*/
package jalview.bin;
+import jalview.api.AlignFrameI;
import jalview.api.AlignViewportI;
import jalview.api.JalviewApp;
+import jalview.api.StructureSelectionManagerProvider;
import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.Preferences;
import jalview.gui.PromptUserConfig;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
import jalview.io.gff.SequenceOntologyFactory;
+import jalview.javascript.JSFunctionExec;
+import jalview.javascript.JalviewLiteJsApi;
+import jalview.javascript.MouseOverStructureListener;
+import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.structure.SelectionSource;
+import jalview.structure.VamsasSource;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
+import java.applet.AppletContext;
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.Hashtable;
import java.util.Map;
import java.util.Vector;
import java.util.logging.ConsoleHandler;
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
+import netscape.javascript.JSObject;
/**
* Main class for Jalview Application <br>
* @author $author$
* @version $Revision$
*/
-public class Jalview implements ApplicationSingletonI
+public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
{
public static Jalview getInstance()
public String appletResourcePath;
+ private JalviewAppLoader appLoader;
+
+ protected JSFunctionExec jsFunctionExec;
+
public static AlignFrame getCurrentAlignFrame()
{
return getInstance().currentAlignFrame;
* configure 'full' SO model if preferences say to,
* else use the default (SO Lite)
*/
- if (Cache.getDefault("USE_FULL_SO", false))
+ if (Cache.getDefault(Preferences.USE_FULL_SO, false))
{
SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
}
}
else
{
- if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+ if (Cache.getProperty(Preferences.NOQUESTIONNAIRES) == null)
{
// Start the desktop questionnaire prompter with the specified
// questionnaire
}
}
-
// script to execute after all loading is
// completed one way or another
// extract groovy argument and execute if necessary
String groovyscript = (isJS ? null
: aparser.getValue(ArgsParser.GROOVY, true));
String file = aparser.getValue(ArgsParser.OPEN, true);
- String file2 = (isJavaAppletTag ? aparser.getAppletValue("file2", null)
- : null);
+ // BH this here to allow split frame; not working as of 5/17/2019
+ String file2 = aparser.getValue(ArgsParser.OPEN2, true);
String fileFormat = (isJavaAppletTag
? aparser.getAppletValue("format", null)
: null);
+
FileFormatI format = null;
DataSourceType protocol = null;
boolean haveImport = checkStartVamas(aparser);
// Finally, deal with the remaining input data.
long progress = -1;
+ if (file == null && isJavaAppletTag)
+ {
+ // Maybe the sequences are added as parameters
+ StringBuffer data = new StringBuffer("PASTE");
+ int i = 1;
+ while ((file = aparser.getAppletValue("sequence" + i, null)) != null)
+ {
+ data.append(file.toString() + "\n");
+ i++;
+ }
+ if (data.length() > 5)
+ {
+ file = data.toString();
+ }
+ }
+
if (file != null)
{
if (!headless)
}
AlignFrame af = new FileLoader(!headless).loadFileWaitTillLoaded(file,
- protocol,
- format);
+ protocol, format);
if (af == null)
{
System.out.println("error");
{
// TODO ?
}
- AlignFrame af2 = new FileLoader(!headless).loadFileWaitTillLoaded(
- file2,
- protocol, format);
+ AlignFrame af2 = new FileLoader(!headless)
+ .loadFileWaitTillLoaded(file2, protocol, format);
if (af2 == null)
{
System.out.println("error");
af.getViewport().getAlignment(),
af2.getViewport().getAlignment(), "",
AlignViewport.SPLIT_FRAME);
+ System.out.println(
+ "CMD [-open2 " + file2 + "] executed successfully!");
}
}
}
startUpAlframe = new FileLoader(!headless)
- .loadFileWaitTillLoaded(file, protocol,
- format);
+ .loadFileWaitTillLoaded(file, protocol, format);
// extract groovy arguments before anything else.
}
*/
public void quit()
{
+ if (jsFunctionExec != null)
+ {
+ jsFunctionExec.tidyUp();
+ jsFunctionExec = null;
+ }
+
if (desktop != null)
{
desktop.quit();
private boolean alignPDBStructures; // From JalviewLite; not implemented
+ private Hashtable<String, Hashtable<String, String[]>> jsmessages;
+
+ private Hashtable<String, int[]> jshashes;
+
@Override
public String getParameter(String name)
{
"Jalview applet interface newFeatureSettings not implemented");
}
+ private Vector<Runnable> jsExecQueue;
+
+ @Override
+ public Vector<Runnable> getJsExecQueue(JSFunctionExec exec)
+ {
+ jsFunctionExec = exec;
+ return (jsExecQueue == null ? (jsExecQueue = new Vector<>())
+ : jsExecQueue);
+ }
+
+ @Override
+ public AppletContext getAppletContext()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public boolean isJsfallbackEnabled()
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public JSObject getJSObject()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public StructureSelectionManagerProvider getStructureSelectionManagerProvider()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void updateColoursFromMouseOver(Object source,
+ MouseOverStructureListener mouseOverStructureListener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public Object[] getSelectionForListener(SequenceGroup seqsel,
+ ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source, Object alignFrame)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String arrayToSeparatorList(String[] array)
+ {
+ return appLoader.arrayToSeparatorList(array);
+ }
+
+ @Override
+ public Hashtable<String, int[]> getJSHashes()
+ {
+ return (jshashes == null
+ ? (jshashes = new Hashtable<>())
+ : jshashes);
+ }
+
+ @Override
+ public Hashtable<String, Hashtable<String, String[]>> getJSMessages()
+ {
+ return (jsmessages == null
+ ? (jsmessages = new Hashtable<>())
+ : jsmessages);
+ }
+
+ @Override
+ public Object getFrameForSource(VamsasSource source)
+ {
+ if (source != null)
+ {
+ AlignFrame af;
+ if (source instanceof jalview.gui.AlignViewport
+ && source == (af = getCurrentAlignFrame()).getViewport())
+ {
+ // should be valid if it just generated an event!
+ return af;
+ }
+ // TODO: ensure that if '_af' is specified along with a handler
+ // function, then only events from that alignFrame are sent to that
+ // function
+ }
+ return null;
+ }
+
+ @Override
+ public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp)
+ {
+ return new jalview.gui.FeatureRenderer((AlignmentPanel) vp);
+ }
+
};
- new JalviewAppLoader(true).load(app);
+ appLoader = new JalviewAppLoader(true);
+ appLoader.load(app);
+ }
+
+ @Override
+ public String getSelectedSequences()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getSelectedSequences(String sep)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getSelectedSequencesFrom(AlignFrameI alf)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getSelectedSequencesFrom(AlignFrameI alf,
+ String sep)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void highlight(String sequenceId, String position,
+ String alignedPosition)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void highlightIn(AlignFrameI alf,
+ String sequenceId, String position, String alignedPosition)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void select(String sequenceIds, String columns)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void select(String sequenceIds, String columns, String sep)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void selectIn(AlignFrameI alf, String sequenceIds,
+ String columns)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void selectIn(AlignFrameI alf, String sequenceIds,
+ String columns, String sep)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignment(String format,
+ String suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignmentFrom(
+ AlignFrameI alf, String format, String suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignmentOrder()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignmentOrderFrom(AlignFrameI alf)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignmentOrderFrom(AlignFrameI alf,
+ String sep)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String orderBy(String order, String undoName)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String orderBy(String order, String undoName, String sep)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String orderAlignmentBy(AlignFrameI alf,
+ String order, String undoName, String sep)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignment(String format)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignmentFrom(AlignFrameI alf,
+ String format)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignment(String format, String suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignmentFrom(AlignFrameI alf,
+ String format, String suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void loadAnnotation(String annotation)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void loadAnnotationFrom(AlignFrameI alf,
+ String annotation)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void loadFeatures(String features, boolean autoenabledisplay)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public boolean loadFeaturesFrom(AlignFrameI alf,
+ String features, boolean autoenabledisplay)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public String getFeatures(String format)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getFeaturesFrom(AlignFrameI alf,
+ String format)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAnnotation()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAnnotationFrom(AlignFrameI alf)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public AlignFrameI newView()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public AlignFrameI newView(String name)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public AlignFrameI newViewFrom(AlignFrameI alf)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public AlignFrameI newViewFrom(AlignFrameI alf, String name)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public AlignFrameI loadAlignment(String text,
+ String title)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setMouseoverListener(String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setMouseoverListener(AlignFrameI af,
+ String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setSelectionListener(String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setSelectionListener(AlignFrameI af,
+ String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setStructureListener(String listener, String modelSet)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void removeJavascriptListener(AlignFrameI af,
+ String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mouseOverStructure(String pdbResNum, String chain,
+ String pdbfile)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public boolean addPdbFile(AlignFrameI alFrame,
+ String sequenceId, String pdbEntryString, String pdbFile)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public void scrollViewToIn(AlignFrameI alf,
+ String topRow, String leftHandColumn)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void scrollViewToRowIn(AlignFrameI alf,
+ String topRow)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void scrollViewToColumnIn(AlignFrameI alf,
+ String leftHandColumn)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public String getFeatureGroups()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getFeatureGroupsOn(AlignFrameI alf)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getFeatureGroupsOfState(boolean visible)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getFeatureGroupsOfStateOn(AlignFrameI alf,
+ boolean visible)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setFeatureGroupStateOn(AlignFrameI alf,
+ String groups, boolean state)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setFeatureGroupState(String groups, boolean state)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public String getSeparator()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setSeparator(String separator)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public String getJsMessage(String messageclass, String viewId)
+ {
+ // TODO Auto-generated method stub
+ return null;
}
}
git://source.jalview.org / jalview.git / blobdiff