import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
+import jalview.gui.CalculationChooser;
import jalview.gui.Desktop;
import jalview.gui.Preferences;
import jalview.gui.PromptUserConfig;
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;
* @author $author$
* @version $Revision$
*/
-public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
+public class Jalview implements ApplicationSingletonI, JalviewJSApi
{
public static Jalview getInstance()
public String appletResourcePath;
- private JalviewAppLoader appLoader;
+ JalviewAppLoader appLoader;
protected JSFunctionExec jsFunctionExec;
+ private boolean noCalculation, noMenuBar, noStatus;
+
+ public boolean getStartCalculations()
+ {
+ return !noCalculation;
+ }
+
+ public boolean getAllowMenuBar()
+ {
+ return !noMenuBar;
+ }
+
+ public boolean getShowStatus()
+ {
+ return !noStatus;
+ }
+
+
public static AlignFrame getCurrentAlignFrame()
{
return getInstance().currentAlignFrame;
getInstance().doMain(args);
}
+
private static void logClass(String name)
{
// BH - for event debugging in JavaScript
}
}
+ parseArguments(aparser, true);
+ }
+
+ /**
+ * Allow an outside entity to initiate the second half of argument parsing
+ * (only).
+ *
+ * @param args
+ * @return null is good
+ */
+ @Override
+ public Object parseArguments(String[] args)
+ {
+
+ try
+ {
+ ArgsParser aparser = new ArgsParser(args);
+ return parseArguments(aparser, false);
+ } catch (Throwable t)
+ {
+ return t;
+ }
+ }
+
+ /**
+ *
+ * @param aparser
+ * @param isStartup
+ * @return
+ */
+ private Object parseArguments(ArgsParser aparser, boolean isStartup)
+ {
+ boolean isJS = Platform.isJS();
+
+ Desktop desktop = (headless ? null : Desktop.getInstance());
// script to execute after all loading is
// completed one way or another
// extract groovy argument and execute if necessary
String fileFormat = (isJavaAppletTag
? aparser.getAppletValue("format", null)
: null);
-
FileFormatI format = null;
DataSourceType protocol = null;
}
}
+ String data;
+
if (file != null)
{
+
if (!headless)
{
desktop.setProgressBar(
// TODO ?
}
+ if (aparser.contains(ArgsParser.SHOWOVERVIEW))
+ {
+ jalview.bin.Cache.setPropertyNoSave(Preferences.SHOW_OVERVIEW,
+ "true");
+
+ System.out.println("CMD [showoverview] executed successfully!");
+ }
+
+ if (aparser.contains(ArgsParser.NOMENUBAR))
+ {
+ noMenuBar = true;
+ System.out.println("CMD [nomenu] executed successfully!");
+ }
+
+ if (aparser.contains(ArgsParser.NOSTATUS))
+ {
+ noStatus = true;
+ System.out.println("CMD [nostatus] executed successfully!");
+ }
+
+ if (aparser.contains(ArgsParser.NOCALCULATION))
+ {
+ noCalculation = true;
+ System.out.println("CMD [nocalculation] executed successfully!");
+ }
+
AlignFrame af = new FileLoader(!headless).loadFileWaitTillLoaded(file,
protocol, format);
if (af == null)
// TODO: file2 How to implement file2 for the applet spit screen?
- String data = aparser.getValue(ArgsParser.COLOUR, true);
+ data = aparser.getValue(ArgsParser.COLOUR, true);
if (data != null)
{
data.replaceAll("%20", " ");
System.out.println("CMD [-sortbytree] executed successfully!");
}
}
+
+ boolean doUpdateAnnotation = false;
+
+
if (aparser.contains(ArgsParser.NOANNOTATION)
|| aparser.contains(ArgsParser.NOANNOTATION2))
{
af.getViewport().setShowAnnotation(false);
if (!af.getViewport().isShowAnnotation())
{
+ doUpdateAnnotation = true;
System.out.println("CMD no-annotation executed successfully!");
}
}
af.getViewport().setSortByTree(false);
if (!af.getViewport().getSortByTree())
{
+ doUpdateAnnotation = true;
System.out
.println("CMD [-nosortbytree] executed successfully!");
}
}
+ if (doUpdateAnnotation)
+ { // BH 2019.07.24
+ af.setMenusForViewport();
+ af.alignPanel.updateLayout();
+ }
data = aparser.getValue(ArgsParser.TREE, true);
if (data != null)
{
}
desktop.setInBatchMode(false);
}
+
+ return null;
}
private boolean checkStartVamas(ArgsParser aparser)
// 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:
+ "Skipping Push for import of data into existing vamsas session.");
+ // TODO:
// enable
// this
// when
JalviewApp app = new JalviewApp()
{
+ // TODO BH 2019
+ //
+ // These are methods that are in JalviewLite that various classes call
+ // but are not in JalviewLiteJsApi. Or, even if they are, other classes
+ // call
+ // them to JalviewLite directly. Some may not be necessary, but they have
+ // to
+ // be at least mentioned here, or the classes calling them should
+ // reference
+ // JalviewLite itself.
+
private boolean alignPDBStructures; // From JalviewLite; not implemented
private Hashtable<String, Hashtable<String, String[]>> jsmessages;
@Override
public StructureSelectionManagerProvider getStructureSelectionManagerProvider()
{
- // TODO Auto-generated method stub
+ // TODO Q: what exactly is this? BH
return null;
}
ColumnSelection colsel, HiddenColumns hidden,
SelectionSource source, Object alignFrame)
{
- // TODO Auto-generated method stub
- return null;
+ return appLoader.getSelectionForListener(getCurrentAlignFrame(),
+ seqsel, colsel, hidden, source, alignFrame);
}
@Override
@Override
public Hashtable<String, int[]> getJSHashes()
{
- return (jshashes == null
- ? (jshashes = new Hashtable<>())
+ return (jshashes == null ? (jshashes = new Hashtable<>())
: jshashes);
}
@Override
public Hashtable<String, Hashtable<String, String[]>> getJSMessages()
{
- return (jsmessages == null
- ? (jsmessages = new Hashtable<>())
+ return (jsmessages == null ? (jsmessages = new Hashtable<>())
: jsmessages);
}
appLoader.load(app);
}
+ /**
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
+ */
@Override
public String getSelectedSequences()
{
- // TODO Auto-generated method stub
- return null;
+ return getSelectedSequencesFrom(getCurrentAlignFrame());
}
+ /**
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
+ */
@Override
public String getSelectedSequences(String sep)
{
- // TODO Auto-generated method stub
- return null;
+ return getSelectedSequencesFrom(getCurrentAlignFrame(), sep);
}
+ /**
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+ * .AlignFrame)
+ */
@Override
public String getSelectedSequencesFrom(AlignFrameI alf)
{
- // TODO Auto-generated method stub
- return null;
+ return getSelectedSequencesFrom(alf, null);
}
+ /**
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+ * .AlignFrame, java.lang.String)
+ */
@Override
- public String getSelectedSequencesFrom(AlignFrameI alf,
- String sep)
+ public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
{
- // TODO Auto-generated method stub
- return null;
+ return appLoader.getSelectedSequencesFrom(alf, sep);
}
+ /**
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+ * .AlignFrame, java.lang.String)
+ */
@Override
public void highlight(String sequenceId, String position,
String alignedPosition)
{
- // TODO Auto-generated method stub
-
+ highlightIn(getCurrentAlignFrame(), sequenceId, position,
+ alignedPosition);
}
@Override
- public void highlightIn(AlignFrameI alf,
- String sequenceId, String position, String alignedPosition)
+ public void highlightIn(AlignFrameI alf, String sequenceId,
+ String position, String alignedPosition)
{
- // TODO Auto-generated method stub
-
+ appLoader.highlightIn(alf, sequenceId, position, alignedPosition);
}
@Override
public void select(String sequenceIds, String columns)
{
- // TODO Auto-generated method stub
-
+ selectIn(getCurrentAlignFrame(), sequenceIds, columns, null);
}
@Override
public void select(String sequenceIds, String columns, String sep)
{
- // TODO Auto-generated method stub
-
+ selectIn(getCurrentAlignFrame(), sequenceIds, columns, sep);
}
@Override
- public void selectIn(AlignFrameI alf, String sequenceIds,
- String columns)
+ public void selectIn(AlignFrameI alf, String sequenceIds, String columns)
{
- // TODO Auto-generated method stub
-
+ selectIn(alf, sequenceIds, columns, null);
}
@Override
- public void selectIn(AlignFrameI alf, String sequenceIds,
- String columns, String sep)
+ public void selectIn(AlignFrameI alf, String sequenceIds, String columns,
+ String sep)
{
- // TODO Auto-generated method stub
-
+ appLoader.selectIn(alf, sequenceIds, columns, sep);
}
@Override
public String getSelectedSequencesAsAlignment(String format,
String suffix)
{
- // TODO Auto-generated method stub
- return null;
+ return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+ format, suffix);
}
@Override
- public String getSelectedSequencesAsAlignmentFrom(
- AlignFrameI alf, String format, String suffix)
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ String format, String sep)
{
- // TODO Auto-generated method stub
- return null;
+ return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep);
}
@Override
public String getAlignmentOrder()
{
- // TODO Auto-generated method stub
- return null;
+ return getAlignmentFrom(getCurrentAlignFrame(), null);
}
@Override
public String getAlignmentOrderFrom(AlignFrameI alf)
{
- // TODO Auto-generated method stub
- return null;
+ return getAlignmentFrom(alf, null);
}
@Override
- public String getAlignmentOrderFrom(AlignFrameI alf,
- String sep)
+ public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
{
- // TODO Auto-generated method stub
- return null;
+ return appLoader.getAlignmentOrderFrom(alf, sep);
}
@Override
public String orderBy(String order, String undoName)
{
- // TODO Auto-generated method stub
- return null;
+ return orderBy(order, undoName, null);
}
@Override
public String orderBy(String order, String undoName, String sep)
{
- // TODO Auto-generated method stub
- return null;
+ return orderAlignmentBy(getCurrentAlignFrame(), order, undoName, sep);
}
@Override
- public String orderAlignmentBy(AlignFrameI alf,
- String order, String undoName, String sep)
+ public String orderAlignmentBy(AlignFrameI alf, String order,
+ String undoName, String sep)
{
- // TODO Auto-generated method stub
- return null;
+ return appLoader.orderAlignmentBy(alf, order, undoName, sep);
}
@Override
public String getAlignment(String format)
{
- // TODO Auto-generated method stub
- return null;
+ return getAlignmentFrom(null, format, null);
}
@Override
- public String getAlignmentFrom(AlignFrameI alf,
- String format)
+ public String getAlignmentFrom(AlignFrameI alf, String format)
{
- // TODO Auto-generated method stub
- return null;
+ return getAlignmentFrom(alf, format, null);
}
@Override
public String getAlignment(String format, String suffix)
{
- // TODO Auto-generated method stub
- return null;
+ return getAlignmentFrom(getCurrentAlignFrame(), format, suffix);
}
@Override
- public String getAlignmentFrom(AlignFrameI alf,
- String format, String suffix)
+ public String getAlignmentFrom(AlignFrameI alf, String format,
+ String suffix)
{
- // TODO Auto-generated method stub
- return null;
+ return appLoader.getAlignmentFrom(alf, format, suffix);
}
@Override
public void loadAnnotation(String annotation)
{
- // TODO Auto-generated method stub
-
+ loadAnnotationFrom(getCurrentAlignFrame(), annotation);
}
@Override
- public void loadAnnotationFrom(AlignFrameI alf,
- String annotation)
+ public void loadAnnotationFrom(AlignFrameI alf, String annotation)
{
- // TODO Auto-generated method stub
-
+ appLoader.loadAnnotationFrom(alf, annotation);
}
@Override
public void loadFeatures(String features, boolean autoenabledisplay)
{
- // TODO Auto-generated method stub
-
+ loadFeaturesFrom(currentAlignFrame, features, autoenabledisplay);
}
@Override
- public boolean loadFeaturesFrom(AlignFrameI alf,
- String features, boolean autoenabledisplay)
+ public boolean loadFeaturesFrom(AlignFrameI alf, String features,
+ boolean autoenabledisplay)
{
- // TODO Auto-generated method stub
- return false;
+ return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay);
}
@Override
public String getFeatures(String format)
{
- // TODO Auto-generated method stub
- return null;
+ return getFeaturesFrom(getCurrentAlignFrame(), format);
}
@Override
- public String getFeaturesFrom(AlignFrameI alf,
- String format)
+ public String getFeaturesFrom(AlignFrameI alf, String format)
{
- // TODO Auto-generated method stub
- return null;
+ return appLoader.getFeaturesFrom(alf, format);
}
@Override
public String getAnnotation()
{
- // TODO Auto-generated method stub
- return null;
+ return getAnnotationFrom(getCurrentAlignFrame());
}
@Override
public String getAnnotationFrom(AlignFrameI alf)
{
- // TODO Auto-generated method stub
- return null;
+ return appLoader.getAnnotationFrom(alf);
}
@Override
public AlignFrameI newView()
{
- // TODO Auto-generated method stub
- return null;
+ return newViewFrom(getCurrentAlignFrame(), null);
}
@Override
public AlignFrameI newView(String name)
{
- // TODO Auto-generated method stub
- return null;
+ return newViewFrom(getCurrentAlignFrame(), name);
}
@Override
public AlignFrameI newViewFrom(AlignFrameI alf)
{
- // TODO Auto-generated method stub
- return null;
+ return newViewFrom(alf, null);
}
@Override
public AlignFrameI newViewFrom(AlignFrameI alf, String name)
{
- // TODO Auto-generated method stub
- return null;
+ return appLoader.newViewFrom(alf, name);
}
@Override
- public AlignFrameI loadAlignment(String text,
- String title)
+ public AlignFrameI loadAlignment(String text, String title)
{
- // TODO Auto-generated method stub
- return null;
+ return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT, title);
}
@Override
- public void setMouseoverListener(String listener)
+ public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
+ String pdbEntryString, String pdbFile)
{
- // TODO Auto-generated method stub
-
+ return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString,
+ pdbFile);
}
@Override
- public void setMouseoverListener(AlignFrameI af,
- String listener)
+ public void scrollViewToIn(AlignFrameI alf, String topRow,
+ String leftHandColumn)
{
- // TODO Auto-generated method stub
-
+ appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
}
@Override
- public void setSelectionListener(String listener)
+ public void scrollViewToRowIn(AlignFrameI alf, String topRow)
{
- // TODO Auto-generated method stub
-
+ appLoader.scrollViewToRowIn(alf, topRow);
}
@Override
- public void setSelectionListener(AlignFrameI af,
- String listener)
+ public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
{
- // TODO Auto-generated method stub
-
+ appLoader.scrollViewToColumnIn(alf, leftHandColumn);
}
@Override
- public void setStructureListener(String listener, String modelSet)
+ public String getFeatureGroups()
{
- // TODO Auto-generated method stub
+ return getFeatureGroupsOn(getCurrentAlignFrame());
+ }
+ @Override
+ public String getFeatureGroupsOn(AlignFrameI alf)
+ {
+ return appLoader.getFeatureGroupsOn(alf);
}
@Override
- public void removeJavascriptListener(AlignFrameI af,
- String listener)
+ public String getFeatureGroupsOfState(boolean visible)
{
- // TODO Auto-generated method stub
+ return getFeatureGroupsOfStateOn(getCurrentAlignFrame(), visible);
+ }
+ @Override
+ public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
+ {
+ return appLoader.getFeatureGroupsOfStateOn(alf, visible);
}
@Override
- public void mouseOverStructure(String pdbResNum, String chain,
- String pdbfile)
+ public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
+ boolean state)
{
- // TODO Auto-generated method stub
+ setFeatureGroupStateOn(alf, groups, state);
+ }
+ @Override
+ public void setFeatureGroupState(String groups, boolean state)
+ {
+ appLoader.setFeatureGroupStateOn(getCurrentAlignFrame(), groups, state);
}
@Override
- public boolean addPdbFile(AlignFrameI alFrame,
- String sequenceId, String pdbEntryString, String pdbFile)
+ public String getSeparator()
{
- // TODO Auto-generated method stub
- return false;
+ return appLoader.getSeparator();
}
@Override
- public void scrollViewToIn(AlignFrameI alf,
- String topRow, String leftHandColumn)
+ public void setSeparator(String separator)
{
- // TODO Auto-generated method stub
+ appLoader.setSeparator(separator);
+ }
+ @Override
+ public String getJsMessage(String messageclass, String viewId)
+ {
+ // see http://www.jalview.org/examples/jalviewLiteJs.html
+ return null;
}
+ /**
+ * Open a new Tree panel on the desktop statically. Params are standard (not
+ * set by Groovy). No dialog is opened.
+ *
+ * @param af
+ * @param treeType
+ * @param modelName
+ * @return null, or the string "label.you_need_at_least_n_sequences" if number
+ * of sequences selected is inappropriate
+ */
@Override
- public void scrollViewToRowIn(AlignFrameI alf,
- String topRow)
+ public Object openTreePanel(AlignFrame af, String treeType,
+ String modelName)
{
- // TODO Auto-generated method stub
+ return CalculationChooser.openTreePanel(af, treeType, modelName, null);
+ }
+ /**
+ * public static method for JalviewJS API to open a PCAPanel without
+ * necessarily using a dialog.
+ *
+ * @param af
+ * @param modelName
+ * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
+ * if number of sequences selected is inappropriate
+ */
+ @Override
+ public Object openPcaPanel(AlignFrame af, String modelName)
+ {
+ return CalculationChooser.openPcaPanel(af, modelName, null);
}
@Override
- public void scrollViewToColumnIn(AlignFrameI alf,
- String leftHandColumn)
+ public String getSelectedSequencesAsAlignment(String format,
+ boolean suffix)
{
- // TODO Auto-generated method stub
+ return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+ format, suffix);
+ }
+ @Override
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ String format, boolean suffix)
+ {
+ return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format,
+ "" + suffix);
}
@Override
- public String getFeatureGroups()
+ public String arrayToSeparatorList(String[] array)
{
- // TODO Auto-generated method stub
- return null;
+ return appLoader.arrayToSeparatorList(array);
}
@Override
- public String getFeatureGroupsOn(AlignFrameI alf)
+ public String[] separatorListToArray(String list)
{
- // TODO Auto-generated method stub
- return null;
+ return appLoader.separatorListToArray(list);
}
+ //// probably not needed in JalviewJS -- From when Jmol and Jalview did not
+ //// have a direct connection?
+
@Override
- public String getFeatureGroupsOfState(boolean visible)
+ public void setMouseoverListener(String listener)
{
// TODO Auto-generated method stub
- return null;
+
}
@Override
- public String getFeatureGroupsOfStateOn(AlignFrameI alf,
- boolean visible)
+ public void setMouseoverListener(AlignFrameI af, String listener)
{
// TODO Auto-generated method stub
- return null;
+
}
@Override
- public void setFeatureGroupStateOn(AlignFrameI alf,
- String groups, boolean state)
+ public void setSelectionListener(String listener)
{
// TODO Auto-generated method stub
}
@Override
- public void setFeatureGroupState(String groups, boolean state)
+ public void setSelectionListener(AlignFrameI af, String listener)
{
// TODO Auto-generated method stub
}
@Override
- public String getSeparator()
+ public void setStructureListener(String listener, String modelSet)
{
// TODO Auto-generated method stub
- return null;
+
}
@Override
- public void setSeparator(String separator)
+ public void removeJavascriptListener(AlignFrameI af, String listener)
{
// TODO Auto-generated method stub
}
@Override
- public String getJsMessage(String messageclass, String viewId)
+ public void mouseOverStructure(String pdbResNum, String chain,
+ String pdbfile)
{
// TODO Auto-generated method stub
- return null;
+
}
+
}
git://source.jalview.org / jalview.git / blobdiff