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Update Jmol version and revert to MMCIF format for JmolPanel #785

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Merged
lafita merged 2 commits into from
Aug 7, 2018
Merged

Update Jmol version and revert to MMCIF format for JmolPanel #785

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b61262a
Update Jmol version to 14.29.17
lafita Jul 26, 2018
00f25a7
Revert to mmCIF for Jmol view
lafita Jul 26, 2018
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2 changes: 1 addition & 1 deletion biojava-structure-gui/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@
<dependency>
<groupId>net.sourceforge.jmol</groupId>
<artifactId>jmol</artifactId>
<version>14.6.2_2016.08.28</version>
<version>14.29.17</version>
</dependency>
<!-- logging dependencies (managed by parent pom, don't set versions or
scopes here) -->
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56 changes: 35 additions & 21 deletions biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -126,30 +126,44 @@ public JmolStatusListener getStatusListener(){
public void executeCmd(String rasmolScript) {
viewer.evalString(rasmolScript);
}

public void setStructure(final Structure s)
{
public void setStructure(final Structure s, boolean useMmtf) {
this.structure = s;
try (
PipedOutputStream out = new PipedOutputStream();
// Viewer requires a BufferedInputStream for reflection
InputStream in = new BufferedInputStream(new PipedInputStream(out));
) {
new Thread((Runnable)() -> {
try {
MmtfActions.writeToOutputStream(s,out);
} catch (Exception e) {
logger.error("Error generating MMTF output for {}",
s.getStructureIdentifier()==null ? s.getStructureIdentifier().getIdentifier() : s.getName(), e);
}
}).start();
viewer.openReader(null, in);
} catch (IOException e) {
logger.error("Error transfering {} to Jmol",
s.getStructureIdentifier()==null ? s.getStructureIdentifier().getIdentifier() : s.getName(), e);

if (useMmtf) {
try (
PipedOutputStream out = new PipedOutputStream();
// Viewer requires a BufferedInputStream for reflection
InputStream in = new BufferedInputStream(new PipedInputStream(out));
) {
new Thread((Runnable)() -> {
try {
MmtfActions.writeToOutputStream(s,out);
} catch (Exception e) {
logger.error("Error generating MMTF output for {}",
s.getStructureIdentifier()==null ? s.getStructureIdentifier().getIdentifier() : s.getName(), e);
}
}).start();
viewer.openReader(null, in);
} catch (IOException e) {
logger.error("Error transfering {} to Jmol",
s.getStructureIdentifier()==null ? s.getStructureIdentifier().getIdentifier() : s.getName(), e);
}
} else {
// Use mmCIF format
String serialized = s.toMMCIF();
viewer.openStringInline(serialized);

}

evalString("save STATE state_1");

}

public void setStructure(final Structure s) {
// Set the default to MMCIF (until issue #629 is fixed)
setStructure(s, false);
}

/** assign a custom color to the Jmol chains command.
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