*/
package jalview.bin;
-import jalview.analysis.AlignmentSorter;
-import jalview.analysis.scoremodels.ScoreModels;
-import jalview.api.StructureSelectionManagerProvider;
-import jalview.ext.ensembl.EnsemblInfo;
+import jalview.api.AlignViewportI;
+import jalview.api.JalviewApp;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
import jalview.ext.so.SequenceOntology;
-import jalview.fts.service.pdb.PDBFTSRestClient;
-import jalview.fts.service.uniprot.UniProtFTSRestClient;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.Preferences;
import jalview.gui.PromptUserConfig;
-import jalview.httpserver.HttpServer;
import jalview.io.AppletFormatAdapter;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
import jalview.io.gff.SequenceOntologyFactory;
-import jalview.io.gff.SequenceOntologyI;
-import jalview.rest.RestHandler;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.structure.StructureImportSettings;
-import jalview.structure.StructureSelectionManager;
-import jalview.urls.IdOrgSettings;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.ws.SequenceFetcher;
-import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
-import jalview.ws.rest.RestClient;
-import jalview.ws.sifts.SiftsSettings;
-import java.awt.Color;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.security.Permissions;
import java.security.Policy;
import java.util.HashMap;
-import java.util.IdentityHashMap;
import java.util.Map;
import java.util.Vector;
import java.util.logging.ConsoleHandler;
* @author $author$
* @version $Revision$
*/
-public class Jalview
+public class Jalview implements ApplicationSingletonI
{
- static
+
+ public static Jalview getInstance()
{
- Platform.getURLCommandArguments();
+ return (Jalview) ApplicationSingletonProvider
+ .getInstance(Jalview.class);
}
- private boolean headless;
-
- public static boolean isHeadlessMode()
+ private Jalview()
{
- return getInstance().headless;
}
- /**
- * singleton instance of this class in Java only
- */
-
- private static Jalview instance;
-
- public static Jalview getInstance()
+ static
{
- Jalview j;
- @SuppressWarnings("unused")
- ThreadGroup g = Thread.currentThread().getThreadGroup();
- /**
- * @j2sNative j = g._jalviewInstance;
- */
- {
- j = instance;
- }
- return j;
+ Platform.getURLCommandArguments();
}
- private static void setInstance(Jalview j)
+ private boolean headless;
+
+ public static boolean isHeadlessMode()
{
- @SuppressWarnings("unused")
- ThreadGroup g = Thread.currentThread().getThreadGroup();
- /**
- * @j2sNative g._jalviewInstance = j;
- */
- {
- instance = j;
- }
+ return getInstance().headless;
}
private Desktop desktop;
private AlignFrame currentAlignFrame;
+ public boolean isJavaAppletTag;
+
+ public String appletResourcePath;
+
public static AlignFrame getCurrentAlignFrame()
{
return getInstance().currentAlignFrame;
public static void main(String[] args)
{
// setLogging(); // BH - for event debugging in JavaScript
- setInstance(new Jalview());
getInstance().doMain(args);
}
String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
Cache.loadProperties(usrPropsFile);
- if (usrPropsFile != null)
+ if (Platform.isJS())
{
+ isJavaAppletTag = aparser.isApplet();
+ if (isJavaAppletTag)
+ {
+ Preferences.setAppletDefaults();
+ Cache.loadProperties(usrPropsFile); // again, because we
+ // might be changing defaults here?
+ }
System.out.println(
- "CMD [-props " + usrPropsFile + "] executed successfully!");
+ "<Applet> found: " + aparser.getValue("Info.j2sAppletID"));
+ appletResourcePath = aparser.getValue("Info.resourcePath");
}
-
- if (!Platform.isJS())
+ else
/**
* Java only
*
* @j2sIgnore
*/
{
+ if (usrPropsFile != null)
+ {
+ System.out.println(
+ "CMD [-props " + usrPropsFile + "] executed successfully!");
+ }
+
if (aparser.contains("help") || aparser.contains("h"))
{
showUsage();
{
try
{
- Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+ Jws2Discoverer.getInstance().setPreferredUrl(jabawsUrl);
System.out.println(
"CMD [-jabaws " + jabawsUrl + "] executed successfully!");
} catch (MalformedURLException e)
*/
if (Cache.getDefault("USE_FULL_SO", false))
{
- SequenceOntologyFactory.setInstance(new SequenceOntology());
+ SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
}
if (!headless)
{
- desktop = new Desktop();
+ desktop = Desktop.getInstance();
desktop.setInBatchMode(true); // indicate we are starting up
desktop.setVisible(true);
+ "] executed successfully!");
groovyscript = null;
}
- String imageName = "unnamed.png";
- while (aparser.getSize() > 1)
+
+ if (isJavaAppletTag)
+ {
+ loadAppletParams(aparser, af);
+ }
+ else
{
- // 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"))
+ String imageName = "unnamed.png";
+ while (aparser.getSize() > 1)
{
- if (file == null)
+ // PNG filename
+ // SVG filename
+ // HTML filename
+ // biojsmsa filename
+ String outputFormat = aparser.nextValue();
+ file = aparser.nextValue();
+
+ if (outputFormat.equalsIgnoreCase("png"))
{
- System.err.println("The output html file must not be null");
- return;
+ af.createPNG(new File(file));
+ imageName = (new File(file)).getName();
+ System.out.println("Creating PNG image: " + file);
+ continue;
}
- try
+ else if (outputFormat.equalsIgnoreCase("svg"))
{
- BioJsHTMLOutput.refreshVersionInfo(
- BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
- } catch (URISyntaxException e)
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ af.createSVG(imageFile);
+ System.out.println("Creating SVG image: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("html"))
{
- e.printStackTrace();
+ 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!!");
}
- 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
+
+ while (aparser.getSize() > 0)
{
- System.out.println("Error writing file " + file + " in "
- + format + " format!!");
+ System.out.println("Unknown arg: " + aparser.nextValue());
}
-
- }
-
- while (aparser.getSize() > 0)
- {
- System.out.println("Unknown arg: " + aparser.nextValue());
}
}
}
}
}
- // singleton instances
+ /**
+ * Get the SwingJS applet ID and combine that with the frameType
+ *
+ * @param frameType
+ * "alignment", "desktop", etc., or null
+ * @return
+ */
+ public static String getAppID(String frameType)
+ {
+ String id = Cache.getProperty("Info.j2sAppletID");
+ if (id == null)
+ {
+ id = "jalview";
+ }
+ return id + (frameType == null ? "" : "-" + frameType);
+ }
- public Cache cache;
+ private void loadAppletParams(ArgsParser aparser, AlignFrame af)
+ {
+ Jalview me = this;
+ JalviewApp app = new JalviewApp()
+ {
- public AlignmentSorter alignmentSorter;
- public EnsemblInfo ensemblInfo;
+ @Override
+ public String getParameter(String name)
+ {
+ return aparser.getAppletValue(name, null);
+ }
- public HttpServer httpServer;
+ @Override
+ public boolean getDefaultParameter(String name, boolean def)
+ {
+ String stn;
+ return ((stn = getParameter(name)) == null ? def
+ : "true".equalsIgnoreCase(stn));
+ }
- public IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> structureSelections;
+ @Override
+ public URL getDocumentBase()
+ {
+ return Platform.getDocumentBase();
+ }
+
+ @Override
+ public URL getCodeBase()
+ {
+ return Platform.getCodeBase();
+ }
+
+ @Override
+ public AlignViewportI getViewport()
+ {
+ return Jalview.getCurrentAlignFrame().getViewport();
+ }
+
+ @Override
+ public boolean loadScoreFile(String sScoreFile) throws IOException
+ {
+ Jalview.getCurrentAlignFrame().loadJalviewDataFile(sScoreFile, null,
+ null, null);
+ return true;
+ }
+
+ @Override
+ public boolean parseFeaturesFile(String filename,
+ DataSourceType protocol)
+ {
+ return af.parseFeaturesFile(filename, protocol);
+ }
+
+ @Override
+ public void loadTree(NewickFile fin, String treeFile)
+ throws IOException
+ {
+ // n/a -- already done
+ }
- public PDBFTSRestClient pdbFTSRestClient;
+ @Override
+ public void setAlignPdbStructures(boolean defaultParameter)
+ {
+ // TODO Auto-generated method stub
- public RestHandler restHandler;
+ }
- public ScoreModels scoreModels;
+ @Override
+ public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
+ String[] chains, DataSourceType protocol)
+ {
+ // TODO Auto-generated method stub
- public SequenceFetcher sequenceFetcher;
+ }
- public SequenceOntologyI sequenceOntology;
+ @Override
+ public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
+ String[][] chains, String[] protocols)
+ {
+ // TODO Auto-generated method stub
- public UniProtFTSRestClient uniprotFTSRestClient;
+ }
- public StructureSelectionManager nullProvider;
+ @Override
+ public void updateForLoader()
+ {
+ // TODO Auto-generated method stub
- public Color[] rnaHelices = null;
+ }
- public StructureImportSettings structureImportSettings;
+ @Override
+ public void setFeatureGroupState(String[] groups, boolean state)
+ {
+ // TODO Auto-generated method stub
- public IdOrgSettings idOrgSettings;
+ }
- public SiftsSettings siftsSettings;
+ @Override
+ public void newFeatureSettings()
+ {
+ // TODO Auto-generated method stub
- public RestClient restClient;
+ }
- public Jws2Discoverer j2s2discoverer;
+ };
- public Jws2InstanceFactory jws2InstanceFactory;
+ new JalviewAppLoader(true).load(app);
- public Discoverer discoverer;
+ }
}
git://source.jalview.org / jalview.git / blobdiff