import java.awt.Color;
import java.awt.Font;
-import java.awt.FontMetrics;
import java.awt.Rectangle;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.bin.Console;
+import jalview.bin.Jalview;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
}
} catch (Exception x)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
+ ref.getSref());
x.printStackTrace();
}
if (unresolved > 0)
{
- System.err.println("Jalview Project Import: There were " + unresolved
+ jalview.bin.Console.errPrintln("Jalview Project Import: There were "
+ + unresolved
+ " forward references left unresolved on the stack.");
}
if (failedtoresolve > 0)
{
- System.err.println("SERIOUS! " + failedtoresolve
+ jalview.bin.Console.errPrintln("SERIOUS! " + failedtoresolve
+ " resolvable forward references failed to resolve.");
}
if (incompleteSeqs != null && incompleteSeqs.size() > 0)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Jalview Project Import: There are " + incompleteSeqs.size()
+ " sequences which may have incomplete metadata.");
if (incompleteSeqs.size() < 10)
{
for (SequenceI s : incompleteSeqs.values())
{
- System.err.println(s.toString());
+ jalview.bin.Console.errPrintln(s.toString());
}
}
else
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Too many to report. Skipping output of incomplete sequences.");
}
}
object.setCreationDate(now);
} catch (DatatypeConfigurationException e)
{
- System.err.println("error writing date: " + e.toString());
+ jalview.bin.Console.errPrintln("error writing date: " + e.toString());
}
object.setVersion(Cache.getDefault("VERSION", "Development Build"));
// HAPPEN! (PF00072.15.stk does this)
// JBPNote: Uncomment to debug writing out of files that do not read
// back in due to ArrayOutOfBoundExceptions.
- // System.err.println("vamsasSeq backref: "+id+"");
- // System.err.println(jds.getName()+"
+ // jalview.bin.Console.errPrintln("vamsasSeq backref: "+id+"");
+ // jalview.bin.Console.errPrintln(jds.getName()+"
// "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
- // System.err.println("Hashcode: "+seqHash(jds));
+ // jalview.bin.Console.errPrintln("Hashcode: "+seqHash(jds));
// SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
- // System.err.println(rsq.getName()+"
+ // jalview.bin.Console.errPrintln(rsq.getName()+"
// "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
- // System.err.println("Hashcode: "+seqHash(rsq));
+ // jalview.bin.Console.errPrintln("Hashcode: "+seqHash(rsq));
}
else
{
* only view *should* be coped with sensibly.
*/
// This must have been loaded, is it still visible?
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- String matchedFile = null;
- for (int f = frames.length - 1; f > -1; f--)
+ List<JalviewStructureDisplayI> viewFrames = new ArrayList<>();
+ if (Desktop.desktop != null)
{
- if (frames[f] instanceof StructureViewerBase)
+ JInternalFrame[] jifs = Desktop.desktop.getAllFrames();
+ if (jifs != null)
{
- StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
- matchedFile = saveStructureViewer(ap, jds, pdb, entry,
- viewIds, matchedFile, viewFrame);
- /*
- * Only store each structure viewer's state once in the project
- * jar. First time through only (storeDS==false)
- */
- String viewId = viewFrame.getViewId();
- String viewerType = viewFrame.getViewerType().toString();
- if (!storeDS && !viewIds.contains(viewId))
+ for (JInternalFrame jif : jifs)
{
- viewIds.add(viewId);
- File viewerState = viewFrame.saveSession();
- if (viewerState != null)
- {
- copyFileToJar(jout, viewerState.getPath(),
- getViewerJarEntryName(viewId), viewerType);
- }
- else
+ if (jif instanceof JalviewStructureDisplayI)
{
- Console.error(
- "Failed to save viewer state for " + viewerType);
+ viewFrames.add((JalviewStructureDisplayI) jif);
}
}
}
}
+ else if (Jalview.isHeadlessMode()
+ && Jalview.getInstance().getCommands() != null)
+ {
+ viewFrames.addAll(
+ StructureViewerBase.getAllStructureViewerBases());
+ }
+
+ String matchedFile = null;
+ for (JalviewStructureDisplayI viewFrame : viewFrames)
+ {
+ matchedFile = saveStructureViewer(ap, jds, pdb, entry, viewIds,
+ matchedFile, viewFrame);
+ /*
+ * Only store each structure viewer's state once in the project
+ * jar. First time through only (storeDS==false)
+ */
+ String viewId = viewFrame.getViewId();
+ String viewerType = viewFrame.getViewerType().toString();
+ if (!storeDS && !viewIds.contains(viewId))
+ {
+ viewIds.add(viewId);
+ File viewerState = viewFrame.saveSession();
+ if (viewerState != null)
+ {
+ copyFileToJar(jout, viewerState.getPath(),
+ getViewerJarEntryName(viewId), viewerType);
+ }
+ else
+ {
+ Console.error(
+ "Failed to save viewer state for " + viewerType);
+ }
+ }
+ }
if (matchedFile != null || entry.getFile() != null)
{
try
{
fileName = fileName.replace('\\', '/');
- System.out.println("Writing jar entry " + fileName);
+ jalview.bin.Console.outPrintln("Writing jar entry " + fileName);
JarEntry entry = new JarEntry(fileName);
jout.putNextEntry(entry);
PrintWriter pout = new PrintWriter(
} catch (Exception ex)
{
// TODO: raise error in GUI if marshalling failed.
- System.err.println("Error writing Jalview project");
+ jalview.bin.Console.errPrintln("Error writing Jalview project");
ex.printStackTrace();
}
}
File file = new File(infilePath);
if (file.exists() && jout != null)
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"Writing jar entry " + jarEntryName + " (" + msg + ")");
jout.putNextEntry(new JarEntry(jarEntryName));
copyAll(is, jout);
*/
protected String saveStructureViewer(AlignmentPanel ap, SequenceI jds,
Pdbids pdb, PDBEntry entry, List<String> viewIds,
- String matchedFile, StructureViewerBase viewFrame)
+ String matchedFile, JalviewStructureDisplayI viewFrame)
{
final AAStructureBindingModel bindingModel = viewFrame.getBinding();
{
StructureState state = new StructureState();
state.setVisible(true);
- state.setXpos(viewFrame.getX());
+ state.setXpos(viewFrame.getY());
state.setYpos(viewFrame.getY());
state.setWidth(viewFrame.getWidth());
state.setHeight(viewFrame.getHeight());
return BitSet.valueOf(newlongvals);
}
+
private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
{
AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
});
} catch (Exception x)
{
- System.err.println("Error loading alignment: " + x.getMessage());
+ jalview.bin.Console
+ .errPrintln("Error loading alignment: " + x.getMessage());
}
}
return af;
{
if (bytes != null)
{
- // System.out.println("Jalview2XML: opening byte jarInputStream for
+ // jalview.bin.Console.outPrintln("Jalview2XML: opening byte
+ // jarInputStream for
// bytes.length=" + bytes.length);
return new JarInputStream(new ByteArrayInputStream(bytes));
}
if (_url != null)
{
- // System.out.println("Jalview2XML: opening url jarInputStream for "
+ // jalview.bin.Console.outPrintln("Jalview2XML: opening url
+ // jarInputStream for "
// + _url);
return new JarInputStream(_url.openStream());
}
else
{
- // System.out.println("Jalview2XML: opening file jarInputStream for
+ // jalview.bin.Console.outPrintln("Jalview2XML: opening file
+ // jarInputStream for
// " + file);
return new JarInputStream(new FileInputStream(file));
}
{
ex.printStackTrace();
errorMessage = "Couldn't locate Jalview XML file : " + file;
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Exception whilst loading jalview XML file : " + ex + "\n");
} catch (Exception ex)
{
- System.err.println("Parsing as Jalview Version 2 file failed.");
+ jalview.bin.Console
+ .errPrintln("Parsing as Jalview Version 2 file failed.");
ex.printStackTrace(System.err);
if (attemptversion1parse)
{
}
if (af != null)
{
- System.out.println("Successfully loaded archive file");
+ jalview.bin.Console.outPrintln("Successfully loaded archive file");
return af;
}
ex.printStackTrace();
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Exception whilst loading jalview XML file : " + ex + "\n");
} catch (OutOfMemoryError e)
{
// Don't use the OOM Window here
errorMessage = "Out of memory loading jalview XML file";
- System.err.println("Out of memory whilst loading jalview XML file");
+ jalview.bin.Console
+ .errPrintln("Out of memory whilst loading jalview XML file");
e.printStackTrace();
}
Desktop.addInternalFrame(af, view.getTitle(),
safeInt(view.getWidth()), safeInt(view.getHeight()));
af.setMenusForViewport();
- System.err.println("Failed to restore view " + view.getTitle()
- + " to split frame");
+ jalview.bin.Console.errPrintln("Failed to restore view "
+ + view.getTitle() + " to split frame");
}
}
}
else
{
- System.err.println("Problem loading Jalview file: " + errorMessage);
+ jalview.bin.Console.errPrintln(
+ "Problem loading Jalview file: " + errorMessage);
}
}
errorMessage = null;
if (tmpSeq.getStart() != jseq.getStart()
|| tmpSeq.getEnd() != jseq.getEnd())
{
- System.err.println(String.format(
+ jalview.bin.Console.errPrintln(String.format(
"Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
tmpSeq.getName(), tmpSeq.getStart(), tmpSeq.getEnd(),
jseq.getStart(), jseq.getEnd()));
// XML.
// and then recover its containing af to allow the settings to be applied.
// TODO: fix for vamsas demo
- System.err.println(
+ jalview.bin.Console.errPrintln(
"About to recover a viewport for existing alignment: Sequence set ID is "
+ uniqueSeqSetId);
Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
if (seqsetobj instanceof String)
{
uniqueSeqSetId = (String) seqsetobj;
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
+ uniqueSeqSetId);
}
else
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Warning : Collision between sequence set ID string and existing jalview object mapping.");
}
{
if (tree.isColumnWise())
{
- AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds
+ AlignmentAnnotation aa = annotationIds
.get(tree.getColumnReference());
if (aa == null)
{
createOrLinkStructureViewer(entry, af, ap, jprovider);
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Error loading structure viewer: " + e.getMessage());
// failed - try the next one
}
|| version.equalsIgnoreCase("Test")
|| version.equalsIgnoreCase("AUTOMATED BUILD"))
{
- System.err.println("Assuming project file with "
+ jalview.bin.Console.errPrintln("Assuming project file with "
+ (version == null ? "null" : version)
+ " is compatible with Jalview version " + supported);
return true;
//
// @Override
// protected void processKeyEvent(java.awt.event.KeyEvent e) {
- // System.out.println("Jalview2XML AF " + e);
+ // jalview.bin.Console.outPrintln("Jalview2XML AF " + e);
// super.processKeyEvent(e);
//
// }
}
if (matchedAnnotation == null)
{
- System.err.println("Failed to match annotation colour scheme for "
- + annotationId);
+ jalview.bin.Console
+ .errPrintln("Failed to match annotation colour scheme for "
+ + annotationId);
return null;
}
// belt-and-braces create a threshold line if the
}
// TODO: merges will never happen if we 'know' we have the real dataset
// sequence - this should be detected when id==dssid
- System.err.println(
+ jalview.bin.Console.errPrintln(
"DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
// + (pre ? "prepended" : "") + " "
// + (post ? "appended" : ""));
}
else
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Warning - making up dataset sequence id for DbRef sequence map reference");
sqid = ((Object) ms).toString(); // make up a new hascode for
// undefined dataset sequence hash
} catch (IllegalStateException e)
{
// mixing AND and OR conditions perhaps
- System.err.println(
+ jalview.bin.Console.errPrintln(
String.format("Error reading filter conditions for '%s': %s",
featureType, e.getMessage()));
// return as much as was parsed up to the error
}
else
{
- System.err.println("Malformed compound filter condition");
+ jalview.bin.Console
+ .errPrintln("Malformed compound filter condition");
}
}
}
git://source.jalview.org / jalview.git / blobdiff