X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=0ec9ee0e685c5e38f347014808b105283af6f945;hb=refs%2Fheads%2FJAL-3253-applet-SwingJS-omnibus;hp=84fec4569df2aad30c78c0ea9171e28f16861235;hpb=418006c3714eb8da78234660698231597eb90fb1;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 84fec45..0ec9ee0 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,6 +20,7 @@
*/
package jalview.bin;
+import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignFrameI;
import jalview.api.AlignViewportI;
import jalview.api.JalviewApp;
@@ -34,6 +35,7 @@ import jalview.ext.so.SequenceOntology;
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;
@@ -51,7 +53,6 @@ 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;
@@ -83,11 +84,9 @@ import java.util.HashMap;
import java.util.Hashtable;
import java.util.Map;
import java.util.Vector;
-import java.util.logging.ConsoleHandler;
-import java.util.logging.Level;
-import java.util.logging.Logger;
import javax.swing.LookAndFeel;
+import javax.swing.SwingUtilities;
import javax.swing.UIManager;
import groovy.lang.Binding;
@@ -109,7 +108,7 @@ import netscape.javascript.JSObject;
* @author $author$
* @version $Revision$
*/
-public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
+public class Jalview implements ApplicationSingletonI, JalviewJSApi
{
public static Jalview getInstance()
@@ -142,10 +141,36 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
public String appletResourcePath;
- private JalviewAppLoader appLoader;
+ JalviewAppLoader appLoader;
protected JSFunctionExec jsFunctionExec;
+ private boolean noCalculation, noMenuBar, noStatus;
+
+ private boolean noAnnotation;
+
+ public static final String TERMINATOR_LINE = "Jalview argument parsing complete.";
+
+ public boolean getStartCalculations()
+ {
+ return !noCalculation;
+ }
+
+ public boolean getAllowMenuBar()
+ {
+ return !noMenuBar;
+ }
+
+ public boolean getShowStatus()
+ {
+ return !noStatus;
+ }
+
+ public boolean getShowAnnotation()
+ {
+ return !noAnnotation;
+ }
+
public static AlignFrame getCurrentAlignFrame()
{
return getInstance().currentAlignFrame;
@@ -251,50 +276,12 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
*/
public static void main(String[] args)
{
- // setLogging(); // BH - for event debugging in JavaScript
+ // Platform.startJavaLogging();
getInstance().doMain(args);
}
- private static void logClass(String name)
- {
- // BH - for event debugging in JavaScript
- ConsoleHandler consoleHandler = new ConsoleHandler();
- consoleHandler.setLevel(Level.ALL);
- Logger logger = Logger.getLogger(name);
- logger.setLevel(Level.ALL);
- logger.addHandler(consoleHandler);
- }
@SuppressWarnings("unused")
- private static void setLogging()
- {
-
- /**
- * @j2sIgnore
- *
- */
- {
- System.out.println("not in js");
- }
-
- // BH - for event debugging in JavaScript (Java mode only)
- if (!Platform.isJS())
- /**
- * Java only
- *
- * @j2sIgnore
- */
- {
- Logger.getLogger("").setLevel(Level.ALL);
- logClass("java.awt.EventDispatchThread");
- logClass("java.awt.EventQueue");
- logClass("java.awt.Component");
- logClass("java.awt.focus.Component");
- logClass("java.awt.focus.DefaultKeyboardFocusManager");
- }
-
- }
-
/**
* @param args
*/
@@ -302,7 +289,11 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
{
boolean isJS = Platform.isJS();
- if (!isJS)
+ if (isJS)
+ {
+ Platform.setAppClass(this);
+ }
+ else
{
System.setSecurityManager(null);
}
@@ -317,6 +308,16 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
Cache.loadProperties(usrPropsFile);
+
+ if (aparser.contains(ArgsParser.NODISPLAY)
+ || aparser.contains(ArgsParser.NOGUI)
+ || aparser.contains(ArgsParser.HEADLESS)
+ || "true".equals(System.getProperty("java.awt.headless")))
+ {
+ headless = true;
+ setSynchronous(true);
+ }
+
if (isJS)
{
isJavaAppletTag = aparser.isApplet();
@@ -348,13 +349,6 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
showUsage();
System.exit(0);
}
- if (aparser.contains(ArgsParser.NODISPLAY)
- || aparser.contains(ArgsParser.NOGUI)
- || aparser.contains(ArgsParser.HEADLESS)
- || "true".equals(System.getProperty("java.awt.headless")))
- {
- headless = true;
- }
// anything else!
@@ -410,7 +404,13 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
try
{
- UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+ if (!isJS && Platform.isWin())
+ {
+ UIManager.setLookAndFeel(
+ headless ? "javax.swing.plaf.metal.MetalLookAndFeel"
+ : UIManager.getSystemLookAndFeelClassName());
+ // UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+ }
} catch (Exception ex)
{
System.err.println("Unexpected Look and Feel Exception");
@@ -463,7 +463,21 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
}
- if (!headless)
+ if (headless)
+ {
+ // If this is not tested, then
+
+ if (aparser.contains(ArgsParser.NOUSAGESTATS))
+ {
+ System.err.println("CMD [-nousagestats] executed successfully!");
+ }
+ if (aparser.contains(ArgsParser.NOQUESTIONNAIRE))
+ {
+ System.err.println("CMD [-noquestionnaire] executed successfully!");
+ }
+
+ }
+ else
{
desktop = Desktop.getInstance();
desktop.setInBatchMode(true); // indicate we are starting up
@@ -529,6 +543,42 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
}
}
+ parseArguments(aparser, true);
+ System.err.println(TERMINATOR_LINE);
+ }
+
+ /**
+ * 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
@@ -540,7 +590,6 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
String fileFormat = (isJavaAppletTag
? aparser.getAppletValue("format", null)
: null);
-
FileFormatI format = null;
DataSourceType protocol = null;
@@ -549,7 +598,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
System.out.println("No files to open!");
System.exit(1);
}
- boolean haveImport = checkStartVamas(aparser);
+ boolean haveImport = false;// checkStartVamas(aparser);
// Finally, deal with the remaining input data.
long progress = -1;
if (file == null && isJavaAppletTag)
@@ -568,8 +617,11 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
}
}
+ String data;
+
if (file != null)
{
+
if (!headless)
{
desktop.setProgressBar(
@@ -616,7 +668,31 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
// TODO ?
}
- AlignFrame af = new FileLoader(!headless).loadFileWaitTillLoaded(file,
+ 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.NOANNOTATION)
+ || aparser.contains(ArgsParser.NOANNOTATION2))
+ {
+ noAnnotation = true;
+ System.out.println("CMD no-annotation 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)
{
@@ -637,7 +713,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
// TODO ?
}
AlignFrame af2 = new FileLoader(!headless)
- .loadFileWaitTillLoaded(file2, protocol, format);
+ .LoadFileWaitTillLoaded(file2, protocol, format);
if (af2 == null)
{
System.out.println("error");
@@ -657,7 +733,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
// 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", " ");
@@ -701,6 +777,13 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
System.out.println(
"CMD [-annotations " + data + "] executed successfully!");
}
+
+ if (aparser.contains(ArgsParser.SHOWOVERVIEW))
+ {
+ af.overviewMenuItem_actionPerformed(null);
+ System.out.println("CMD [showoverview] executed successfully!");
+ }
+
// set or clear the sortbytree flag.
if (aparser.contains(ArgsParser.SORTBYTREE))
{
@@ -710,13 +793,30 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
System.out.println("CMD [-sortbytree] executed successfully!");
}
}
- if (aparser.contains(ArgsParser.NOANNOTATION)
- || aparser.contains(ArgsParser.NOANNOTATION2))
+
+ boolean doUpdateAnnotation = false;
+
+ /**
+ * we do this earlier in JalviewJS because of a complication with
+ * SHOWOVERVIEW
+ *
+ * For now, just fixing this in JalviewJS.
+ *
+ *
+ * @j2sIgnore
+ *
+ */
{
- af.getViewport().setShowAnnotation(false);
- if (!af.getViewport().isShowAnnotation())
+ if (aparser.contains(ArgsParser.NOANNOTATION)
+ || aparser.contains(ArgsParser.NOANNOTATION2))
{
- System.out.println("CMD no-annotation executed successfully!");
+ af.getViewport().setShowAnnotation(false);
+ if (!af.getViewport().isShowAnnotation())
+ {
+ doUpdateAnnotation = true;
+ System.out
+ .println("CMD no-annotation executed successfully!");
+ }
}
}
if (aparser.contains(ArgsParser.NOSORTBYTREE))
@@ -724,10 +824,16 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
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)
{
@@ -770,11 +876,11 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
+ "] executed successfully!");
groovyscript = null;
}
- checkOutputFile(aparser, af, format);
- while (aparser.getSize() > 0)
- {
- System.out.println("Unknown arg: " + aparser.nextValue());
- }
+ }
+ createOutputFiles(aparser, af, format);
+ while (aparser.getSize() > 0)
+ {
+ System.out.println("Unknown arg: " + aparser.nextValue());
}
}
}
@@ -827,7 +933,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
}
startUpAlframe = new FileLoader(!headless)
- .loadFileWaitTillLoaded(file, protocol, format);
+ .LoadFileWaitTillLoaded(file, protocol, format);
// extract groovy arguments before anything else.
}
@@ -855,112 +961,39 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
}
desktop.setInBatchMode(false);
}
- }
-
- 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;
+ return null;
}
- private void checkOutputFile(ArgsParser aparser, AlignFrame af,
+ /**
+ * Writes an output file for each format (if any) specified in the
+ * command-line arguments. Supported formats are currently
+ *
+ * - png
+ * - svg
+ * - html
+ * - biojsmsa
+ * - imgMap
+ * - eps
+ *
+ * A format parameter should be followed by a parameter specifying the output
+ * file name. {@code imgMap} parameters should follow those for the
+ * corresponding alignment image output.
+ *
+ * @param aparser
+ * @param af
+ * @param format
+ */
+ private void createOutputFiles(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();
+ // System.out.println("format " + outputFormat);
+
if (outputFormat.equalsIgnoreCase("png"))
{
af.createPNG(new File(file));
@@ -1261,23 +1294,6 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
}
/**
- * 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);
- }
-
- /**
* Handle all JalviewLite applet parameters
*
* @param aparser
@@ -1288,6 +1304,17 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
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> jsmessages;
@@ -1439,7 +1466,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
@Override
public StructureSelectionManagerProvider getStructureSelectionManagerProvider()
{
- // TODO Auto-generated method stub
+ // TODO Q: what exactly is this? BH
return null;
}
@@ -1456,8 +1483,8 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
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
@@ -1469,16 +1496,14 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
@Override
public Hashtable getJSHashes()
{
- return (jshashes == null
- ? (jshashes = new Hashtable<>())
+ return (jshashes == null ? (jshashes = new Hashtable<>())
: jshashes);
}
@Override
public Hashtable> getJSMessages()
{
- return (jsmessages == null
- ? (jsmessages = new Hashtable<>())
+ return (jsmessages == null ? (jsmessages = new Hashtable<>())
: jsmessages);
}
@@ -1513,414 +1538,639 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
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;
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ 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;
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ 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(null, 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
-
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ 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(null, 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
-
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.selectIn(alf, sequenceIds, columns, sep);
}
@Override
public String getSelectedSequencesAsAlignment(String format,
String suffix)
{
- // TODO Auto-generated method stub
- return null;
+ return getSelectedSequencesAsAlignmentFrom(null,
+ 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;
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ 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;
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ 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;
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ 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
-
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ 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;
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay);
}
@Override
public String getFeatures(String format)
{
- // TODO Auto-generated method stub
- return null;
+ return getFeaturesFrom(null, format);
}
@Override
- public String getFeaturesFrom(AlignFrameI alf,
- String format)
+ public String getFeaturesFrom(AlignFrameI alf, String format)
{
- // TODO Auto-generated method stub
- return null;
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getFeaturesFrom(alf, format, true, false);
}
@Override
public String getAnnotation()
{
- // TODO Auto-generated method stub
- return null;
+ return getAnnotationFrom(null);
}
@Override
public String getAnnotationFrom(AlignFrameI alf)
{
- // TODO Auto-generated method stub
- return null;
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getAnnotationFrom(alf);
}
@Override
public AlignFrameI newView()
{
- // TODO Auto-generated method stub
- return null;
+ return newViewFrom(null, null);
}
@Override
public AlignFrameI newView(String name)
{
- // TODO Auto-generated method stub
- return null;
+ return newViewFrom(null, 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;
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ 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
-
+ if (alFrame == null)
+ {
+ alFrame = getCurrentAlignFrame();
+ }
+ 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
-
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
}
@Override
- public void setSelectionListener(String listener)
+ public void scrollViewToRowIn(AlignFrameI alf, String topRow)
{
- // TODO Auto-generated method stub
-
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.scrollViewToRowIn(alf, topRow);
}
@Override
- public void setSelectionListener(AlignFrameI af,
- String listener)
+ public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
{
- // TODO Auto-generated method stub
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.scrollViewToColumnIn(alf, leftHandColumn);
+ }
+ @Override
+ public String getFeatureGroups()
+ {
+ return getFeatureGroupsOn(null);
}
@Override
- public void setStructureListener(String listener, String modelSet)
+ public String getFeatureGroupsOn(AlignFrameI alf)
{
- // TODO Auto-generated method stub
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getFeatureGroupsOn(alf);
+ }
+ @Override
+ public String getFeatureGroupsOfState(boolean visible)
+ {
+ return getFeatureGroupsOfStateOn(null, visible);
}
@Override
- public void removeJavascriptListener(AlignFrameI af,
- String listener)
+ public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
{
- // TODO Auto-generated method stub
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getFeatureGroupsOfStateOn(alf, visible);
+ }
+ @Override
+ public void setFeatureGroupState(String groups, boolean state)
+ { // JalviewLite API
+ setFeatureGroupStateOn(null, groups, state);
}
@Override
- public void mouseOverStructure(String pdbResNum, String chain,
- String pdbfile)
+ public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
+ boolean state)
{
- // TODO Auto-generated method stub
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.setFeatureGroupStateOn(alf, groups, state);
+ }
+ @Override
+ public String getSeparator()
+ {
+ return appLoader.getSeparator();
}
@Override
- public boolean addPdbFile(AlignFrameI alFrame,
- String sequenceId, String pdbEntryString, String pdbFile)
+ public void setSeparator(String separator)
{
- // TODO Auto-generated method stub
- return false;
+ appLoader.setSeparator(separator);
}
@Override
- public void scrollViewToIn(AlignFrameI alf,
- String topRow, String leftHandColumn)
+ public String getJsMessage(String messageclass, String viewId)
{
- // TODO Auto-generated method stub
+ // 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 Object openTreePanel(AlignFrame af, String treeType,
+ String modelName)
+ { // JalviewJS api
+ if (af == null)
+ {
+ af = getCurrentAlignFrame();
+ }
+ 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 void scrollViewToRowIn(AlignFrameI alf,
- String topRow)
+ public Object openPcaPanel(AlignFrame af, String modelName)
{
- // TODO Auto-generated method stub
+ if (af == null)
+ {
+ af = getCurrentAlignFrame();
+ }
+ return CalculationChooser.openPcaPanel(af, modelName, null);
+ }
+ @Override
+ public String getSelectedSequencesAsAlignment(String format,
+ boolean suffix)
+ {
+ return getSelectedSequencesAsAlignmentFrom(null,
+ format, suffix);
}
@Override
- public void scrollViewToColumnIn(AlignFrameI alf,
- String leftHandColumn)
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ String format, boolean suffix)
{
- // TODO Auto-generated method stub
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format,
+ "" + suffix);
+ }
+ @Override
+ public String arrayToSeparatorList(String[] array)
+ {
+ return appLoader.arrayToSeparatorList(array);
}
@Override
- public String getFeatureGroups()
+ 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 getFeatureGroupsOn(AlignFrameI alf)
+ public void setMouseoverListener(String listener)
{
// TODO Auto-generated method stub
- return null;
+
}
@Override
- public String getFeatureGroupsOfState(boolean visible)
+ public void setMouseoverListener(AlignFrameI af, String listener)
{
// TODO Auto-generated method stub
- return null;
+
}
@Override
- public String getFeatureGroupsOfStateOn(AlignFrameI alf,
- boolean visible)
+ public void setSelectionListener(String listener)
{
// TODO Auto-generated method stub
- return null;
+
}
@Override
- public void setFeatureGroupStateOn(AlignFrameI alf,
- String groups, boolean state)
+ public void setSelectionListener(AlignFrameI af, String listener)
{
// TODO Auto-generated method stub
}
@Override
- public void setFeatureGroupState(String groups, boolean state)
+ public void setStructureListener(String listener, String modelSet)
{
// TODO Auto-generated method stub
}
@Override
- public String getSeparator()
+ public void removeJavascriptListener(AlignFrameI af, String listener)
{
// TODO Auto-generated method stub
- return null;
+
}
@Override
- public void setSeparator(String separator)
+ public void mouseOverStructure(String pdbResNum, String chain,
+ String pdbfile)
{
// TODO Auto-generated method stub
}
@Override
- public String getJsMessage(String messageclass, String viewId)
+ public void showOverview()
{
- // TODO Auto-generated method stub
- return null;
+ currentAlignFrame.overviewMenuItem_actionPerformed(null);
+ }
+
+ public void notifyWorker(AlignCalcWorkerI worker, String status)
+ {
+ // System.out.println("Jalview worker " + worker.getClass().getSimpleName()
+ // + " " + status);
+ }
+
+ /**
+ * flag to allow selected Runnable and Thread processes to run synchronously
+ *
+ * JAL-3563
+ *
+ */
+ private static boolean isSynchronous = false;
+
+ /**
+ * Set Jalview to run selected processes synchronously in test and headless
+ * environments.
+ *
+ * JAL-3563
+ *
+ * @param b
+ * @author Bob Hanson
+ */
+ public static void setSynchronous(boolean b)
+ {
+ isSynchronous = b;
+ }
+
+ /**
+ * Allows optional synchronous running of a Runnable that would otherwise use
+ * SwingUtilities.invokeLater.
+ *
+ * JAL-3563
+ *
+ * @param t
+ * @author Bob Hanson
+ */
+ public static boolean isSynchronous()
+ {
+ return isSynchronous;
+ }
+
+ /**
+ * Allows optional synchronous running of a Runnable that would otherwise use
+ * SwingUtilities.invokeLater.
+ *
+ * JAL-3563
+ *
+ * @param t
+ * @author Bob Hanson
+ */
+ public static void execRunnable(Runnable r)
+ {
+ if (isSynchronous())
+ {
+ r.run();
+ }
+ else
+ {
+ SwingUtilities.invokeLater(r);
+ }
+ }
+
+ /**
+ * Allows optional synchronous running of a thread that would otherwise be run
+ * using start().
+ *
+ * JAL-3563
+ *
+ * @param t
+ * @author Bob Hanson
+ */
+ public static void execThread(Thread t)
+ {
+ if (isSynchronous())
+ {
+ t.run();
+ }
+ else
+ {
+ t.start();
+ }
+ }
+
+ /**
+ * 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);
}
-}
+}
\ No newline at end of file