import jalview.gui.Desktop;
import jalview.gui.Preferences;
import jalview.gui.PromptUserConfig;
+import jalview.gui.StructureViewer;
import jalview.io.AppletFormatAdapter;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
void doMain(String[] args)
{
- if (!Platform.isJS())
+ boolean isJS = Platform.isJS();
+ if (!isJS)
{
System.setSecurityManager(null);
}
String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
Cache.loadProperties(usrPropsFile);
- if (Platform.isJS())
+ if (isJS)
{
isJavaAppletTag = aparser.isApplet();
if (isJavaAppletTag)
else
{
System.out.println("Executing setprop argument: " + defs);
- if (Platform.isJS())
+ if (isJS)
{
Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
}
desktop.setInBatchMode(true); // indicate we are starting up
desktop.setVisible(true);
- if (!Platform.isJS())
+ if (!isJS)
/**
* Java only
*
}
String data = null;
- FileFormatI format = null;
- DataSourceType protocol = null;
FileLoader fileLoader = new FileLoader(!headless);
// script to execute after all loading is
// completed one way or another
// extract groovy argument and execute if necessary
- String groovyscript = aparser.getValue(ArgsParser.GROOVY, true);
+ String groovyscript = (isJS ? null
+ : aparser.getValue(ArgsParser.GROOVY, true));
String file = aparser.getValue(ArgsParser.OPEN, true);
+ String file2 = (isJavaAppletTag ? aparser.getAppletValue("file2", null)
+ : null);
+ String fileFormat = (isJavaAppletTag
+ ? aparser.getAppletValue("format", null)
+ : null);
+ FileFormatI format = null;
+ DataSourceType protocol = null;
if (file == null && desktop == null)
{
System.out.println("No files to open!");
System.exit(1);
}
- String vamsasImport = aparser.getValue(ArgsParser.VDOC);
- String vamsasSession = aparser.getValue(ArgsParser.VSESS);
- if (vamsasImport != null || vamsasSession != null)
- {
- if (desktop == null || headless)
- {
- System.out.println(
- "Headless vamsas sessions not yet supported. Sorry.");
- System.exit(1);
- }
- // if we have a file, start a new session and import it.
- boolean inSession = false;
- if (vamsasImport != null)
- {
- try
- {
- DataSourceType viprotocol = AppletFormatAdapter
- .checkProtocol(vamsasImport);
- if (viprotocol == DataSourceType.FILE)
- {
- inSession = desktop.vamsasImport(new File(vamsasImport));
- }
- else if (viprotocol == DataSourceType.URL)
- {
- inSession = desktop.vamsasImport(new URL(vamsasImport));
- }
-
- } catch (Exception e)
- {
- System.err.println("Exeption when importing " + vamsasImport
- + " as a vamsas document.");
- e.printStackTrace();
- }
- if (!inSession)
- {
- System.err.println("Failed to import " + vamsasImport
- + " as a vamsas document.");
- }
- else
- {
- System.out.println("Imported Successfully into new session "
- + desktop.getVamsasApplication().getCurrentSession());
- }
- }
- if (vamsasSession != null)
- {
- if (vamsasImport != null)
- {
- // close the newly imported session and import the Jalview specific
- // remnants into the new session later on.
- desktop.vamsasStop_actionPerformed(null);
- }
- // now join the new session
- try
- {
- if (desktop.joinVamsasSession(vamsasSession))
- {
- System.out.println(
- "Successfully joined vamsas session " + vamsasSession);
- }
- else
- {
- System.err.println("WARNING: Failed to join vamsas session "
- + vamsasSession);
- }
- } catch (Exception e)
- {
- System.err.println(
- "ERROR: Failed to join vamsas session " + vamsasSession);
- e.printStackTrace();
- }
- if (vamsasImport != null)
- {
- // the Jalview specific remnants can now be imported into the new
- // session at the user's leisure.
- Cache.log.info(
- "Skipping Push for import of data into existing vamsas session."); // TODO:
- // enable
- // this
- // when
- // debugged
- // desktop.getVamsasApplication().push_update();
- }
- }
- }
- long progress = -1;
+ boolean haveImport = checkStartVamas(aparser);
// Finally, deal with the remaining input data.
+ long progress = -1;
if (file != null)
{
if (!headless)
}
System.out.println("CMD [-open " + file + "] executed successfully!");
- if (!Platform.isJS())
+ if (!isJS)
/**
* ignore in JavaScript -- can't just check file existence - could load
* it?
try
{
- format = new IdentifyFile().identify(file, protocol);
+ format = (isJavaAppletTag && fileFormat != null
+ ? FileFormats.getInstance().forName(fileFormat)
+ : null);
+ if (format == null)
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ }
} catch (FileFormatException e1)
{
// TODO ?
else
{
setCurrentAlignFrame(af);
+
+ // TODO: file2 How to implement file2 for the applet spit screen?
+
data = aparser.getValue(ArgsParser.COLOUR, true);
if (data != null)
{
// TODO - load PDB structure(s) to alignment JAL-629
// (associate with identical sequence in alignment, or a specified
// sequence)
- if (groovyscript != null)
- {
- // Execute the groovy script after we've done all the rendering stuff
- // and before any images or figures are generated.
- System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, af);
- System.out.println("CMD groovy[" + groovyscript
- + "] executed successfully!");
- groovyscript = null;
- }
-
if (isJavaAppletTag)
{
loadAppletParams(aparser, af);
}
- else
+ else if (!isJS)
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
-
- String imageName = "unnamed.png";
- while (aparser.getSize() > 1)
+ if (groovyscript != null)
{
- // PNG filename
- // SVG filename
- // HTML filename
- // biojsmsa filename
- String outputFormat = aparser.nextValue();
- file = aparser.nextValue();
-
- if (outputFormat.equalsIgnoreCase("png"))
- {
- af.createPNG(new File(file));
- imageName = (new File(file)).getName();
- System.out.println("Creating PNG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("svg"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
- af.createSVG(imageFile);
- System.out.println("Creating SVG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("html"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
- HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.exportHTML(file);
-
- System.out.println("Creating HTML image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("biojsmsa"))
- {
- if (file == null)
- {
- System.err.println("The output html file must not be null");
- return;
- }
- try
- {
- BioJsHTMLOutput.refreshVersionInfo(
- BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
- } catch (URISyntaxException e)
- {
- e.printStackTrace();
- }
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
- bjs.exportHTML(file);
- System.out.println(
- "Creating BioJS MSA Viwer HTML file: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("imgMap"))
- {
- af.createImageMap(new File(file), imageName);
- System.out.println("Creating image map: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("eps"))
- {
- File outputFile = new File(file);
- System.out.println(
- "Creating EPS file: " + outputFile.getAbsolutePath());
- af.createEPS(outputFile);
- continue;
- }
-
- af.saveAlignment(file, format);
- if (af.isSaveAlignmentSuccessful())
- {
- System.out.println("Written alignment in " + format
- + " format to " + file);
- }
- else
- {
- System.out.println("Error writing file " + file + " in "
- + format + " format!!");
- }
-
+ // Execute the groovy script after we've done all the rendering stuff
+ // and before any images or figures are generated.
+ System.out.println("Executing script " + groovyscript);
+ executeGroovyScript(groovyscript, af);
+ System.out.println("CMD groovy[" + groovyscript
+ + "] executed successfully!");
+ groovyscript = null;
}
-
+ checkOutputFile(aparser, af, format);
while (aparser.getSize() > 0)
{
System.out.println("Unknown arg: " + aparser.nextValue());
// And the user
// ////////////////////
- if (!Platform.isJS() && !headless && file == null
- && vamsasImport == null
+ if (!isJS && !headless && file == null && !haveImport
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
/**
* Java only
}
}
+ private boolean checkStartVamas(ArgsParser aparser)
+ {
+ String vamsasImport = aparser.getValue(ArgsParser.VDOC);
+ String vamsasSession = aparser.getValue(ArgsParser.VSESS);
+ if (vamsasImport == null && vamsasSession == null)
+ {
+ return false;
+ }
+ if (desktop == null || headless)
+ {
+ System.out.println(
+ "Headless vamsas sessions not yet supported. Sorry.");
+ System.exit(1);
+ }
+ boolean haveImport = (vamsasImport != null);
+ if (haveImport)
+ {
+ // if we have a file, start a new session and import it.
+ boolean inSession = false;
+ try
+ {
+ DataSourceType viprotocol = AppletFormatAdapter
+ .checkProtocol(vamsasImport);
+ if (viprotocol == DataSourceType.FILE)
+ {
+ inSession = desktop.vamsasImport(new File(vamsasImport));
+ }
+ else if (viprotocol == DataSourceType.URL)
+ {
+ inSession = desktop.vamsasImport(new URL(vamsasImport));
+ }
+
+ } catch (Exception e)
+ {
+ System.err.println("Exeption when importing " + vamsasImport
+ + " as a vamsas document.");
+ e.printStackTrace();
+ }
+ if (!inSession)
+ {
+ System.err.println("Failed to import " + vamsasImport
+ + " as a vamsas document.");
+ }
+ else
+ {
+ System.out.println("Imported Successfully into new session "
+ + desktop.getVamsasApplication().getCurrentSession());
+ }
+ }
+ if (vamsasSession != null)
+ {
+ if (vamsasImport != null)
+ {
+ // close the newly imported session and import the Jalview specific
+ // remnants into the new session later on.
+ desktop.vamsasStop_actionPerformed(null);
+ }
+ // now join the new session
+ try
+ {
+ if (desktop.joinVamsasSession(vamsasSession))
+ {
+ System.out.println(
+ "Successfully joined vamsas session " + vamsasSession);
+ }
+ else
+ {
+ System.err.println("WARNING: Failed to join vamsas session "
+ + vamsasSession);
+ }
+ } catch (Exception e)
+ {
+ System.err.println(
+ "ERROR: Failed to join vamsas session " + vamsasSession);
+ e.printStackTrace();
+ }
+ if (vamsasImport != null)
+ {
+ // the Jalview specific remnants can now be imported into the new
+ // session at the user's leisure.
+ Cache.log.info(
+ "Skipping Push for import of data into existing vamsas session."); // TODO:
+ // enable
+ // this
+ // when
+ // debugged
+ // desktop.getVamsasApplication().push_update();
+ }
+ }
+ return haveImport;
+ }
+
+ private void checkOutputFile(ArgsParser aparser, AlignFrame af,
+ FileFormatI format)
+ {
+ String imageName = "unnamed.png";
+ while (aparser.getSize() > 1)
+ {
+ // PNG filename
+ // SVG filename
+ // HTML filename
+ // biojsmsa filename
+ String outputFormat = aparser.nextValue();
+ String file = aparser.nextValue();
+ if (outputFormat.equalsIgnoreCase("png"))
+ {
+ af.createPNG(new File(file));
+ imageName = (new File(file)).getName();
+ System.out.println("Creating PNG image: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("svg"))
+ {
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ af.createSVG(imageFile);
+ System.out.println("Creating SVG image: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("html"))
+ {
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(file);
+
+ System.out.println("Creating HTML image: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("biojsmsa"))
+ {
+ if (file == null)
+ {
+ System.err.println("The output html file must not be null");
+ return;
+ }
+ try
+ {
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(file);
+ System.out.println("Creating BioJS MSA Viwer HTML file: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("imgMap"))
+ {
+ af.createImageMap(new File(file), imageName);
+ System.out.println("Creating image map: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("eps"))
+ {
+ File outputFile = new File(file);
+ System.out.println(
+ "Creating EPS file: " + outputFile.getAbsolutePath());
+ af.createEPS(outputFile);
+ continue;
+ }
+
+ af.saveAlignment(file, format);
+ if (af.isSaveAlignmentSuccessful())
+ {
+ System.out.println(
+ "Written alignment in " + format + " format to " + file);
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in " + format
+ + " format!!");
+ }
+
+ }
+ }
+
private static void showUsage()
{
System.out.println(
*/
private void loadAppletParams(ArgsParser aparser, AlignFrame af)
{
- Jalview me = this;
JalviewApp app = new JalviewApp()
{
+ private boolean alignPDBStructures; // From JalviewLite; not implemented
+
@Override
public String getParameter(String name)
{
@Override
public AlignViewportI getViewport()
{
- return Jalview.getCurrentAlignFrame().getViewport();
+ return af.getViewport();
}
/**
@Override
public boolean loadScoreFile(String sScoreFile) throws IOException
{
- Jalview.getCurrentAlignFrame().loadJalviewDataFile(sScoreFile, null,
+ af.loadJalviewDataFile(sScoreFile, null,
null, null);
return true;
}
@Override
public void updateForAnnotations()
{
- Jalview.getCurrentAlignFrame().updateForAnnotations();
+ af.updateForAnnotations();
}
@Override
@Override
public void setAlignPdbStructures(boolean defaultParameter)
{
- // TODO Auto-generated method stub
-
+ alignPDBStructures = true;
}
@Override
public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
String[] chains, DataSourceType protocol)
{
- // TODO Auto-generated method stub
-
+ StructureViewer.launchStructureViewer(af.alignPanel, pdb, seqs);
}
@Override
- public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
- String[][] chains, String[] protocols)
+ public void setFeatureGroupState(String[] groups, boolean state)
{
- // TODO Auto-generated method stub
-
+ af.setFeatureGroupState(groups, state);
}
@Override
- public void setFeatureGroupState(String[] groups, boolean state)
+ public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
+ String[][] chains, String[] protocols)
{
- // TODO Auto-generated method stub
-
+ System.err.println(
+ "Jalview applet interface alignedStructureView not implemented");
}
@Override
public void newFeatureSettings()
{
- // TODO Auto-generated method stub
-
+ System.err.println(
+ "Jalview applet interface newFeatureSettings not implemented");
}
};
git://source.jalview.org / jalview.git / commitdiff