
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209 |
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210 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
211 |
0 |
@Override... |
212 |
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public float[][] functionXY(String functionName, int x, int y) |
213 |
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{ |
214 |
0 |
return null; |
215 |
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} |
216 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
217 |
0 |
@Override... |
218 |
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public float[][][] functionXYZ(String functionName, int nx, int ny, |
219 |
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int nz) |
220 |
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{ |
221 |
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222 |
0 |
return null; |
223 |
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} |
224 |
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225 |
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226 |
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227 |
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228 |
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229 |
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230 |
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private int _modelFileNameMap[]; |
231 |
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| 100% |
Uncovered Elements: 0 (23) |
Complexity: 7 |
Complexity Density: 0.54 |
|
232 |
1053 |
@Override... |
233 |
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public synchronized String[] getStructureFiles() |
234 |
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{ |
235 |
1053 |
if (jmolViewer == null) |
236 |
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{ |
237 |
52 |
return new String[0]; |
238 |
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} |
239 |
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|
240 |
1001 |
if (modelFileNames == null) |
241 |
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{ |
242 |
202 |
int modelCount = jmolViewer.ms.mc; |
243 |
202 |
String filePath = null; |
244 |
202 |
List<String> mset = new ArrayList<>(); |
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405 |
for (int i = 0; i < modelCount; ++i) |
246 |
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{ |
247 |
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248 |
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249 |
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250 |
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251 |
203 |
filePath = jmolViewer.ms.getModelFileName(i); |
252 |
203 |
if (filePath != null && !mset.contains(filePath)) |
253 |
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{ |
254 |
70 |
mset.add(filePath); |
255 |
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} |
256 |
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} |
257 |
202 |
if (!mset.isEmpty()) |
258 |
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{ |
259 |
69 |
modelFileNames = mset.toArray(new String[mset.size()]); |
260 |
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} |
261 |
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} |
262 |
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|
263 |
1001 |
return modelFileNames; |
264 |
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} |
265 |
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266 |
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267 |
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|
268 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
269 |
0 |
@Override... |
270 |
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public Map<String, Object> getRegistryInfo() |
271 |
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{ |
272 |
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|
273 |
0 |
return null; |
274 |
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} |
275 |
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|
276 |
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277 |
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|
278 |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
279 |
0 |
public void handlePopupMenu(int x, int y)... |
280 |
|
{ |
281 |
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|
282 |
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|
283 |
|
} |
284 |
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|
285 |
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|
286 |
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|
287 |
|
|
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| 0% |
Uncovered Elements: 25 (25) |
Complexity: 6 |
Complexity Density: 0.4 |
|
288 |
0 |
@Override... |
289 |
|
public void highlightAtoms(List<AtomSpec> atoms) |
290 |
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{ |
291 |
0 |
if (atoms != null) |
292 |
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{ |
293 |
0 |
if (resetLastRes.length() > 0) |
294 |
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{ |
295 |
0 |
jmolScript(resetLastRes.toString()); |
296 |
0 |
resetLastRes.setLength(0); |
297 |
|
} |
298 |
0 |
StringBuilder highlightCommands = null; |
299 |
0 |
for (AtomSpec atom : atoms) |
300 |
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{ |
301 |
0 |
StringBuilder thisAtom = highlightAtom(atom.getAtomIndex(), |
302 |
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atom.getPdbResNum(), atom.getChain(), atom.getPdbFile()); |
303 |
0 |
if (thisAtom != null) |
304 |
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{ |
305 |
0 |
if (highlightCommands == null) |
306 |
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{ |
307 |
0 |
highlightCommands = thisAtom; |
308 |
|
} |
309 |
|
else |
310 |
|
{ |
311 |
0 |
highlightCommands.append(thisAtom); |
312 |
|
} |
313 |
|
} |
314 |
|
} |
315 |
0 |
if (highlightCommands != null) |
316 |
|
{ |
317 |
0 |
jmolHistory(false); |
318 |
0 |
jmolScript(highlightCommands.toString()); |
319 |
0 |
jmolHistory(true); |
320 |
|
} |
321 |
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322 |
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323 |
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324 |
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325 |
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|
326 |
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327 |
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328 |
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329 |
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|
330 |
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|
331 |
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|
332 |
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|
333 |
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|
334 |
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|
335 |
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|
336 |
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|
337 |
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|
338 |
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|
339 |
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|
340 |
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|
341 |
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|
342 |
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|
343 |
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|
344 |
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} |
345 |
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|
346 |
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} |
347 |
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|
348 |
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|
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|
| 0% |
Uncovered Elements: 17 (17) |
Complexity: 3 |
Complexity Density: 0.23 |
|
349 |
0 |
private StringBuilder highlightAtom(int atomIndex, int pdbResNum,... |
350 |
|
String chain, String pdbfile) |
351 |
|
{ |
352 |
0 |
String modelId = getModelIdForFile(pdbfile); |
353 |
0 |
if (modelId.isEmpty()) |
354 |
|
{ |
355 |
0 |
return null; |
356 |
|
} |
357 |
|
|
358 |
0 |
StringBuilder selection = new StringBuilder(32); |
359 |
0 |
StringBuilder cmd = new StringBuilder(64); |
360 |
0 |
selection.append("select ").append(String.valueOf(pdbResNum)); |
361 |
0 |
selection.append(":"); |
362 |
0 |
if (!chain.equals(" ")) |
363 |
|
{ |
364 |
0 |
selection.append(chain); |
365 |
|
} |
366 |
0 |
selection.append(" /").append(modelId); |
367 |
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|
368 |
0 |
cmd.append(selection).append(";wireframe 100;").append(selection) |
369 |
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.append(" and not hetero;").append("spacefill 200;select none"); |
370 |
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|
371 |
0 |
resetLastRes.append(selection).append(";wireframe 0;").append(selection) |
372 |
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.append(" and not hetero; spacefill 0;"); |
373 |
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|
374 |
0 |
return cmd; |
375 |
|
} |
376 |
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|
377 |
|
private boolean debug = true; |
378 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
379 |
808 |
private void jmolHistory(boolean enable)... |
380 |
|
{ |
381 |
808 |
jmolHistory(enable, false); |
382 |
|
} |
383 |
|
|
|
|
| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 3 |
Complexity Density: 3 |
|
384 |
808 |
private void jmolHistory(boolean enable, boolean useScriptWait)... |
385 |
|
{ |
386 |
808 |
jmolScript("History " + ((debug || enable) ? "on" : "off"), |
387 |
|
useScriptWait); |
388 |
|
} |
389 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
390 |
0 |
public void loadInline(String string)... |
391 |
|
{ |
392 |
0 |
loadedInline = true; |
393 |
|
|
394 |
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|
395 |
|
|
396 |
|
|
397 |
|
|
398 |
|
|
399 |
|
|
400 |
|
|
401 |
0 |
jmolViewer.openStringInline(string); |
402 |
|
} |
403 |
|
|
|
|
| 50.8% |
Uncovered Elements: 32 (65) |
Complexity: 16 |
Complexity Density: 0.39 |
|
404 |
1 |
protected void mouseOverStructure(int atomIndex, final String strInfo)... |
405 |
|
{ |
406 |
1 |
int pdbResNum; |
407 |
1 |
int alocsep = strInfo.indexOf("^"); |
408 |
1 |
int mdlSep = strInfo.indexOf("/"); |
409 |
1 |
int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1; |
410 |
|
|
411 |
1 |
if (chainSeparator == -1) |
412 |
|
{ |
413 |
0 |
chainSeparator = strInfo.indexOf("."); |
414 |
0 |
if (mdlSep > -1 && mdlSep < chainSeparator) |
415 |
|
{ |
416 |
0 |
chainSeparator1 = chainSeparator; |
417 |
0 |
chainSeparator = mdlSep; |
418 |
|
} |
419 |
|
} |
420 |
|
|
421 |
1 |
if (alocsep != -1) |
422 |
|
{ |
423 |
0 |
pdbResNum = Integer.parseInt( |
424 |
|
strInfo.substring(strInfo.indexOf("]") + 1, alocsep)); |
425 |
|
|
426 |
|
} |
427 |
|
else |
428 |
|
{ |
429 |
1 |
pdbResNum = Integer.parseInt( |
430 |
|
strInfo.substring(strInfo.indexOf("]") + 1, chainSeparator)); |
431 |
|
} |
432 |
1 |
String chainId; |
433 |
|
|
434 |
1 |
if (strInfo.indexOf(":") > -1) |
435 |
|
{ |
436 |
1 |
chainId = strInfo.substring(strInfo.indexOf(":") + 1, |
437 |
|
strInfo.indexOf(".")); |
438 |
|
} |
439 |
|
else |
440 |
|
{ |
441 |
0 |
chainId = " "; |
442 |
|
} |
443 |
|
|
444 |
1 |
String pdbfilename = modelFileNames[0]; |
445 |
1 |
if (mdlSep > -1) |
446 |
|
{ |
447 |
1 |
if (chainSeparator1 == -1) |
448 |
|
{ |
449 |
1 |
chainSeparator1 = strInfo.indexOf(".", mdlSep); |
450 |
|
} |
451 |
1 |
String mdlId = (chainSeparator1 > -1) |
452 |
|
? strInfo.substring(mdlSep + 1, chainSeparator1) |
453 |
|
: strInfo.substring(mdlSep + 1); |
454 |
1 |
try |
455 |
|
{ |
456 |
|
|
457 |
1 |
int mnumber = Integer.valueOf(mdlId).intValue() - 1; |
458 |
1 |
if (_modelFileNameMap != null) |
459 |
|
{ |
460 |
0 |
int _mp = _modelFileNameMap.length - 1; |
461 |
|
|
462 |
0 |
while (mnumber < _modelFileNameMap[_mp]) |
463 |
|
{ |
464 |
0 |
_mp--; |
465 |
|
} |
466 |
0 |
pdbfilename = modelFileNames[_mp]; |
467 |
|
} |
468 |
|
else |
469 |
|
{ |
470 |
1 |
if (mnumber >= 0 && mnumber < modelFileNames.length) |
471 |
|
{ |
472 |
1 |
pdbfilename = modelFileNames[mnumber]; |
473 |
|
} |
474 |
|
|
475 |
1 |
if (pdbfilename == null) |
476 |
|
{ |
477 |
0 |
pdbfilename = new File(jmolViewer.ms.getModelFileName(mnumber)) |
478 |
|
.getAbsolutePath(); |
479 |
|
} |
480 |
|
} |
481 |
|
} catch (Exception e) |
482 |
|
{ |
483 |
|
} |
484 |
|
} |
485 |
|
|
486 |
|
|
487 |
|
|
488 |
|
|
489 |
|
|
490 |
1 |
String label = getSsm().mouseOverStructure(pdbResNum, chainId, |
491 |
|
pdbfilename); |
492 |
1 |
if (label != null) |
493 |
|
{ |
494 |
|
|
495 |
0 |
label = label.replace(',', '|'); |
496 |
0 |
StringTokenizer toks = new StringTokenizer(strInfo, " "); |
497 |
0 |
StringBuilder sb = new StringBuilder(); |
498 |
0 |
sb.append("select ").append(String.valueOf(pdbResNum)).append(":") |
499 |
|
.append(chainId).append("/1"); |
500 |
0 |
sb.append(";set hoverLabel \"").append(toks.nextToken()).append(" ") |
501 |
|
.append(toks.nextToken()); |
502 |
0 |
sb.append("|").append(label).append("\""); |
503 |
0 |
executeCommand(new StructureCommand(sb.toString()), false); |
504 |
|
} |
505 |
|
} |
506 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
507 |
0 |
public void notifyAtomHovered(int atomIndex, String strInfo, String data)... |
508 |
|
{ |
509 |
0 |
if (strInfo.equals(lastMessage)) |
510 |
|
{ |
511 |
0 |
return; |
512 |
|
} |
513 |
0 |
lastMessage = strInfo; |
514 |
0 |
if (data != null) |
515 |
|
{ |
516 |
0 |
jalview.bin.Console.errPrintln( |
517 |
|
"Ignoring additional hover info: " + data + " (other info: '" |
518 |
|
+ strInfo + "' pos " + atomIndex + ")"); |
519 |
|
} |
520 |
0 |
mouseOverStructure(atomIndex, strInfo); |
521 |
|
} |
522 |
|
|
523 |
|
|
524 |
|
|
525 |
|
|
526 |
|
|
527 |
|
|
528 |
|
|
|
|
| 0% |
Uncovered Elements: 30 (30) |
Complexity: 6 |
Complexity Density: 0.3 |
|
529 |
0 |
public void notifyAtomPicked(int atomIndex, String strInfo,... |
530 |
|
String strData) |
531 |
|
{ |
532 |
|
|
533 |
|
|
534 |
|
|
535 |
|
|
536 |
0 |
if (strData != null) |
537 |
|
{ |
538 |
0 |
jalview.bin.Console.errPrintln( |
539 |
|
"Ignoring additional pick data string " + strData); |
540 |
|
} |
541 |
0 |
int chainSeparator = strInfo.indexOf(":"); |
542 |
0 |
int p = 0; |
543 |
0 |
if (chainSeparator == -1) |
544 |
|
{ |
545 |
0 |
chainSeparator = strInfo.indexOf("."); |
546 |
|
} |
547 |
|
|
548 |
0 |
String picked = strInfo.substring(strInfo.indexOf("]") + 1, |
549 |
|
chainSeparator); |
550 |
0 |
String mdlString = ""; |
551 |
0 |
if ((p = strInfo.indexOf(":")) > -1) |
552 |
|
{ |
553 |
0 |
picked += strInfo.substring(p, strInfo.indexOf(".")); |
554 |
|
} |
555 |
|
|
556 |
0 |
if ((p = strInfo.indexOf("/")) > -1) |
557 |
|
{ |
558 |
0 |
mdlString += strInfo.substring(p, strInfo.indexOf(" #")); |
559 |
|
} |
560 |
0 |
picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P" |
561 |
|
+ mdlString + "))"; |
562 |
0 |
jmolHistory(false); |
563 |
|
|
564 |
0 |
if (!atomsPicked.contains(picked)) |
565 |
|
{ |
566 |
0 |
jmolScript("select " + picked + ";label %n %r:%c"); |
567 |
0 |
atomsPicked.addElement(picked); |
568 |
|
} |
569 |
|
else |
570 |
|
{ |
571 |
0 |
jmolViewer.evalString("select " + picked + ";label off"); |
572 |
0 |
atomsPicked.removeElement(picked); |
573 |
|
} |
574 |
0 |
jmolHistory(true); |
575 |
|
|
576 |
|
|
577 |
|
|
578 |
|
|
579 |
|
|
580 |
|
|
581 |
|
|
582 |
|
|
583 |
|
} |
584 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
585 |
159 |
@Override... |
586 |
|
public void notifyCallback(CBK type, Object[] data) |
587 |
|
{ |
588 |
|
|
589 |
|
|
590 |
|
|
591 |
159 |
SwingUtilities.invokeLater(new Runnable() |
592 |
|
{ |
593 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
594 |
159 |
@Override... |
595 |
|
public void run() |
596 |
|
{ |
597 |
159 |
processCallback(type, data); |
598 |
|
} |
599 |
|
}); |
600 |
|
} |
601 |
|
|
602 |
|
|
603 |
|
|
604 |
|
|
605 |
|
@param |
606 |
|
@param |
607 |
|
|
|
|
| 55.9% |
Uncovered Elements: 15 (34) |
Complexity: 14 |
Complexity Density: 0.44 |
|
608 |
159 |
protected void processCallback(CBK type, Object[] data)... |
609 |
|
{ |
610 |
159 |
try |
611 |
|
{ |
612 |
159 |
switch (type) |
613 |
|
{ |
614 |
60 |
case LOADSTRUCT: |
615 |
60 |
notifyFileLoaded((String) data[1], (String) data[2], |
616 |
|
(String) data[3], (String) data[4], |
617 |
|
((Integer) data[5]).intValue()); |
618 |
|
|
619 |
59 |
break; |
620 |
0 |
case PICK: |
621 |
0 |
notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], |
622 |
|
(String) data[0]); |
623 |
|
|
624 |
|
|
625 |
0 |
case HOVER: |
626 |
0 |
notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], |
627 |
|
(String) data[0]); |
628 |
0 |
break; |
629 |
8 |
case SCRIPT: |
630 |
8 |
notifyScriptTermination((String) data[2], |
631 |
|
((Integer) data[3]).intValue()); |
632 |
8 |
break; |
633 |
32 |
case ECHO: |
634 |
32 |
sendConsoleEcho((String) data[1]); |
635 |
32 |
break; |
636 |
0 |
case MESSAGE: |
637 |
0 |
sendConsoleMessage( |
638 |
0 |
(data == null) ? ((String) null) : (String) data[1]); |
639 |
0 |
break; |
640 |
0 |
case ERROR: |
641 |
|
|
642 |
0 |
break; |
643 |
52 |
case SYNC: |
644 |
0 |
case RESIZE: |
645 |
52 |
refreshGUI(); |
646 |
52 |
break; |
647 |
7 |
case MEASURE: |
648 |
|
|
649 |
0 |
case CLICK: |
650 |
0 |
default: |
651 |
7 |
jalview.bin.Console.errPrintln( |
652 |
|
"Unhandled callback " + type + " " + data[1].toString()); |
653 |
7 |
break; |
654 |
|
} |
655 |
|
} catch (Exception e) |
656 |
|
{ |
657 |
1 |
jalview.bin.Console |
658 |
|
.errPrintln("Squashed Jmol callback handler error:"); |
659 |
1 |
e.printStackTrace(); |
660 |
|
} |
661 |
|
} |
662 |
|
|
|
|
| 66.7% |
Uncovered Elements: 4 (12) |
Complexity: 9 |
Complexity Density: 0.75 |
|
663 |
360 |
@Override... |
664 |
|
public boolean notifyEnabled(CBK callbackPick) |
665 |
|
{ |
666 |
360 |
switch (callbackPick) |
667 |
|
{ |
668 |
32 |
case ECHO: |
669 |
60 |
case LOADSTRUCT: |
670 |
7 |
case MEASURE: |
671 |
0 |
case MESSAGE: |
672 |
0 |
case PICK: |
673 |
8 |
case SCRIPT: |
674 |
0 |
case HOVER: |
675 |
0 |
case ERROR: |
676 |
107 |
return true; |
677 |
253 |
default: |
678 |
253 |
return false; |
679 |
|
} |
680 |
|
} |
681 |
|
|
682 |
|
|
683 |
|
|
684 |
|
|
685 |
|
private long loadNotifiesHandled = 0; |
686 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
687 |
62 |
public long getLoadNotifiesHandled()... |
688 |
|
{ |
689 |
62 |
return loadNotifiesHandled; |
690 |
|
} |
691 |
|
|
|
|
| 75% |
Uncovered Elements: 28 (112) |
Complexity: 26 |
Complexity Density: 0.37 |
|
692 |
60 |
public void notifyFileLoaded(String fullPathName, String fileName2,... |
693 |
|
String modelName, String errorMsg, int modelParts) |
694 |
|
{ |
695 |
60 |
if (errorMsg != null) |
696 |
|
{ |
697 |
7 |
fileLoadingError = errorMsg; |
698 |
7 |
refreshGUI(); |
699 |
7 |
return; |
700 |
|
} |
701 |
|
|
702 |
|
|
703 |
|
|
704 |
|
|
705 |
|
|
706 |
|
|
707 |
53 |
fileLoadingError = null; |
708 |
53 |
String[] oldmodels = modelFileNames; |
709 |
53 |
modelFileNames = null; |
710 |
53 |
boolean notifyLoaded = false; |
711 |
53 |
String[] modelfilenames = getStructureFiles(); |
712 |
53 |
if (modelfilenames == null) |
713 |
|
{ |
714 |
|
|
715 |
6 |
return; |
716 |
|
} |
717 |
|
|
718 |
47 |
if (oldmodels != null && oldmodels.length > 0) |
719 |
|
{ |
720 |
24 |
int oldm = 0; |
721 |
48 |
for (int i = 0; i < oldmodels.length; i++) |
722 |
|
{ |
723 |
24 |
for (int n = 0; n < modelfilenames.length; n++) |
724 |
|
{ |
725 |
24 |
if (modelfilenames[n] == oldmodels[i]) |
726 |
|
{ |
727 |
24 |
oldmodels[i] = null; |
728 |
24 |
break; |
729 |
|
} |
730 |
|
} |
731 |
24 |
if (oldmodels[i] != null) |
732 |
|
{ |
733 |
0 |
oldm++; |
734 |
|
} |
735 |
|
} |
736 |
24 |
if (oldm > 0) |
737 |
|
{ |
738 |
0 |
String[] oldmfn = new String[oldm]; |
739 |
0 |
oldm = 0; |
740 |
0 |
for (int i = 0; i < oldmodels.length; i++) |
741 |
|
{ |
742 |
0 |
if (oldmodels[i] != null) |
743 |
|
{ |
744 |
0 |
oldmfn[oldm++] = oldmodels[i]; |
745 |
|
} |
746 |
|
} |
747 |
|
|
748 |
|
|
749 |
0 |
getSsm().removeStructureViewerListener(this, oldmfn); |
750 |
|
} |
751 |
|
} |
752 |
47 |
refreshPdbEntries(); |
753 |
95 |
for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++) |
754 |
|
{ |
755 |
48 |
String fileName = modelfilenames[modelnum]; |
756 |
48 |
boolean foundEntry = false; |
757 |
48 |
StructureFile pdb = null; |
758 |
48 |
String pdbfile = null; |
759 |
|
|
760 |
48 |
if (loadedInline) |
761 |
|
{ |
762 |
|
|
763 |
|
|
764 |
|
|
765 |
0 |
pdbfile = jmolViewer.getData( |
766 |
|
"" + (1 + _modelFileNameMap[modelnum]) + ".0", "PDB"); |
767 |
|
} |
768 |
|
|
769 |
|
|
770 |
98 |
for (int pe = 0; pe < getPdbCount(); pe++) |
771 |
|
{ |
772 |
50 |
boolean matches = false; |
773 |
50 |
addSequence(pe, getSequence()[pe]); |
774 |
50 |
if (fileName == null) |
775 |
|
{ |
776 |
0 |
if (false) |
777 |
|
|
778 |
|
{ |
779 |
0 |
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe], |
780 |
|
pdbfile, DataSourceType.PASTE, getIProgressIndicator()); |
781 |
0 |
getPdbEntry(modelnum).setFile("INLINE" + pdb.getId()); |
782 |
0 |
matches = true; |
783 |
0 |
foundEntry = true; |
784 |
|
} |
785 |
|
} |
786 |
|
else |
787 |
|
{ |
788 |
50 |
File fl = new File(getPdbEntry(pe).getFile()); |
789 |
50 |
matches = fl.equals(new File(fileName)); |
790 |
50 |
if (matches) |
791 |
|
{ |
792 |
45 |
foundEntry = true; |
793 |
|
|
794 |
|
|
795 |
|
|
796 |
|
|
797 |
|
|
798 |
45 |
DataSourceType protocol = DataSourceType.URL; |
799 |
45 |
try |
800 |
|
{ |
801 |
45 |
if (fl.exists()) |
802 |
|
{ |
803 |
45 |
protocol = DataSourceType.FILE; |
804 |
|
} |
805 |
|
} catch (Exception e) |
806 |
|
{ |
807 |
|
} catch (Error e) |
808 |
|
{ |
809 |
|
} |
810 |
|
|
811 |
45 |
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe], |
812 |
|
fileName, protocol, getIProgressIndicator()); |
813 |
|
|
814 |
|
|
815 |
|
} |
816 |
|
} |
817 |
50 |
if (matches) |
818 |
|
{ |
819 |
45 |
stashFoundChains(pdb, fileName); |
820 |
45 |
notifyLoaded = true; |
821 |
|
} |
822 |
|
} |
823 |
|
|
824 |
48 |
if (!foundEntry && associateNewStructs) |
825 |
|
{ |
826 |
|
|
827 |
|
|
828 |
|
|
829 |
0 |
String pdbcontent = jmolViewer.getData("/" + (modelnum + 1) + ".1", |
830 |
|
"PDB"); |
831 |
|
|
832 |
|
|
833 |
|
|
834 |
|
|
835 |
0 |
notifyLoaded = true; |
836 |
|
|
837 |
|
} |
838 |
|
} |
839 |
|
|
840 |
|
|
841 |
|
|
842 |
|
|
843 |
|
|
844 |
|
|
845 |
|
|
846 |
47 |
if (!isLoadingFromArchive()) |
847 |
|
{ |
848 |
40 |
jmolScript( |
849 |
|
"model *; select backbone;restrict;cartoon;wireframe off;spacefill off"); |
850 |
|
} |
851 |
|
|
852 |
|
|
853 |
47 |
getSsm().addStructureViewerListener(this); |
854 |
47 |
if (notifyLoaded) |
855 |
|
{ |
856 |
44 |
FeatureRenderer fr = getFeatureRenderer(null); |
857 |
43 |
if (fr != null) |
858 |
|
{ |
859 |
43 |
FeatureSettingsModelI colours = new Pdb().getFeatureColourScheme(); |
860 |
43 |
((AppJmol) getViewer()).getAlignmentPanel().av |
861 |
|
.applyFeaturesStyle(colours); |
862 |
|
} |
863 |
43 |
refreshGUI(); |
864 |
43 |
loadNotifiesHandled++; |
865 |
|
} |
866 |
46 |
setLoadingFromArchive(false); |
867 |
|
} |
868 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
869 |
45 |
protected IProgressIndicator getIProgressIndicator()... |
870 |
|
{ |
871 |
45 |
return null; |
872 |
|
} |
873 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
874 |
0 |
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)... |
875 |
|
{ |
876 |
0 |
notifyAtomPicked(iatom, strMeasure, null); |
877 |
|
} |
878 |
|
|
879 |
|
public abstract void notifyScriptTermination(String strStatus, |
880 |
|
int msWalltime); |
881 |
|
|
882 |
|
|
883 |
|
|
884 |
|
|
885 |
|
@param |
886 |
|
|
887 |
|
public abstract void sendConsoleEcho(String strEcho); |
888 |
|
|
889 |
|
|
890 |
|
|
891 |
|
|
892 |
|
|
893 |
|
|
894 |
|
|
895 |
|
|
896 |
|
|
897 |
|
@param |
898 |
|
|
899 |
|
|
900 |
|
|
901 |
|
public abstract void sendConsoleMessage(String strStatus); |
902 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
903 |
0 |
@Override... |
904 |
|
public void setCallbackFunction(String callbackType, |
905 |
|
String callbackFunction) |
906 |
|
{ |
907 |
0 |
jalview.bin.Console |
908 |
|
.errPrintln("Ignoring set-callback request to associate " |
909 |
|
+ callbackType + " with function " + callbackFunction); |
910 |
|
|
911 |
|
} |
912 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
913 |
0 |
public void showHelp()... |
914 |
|
{ |
915 |
0 |
showUrl("http://wiki.jmol.org" |
916 |
|
|
917 |
|
, "jmolHelp"); |
918 |
|
} |
919 |
|
|
920 |
|
|
921 |
|
|
922 |
|
|
923 |
|
@param |
924 |
|
|
925 |
|
public abstract void showUrl(String url, String target); |
926 |
|
|
927 |
|
|
928 |
|
|
929 |
|
|
930 |
|
@param |
931 |
|
|
932 |
|
public abstract void showConsole(boolean show); |
933 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
934 |
176 |
public static Viewer getJmolData(JmolParser jmolParser)... |
935 |
|
{ |
936 |
176 |
return (Viewer) JmolViewer.allocateViewer(null, null, null, null, null, |
937 |
|
"-x -o -n", jmolParser); |
938 |
|
} |
939 |
|
|
940 |
|
|
941 |
|
|
942 |
|
|
943 |
|
|
944 |
|
@param |
945 |
|
@param |
946 |
|
|
947 |
|
|
948 |
|
@param |
949 |
|
@param |
950 |
|
@param |
951 |
|
@param |
952 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
953 |
0 |
public void allocateViewer(Container renderPanel, boolean jmolfileio,... |
954 |
|
String htmlName, URL documentBase, URL codeBase, |
955 |
|
String commandOptions) |
956 |
|
{ |
957 |
0 |
allocateViewer(renderPanel, jmolfileio, htmlName, documentBase, |
958 |
|
codeBase, commandOptions, null, null); |
959 |
|
} |
960 |
|
|
961 |
|
|
962 |
|
|
963 |
|
@param |
964 |
|
@param |
965 |
|
|
966 |
|
|
967 |
|
@param |
968 |
|
@param |
969 |
|
@param |
970 |
|
@param |
971 |
|
@param |
972 |
|
|
973 |
|
@param |
974 |
|
|
975 |
|
|
|
|
| 64.7% |
Uncovered Elements: 6 (17) |
Complexity: 5 |
Complexity Density: 0.45 |
|
976 |
45 |
public void allocateViewer(Container renderPanel, boolean jmolfileio,... |
977 |
|
String htmlName, URL documentBase, URL codeBase, |
978 |
|
String commandOptions, final Container consolePanel, |
979 |
|
String buttonsToShow) |
980 |
|
{ |
981 |
|
|
982 |
45 |
jalview.bin.Console |
983 |
|
.errPrintln("Allocating Jmol Viewer: " + commandOptions); |
984 |
|
|
985 |
45 |
if (commandOptions == null) |
986 |
|
{ |
987 |
0 |
commandOptions = ""; |
988 |
|
} |
989 |
45 |
jmolViewer = (Viewer) JmolViewer.allocateViewer(renderPanel, |
990 |
45 |
(jmolfileio ? new SmarterJmolAdapter() : null), |
991 |
|
htmlName + ((Object) this).toString(), documentBase, codeBase, |
992 |
|
commandOptions, this); |
993 |
|
|
994 |
45 |
jmolViewer.setJmolStatusListener(this); |
995 |
|
|
996 |
45 |
try |
997 |
|
{ |
998 |
45 |
console = createJmolConsole(consolePanel, buttonsToShow); |
999 |
|
} catch (Throwable e) |
1000 |
|
{ |
1001 |
0 |
jalview.bin.Console |
1002 |
|
.errPrintln("Could not create Jmol application console. " |
1003 |
|
+ e.getMessage()); |
1004 |
0 |
e.printStackTrace(); |
1005 |
|
} |
1006 |
45 |
if (consolePanel != null) |
1007 |
|
{ |
1008 |
45 |
consolePanel.addComponentListener(this); |
1009 |
|
|
1010 |
|
} |
1011 |
|
|
1012 |
|
} |
1013 |
|
|
1014 |
|
protected abstract JmolAppConsoleInterface createJmolConsole( |
1015 |
|
Container consolePanel, String buttonsToShow); |
1016 |
|
|
1017 |
|
|
1018 |
|
|
1019 |
|
|
1020 |
|
protected org.jmol.api.JmolAppConsoleInterface console = null; |
1021 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1022 |
0 |
@Override... |
1023 |
|
public int[] resizeInnerPanel(String data) |
1024 |
|
{ |
1025 |
|
|
1026 |
0 |
return null; |
1027 |
|
} |
1028 |
|
|
1029 |
|
|
1030 |
|
|
1031 |
|
|
|
|
| 85.7% |
Uncovered Elements: 1 (7) |
Complexity: 4 |
Complexity Density: 0.8 |
|
1032 |
23 |
protected void closeConsole()... |
1033 |
|
{ |
1034 |
23 |
if (console != null) |
1035 |
|
{ |
1036 |
23 |
try |
1037 |
|
{ |
1038 |
23 |
console.setVisible(false); |
1039 |
|
} catch (Error e) |
1040 |
|
{ |
1041 |
|
} catch (Exception x) |
1042 |
|
{ |
1043 |
|
} |
1044 |
23 |
; |
1045 |
23 |
console = null; |
1046 |
|
} |
1047 |
|
} |
1048 |
|
|
1049 |
|
|
1050 |
|
|
1051 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1052 |
0 |
@Override... |
1053 |
|
public void componentMoved(ComponentEvent e) |
1054 |
|
{ |
1055 |
|
} |
1056 |
|
|
1057 |
|
|
1058 |
|
|
1059 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1060 |
0 |
@Override... |
1061 |
|
public void componentResized(ComponentEvent e) |
1062 |
|
{ |
1063 |
|
} |
1064 |
|
|
1065 |
|
|
1066 |
|
|
1067 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1068 |
0 |
@Override... |
1069 |
|
public void componentShown(ComponentEvent e) |
1070 |
|
{ |
1071 |
0 |
showConsole(true); |
1072 |
|
} |
1073 |
|
|
1074 |
|
|
1075 |
|
|
1076 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1077 |
0 |
@Override... |
1078 |
|
public void componentHidden(ComponentEvent e) |
1079 |
|
{ |
1080 |
0 |
showConsole(false); |
1081 |
|
} |
1082 |
|
|
|
|
| 66.7% |
Uncovered Elements: 4 (12) |
Complexity: 4 |
Complexity Density: 0.67 |
|
1083 |
269 |
@Override... |
1084 |
|
protected String getModelIdForFile(String pdbFile) |
1085 |
|
{ |
1086 |
269 |
if (modelFileNames == null) |
1087 |
|
{ |
1088 |
0 |
return ""; |
1089 |
|
} |
1090 |
272 |
for (int i = 0; i < modelFileNames.length; i++) |
1091 |
|
{ |
1092 |
272 |
if (modelFileNames[i].equalsIgnoreCase(pdbFile)) |
1093 |
|
{ |
1094 |
269 |
return String.valueOf(i + 1); |
1095 |
|
} |
1096 |
|
} |
1097 |
0 |
return ""; |
1098 |
|
} |
1099 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1100 |
2 |
@Override... |
1101 |
|
protected ViewerType getViewerType() |
1102 |
|
{ |
1103 |
2 |
return ViewerType.JMOL; |
1104 |
|
} |
1105 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1106 |
0 |
@Override... |
1107 |
|
protected String getModelId(int pdbfnum, String file) |
1108 |
|
{ |
1109 |
0 |
return String.valueOf(pdbfnum + 1); |
1110 |
|
} |
1111 |
|
|
1112 |
|
|
1113 |
|
|
1114 |
|
|
1115 |
|
@return |
1116 |
|
@see |
1117 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1118 |
2 |
@Override... |
1119 |
|
public String getSessionFileExtension() |
1120 |
|
{ |
1121 |
2 |
return ".spt"; |
1122 |
|
} |
1123 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1124 |
0 |
@Override... |
1125 |
|
public void selectionChanged(BS arg0) |
1126 |
|
{ |
1127 |
|
|
1128 |
|
|
1129 |
|
} |
1130 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1131 |
0 |
@Override... |
1132 |
|
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp) |
1133 |
|
{ |
1134 |
0 |
return new jalview.gui.SequenceRenderer(avp.getAlignViewport()); |
1135 |
|
} |
1136 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1137 |
0 |
@Override... |
1138 |
|
public String getHelpURL() |
1139 |
|
{ |
1140 |
0 |
return "http://wiki.jmol.org"; |
1141 |
|
} |
1142 |
|
} |