git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (from parent 1:
4499c22
)
JAL-3056 suppress menu options, and repoint Help, for JalviewJS
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Mon, 23 Jul 2018 13:42:08 +0000
(14:42 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Mon, 23 Jul 2018 13:42:08 +0000
(14:42 +0100)
src/jalview/bin/Jalview.java
patch
|
blob
|
history
src/jalview/gui/Desktop.java
patch
|
blob
|
history
src/jalview/io/AppletFormatAdapter.java
patch
|
blob
|
history
src/jalview/jbgui/GAlignFrame.java
patch
|
blob
|
history
src/jalview/jbgui/GDesktop.java
patch
|
blob
|
history
src/jalview/jbgui/GUserDefinedColours.java
patch
|
blob
|
history
diff --git
a/src/jalview/bin/Jalview.java
b/src/jalview/bin/Jalview.java
index
e890cb8
..
3e6e545
100755
(executable)
--- a/
src/jalview/bin/Jalview.java
+++ b/
src/jalview/bin/Jalview.java
@@
-89,13
+89,21
@@
public class Jalview
public static AlignFrame currentAlignFrame;
public static AlignFrame currentAlignFrame;
- public static boolean isJS = /** @j2sNative true || */ // BH 2018
- false;
+ /**
+ * Answers true if Jalview is running as Javascript, else false. The value is
+ * set at compile time.
+ *
+ * @return
+ */
+ public static boolean isJS()
+ {
+ return /** @j2sNative true || */
+ false;
+ }
static
{
static
{
-
- if (!isJS)
+ if (!isJS())
{ // BH 2018
// grab all the rights we can the JVM
Policy.setPolicy(new Policy()
{ // BH 2018
// grab all the rights we can the JVM
Policy.setPolicy(new Policy()
@@
-199,7
+207,7
@@
public class Jalview
void doMain(String[] args)
{
void doMain(String[] args)
{
- if (!isJS)
+ if (!isJS())
{
System.setSecurityManager(null);
}
{
System.setSecurityManager(null);
}
@@
-530,7
+538,7
@@
public class Jalview
}
System.out.println("CMD [-open " + file + "] executed successfully!");
}
System.out.println("CMD [-open " + file + "] executed successfully!");
- if (!isJS && !file.startsWith("http://"))
+ if (!isJS() && !file.startsWith("http://"))
{
if (!(new File(file)).exists())
{
{
if (!(new File(file)).exists())
{
diff --git
a/src/jalview/gui/Desktop.java
b/src/jalview/gui/Desktop.java
index
81aacda
..
564f04a
100644
(file)
--- a/
src/jalview/gui/Desktop.java
+++ b/
src/jalview/gui/Desktop.java
@@
-41,6
+41,7
@@
import jalview.jbgui.GSplitFrame;
import jalview.jbgui.GStructureViewer;
import jalview.structure.StructureSelectionManager;
import jalview.urls.IdOrgSettings;
import jalview.jbgui.GStructureViewer;
import jalview.structure.StructureSelectionManager;
import jalview.urls.IdOrgSettings;
+import jalview.util.BrowserLauncher;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
@@
-1377,19
+1378,24
@@
public class Desktop extends jalview.jbgui.GDesktop
}
/**
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action on requesting Help documentation
*/
@Override
*/
@Override
- public void documentationMenuItem_actionPerformed(ActionEvent e)
+ public void documentationMenuItem_actionPerformed()
{
try
{
{
try
{
- Help.showHelpWindow();
+ if (Jalview.isJS())
+ {
+ BrowserLauncher.openURL("http://www.jalview.org/help.html");
+ }
+ else
+ {
+ Help.showHelpWindow();
+ }
} catch (Exception ex)
{
} catch (Exception ex)
{
+ System.err.println("Error opening help: " + ex.getMessage());
}
}
}
}
@@
-1593,16
+1599,12
@@
public class Desktop extends jalview.jbgui.GDesktop
}
/**
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Prompts the user to choose a file and then saves the Jalview state as a
+ * Jalview project file
*/
@Override
*/
@Override
- public void saveState_actionPerformed(ActionEvent e)
+ public void saveState_actionPerformed()
{
{
- // TODO: JAL-3048 not needed for Jalview-JS
-
JalviewFileChooser chooser = new JalviewFileChooser("jvp",
"Jalview Project");
JalviewFileChooser chooser = new JalviewFileChooser("jvp",
"Jalview Project");
@@
-1668,16
+1670,11
@@
public class Desktop extends jalview.jbgui.GDesktop
}
/**
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Prompts the user to choose a file and loads in as a Jalview project file
*/
@Override
*/
@Override
- public void loadState_actionPerformed(ActionEvent e)
+ public void loadState_actionPerformed()
{
{
- // TODO: JAL-3048 not needed for Jalview-JS
-
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"), new String[]
{ "jvp", "jar" },
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"), new String[]
{ "jvp", "jar" },
diff --git
a/src/jalview/io/AppletFormatAdapter.java
b/src/jalview/io/AppletFormatAdapter.java
index
b0fee88
..
95cbb61
100755
(executable)
--- a/
src/jalview/io/AppletFormatAdapter.java
+++ b/
src/jalview/io/AppletFormatAdapter.java
@@
-444,7
+444,7
@@
public class AppletFormatAdapter
{
protocol = DataSourceType.URL;
}
{
protocol = DataSourceType.URL;
}
- else if (jalview.bin.Jalview.isJS)
+ else if (jalview.bin.Jalview.isJS())
{
protocol = DataSourceType.RELATIVE_URL;
}
{
protocol = DataSourceType.RELATIVE_URL;
}
diff --git
a/src/jalview/jbgui/GAlignFrame.java
b/src/jalview/jbgui/GAlignFrame.java
index
a83c688
..
1910930
100755
(executable)
--- a/
src/jalview/jbgui/GAlignFrame.java
+++ b/
src/jalview/jbgui/GAlignFrame.java
@@
-23,6
+23,7
@@
package jalview.jbgui;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.api.SplitContainerI;
import jalview.bin.Cache;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.api.SplitContainerI;
import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
import jalview.io.FileFormats;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
import jalview.io.FileFormats;
@@
-1716,7
+1717,10
@@
public class GAlignFrame extends JInternalFrame
alignFrameMenuBar.add(formatMenu);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
alignFrameMenuBar.add(formatMenu);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
- alignFrameMenuBar.add(webService);
+ if (!Jalview.isJS())
+ {
+ alignFrameMenuBar.add(webService);
+ }
fileMenu.add(fetchSequence);
fileMenu.add(addSequenceMenu);
fileMenu.add(fetchSequence);
fileMenu.add(addSequenceMenu);
@@
-1734,10
+1738,7
@@
public class GAlignFrame extends JInternalFrame
fileMenu.add(exportAnnotations);
fileMenu.add(loadTreeMenuItem);
fileMenu.add(associatedData);
fileMenu.add(exportAnnotations);
fileMenu.add(loadTreeMenuItem);
fileMenu.add(associatedData);
- /*
- * No VCF import in Jalview-JS
- * @j2sNative
- */
+ if (!Jalview.isJS())
{
fileMenu.add(loadVcf);
}
{
fileMenu.add(loadVcf);
}
@@
-1774,8
+1775,11
@@
public class GAlignFrame extends JInternalFrame
hideMenu.add(hideAllSelection);
hideMenu.add(hideAllButSelection);
viewMenu.add(newView);
hideMenu.add(hideAllSelection);
hideMenu.add(hideAllButSelection);
viewMenu.add(newView);
- viewMenu.add(expandViews);
- viewMenu.add(gatherViews);
+ if (!Jalview.isJS())
+ {
+ viewMenu.add(expandViews);
+ viewMenu.add(gatherViews);
+ }
viewMenu.addSeparator();
viewMenu.add(showMenu);
viewMenu.add(hideMenu);
viewMenu.addSeparator();
viewMenu.add(showMenu);
viewMenu.add(hideMenu);
@@
-1835,17
+1839,26
@@
public class GAlignFrame extends JInternalFrame
calculateMenu.addSeparator();
calculateMenu.add(expandAlignment);
calculateMenu.add(extractScores);
calculateMenu.addSeparator();
calculateMenu.add(expandAlignment);
calculateMenu.add(extractScores);
- calculateMenu.addSeparator();
- calculateMenu.add(runGroovy);
+ if (!Jalview.isJS())
+ {
+ calculateMenu.addSeparator();
+ calculateMenu.add(runGroovy);
+ }
webServiceNoServices = new JMenuItem(
MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
webServiceNoServices = new JMenuItem(
MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
- exportImageMenu.add(htmlMenuItem);
+ if (!Jalview.isJS())
+ {
+ exportImageMenu.add(htmlMenuItem);
+ }
exportImageMenu.add(epsFile);
exportImageMenu.add(createPNG);
exportImageMenu.add(createBioJS);
exportImageMenu.add(epsFile);
exportImageMenu.add(createPNG);
exportImageMenu.add(createBioJS);
- exportImageMenu.add(createSVG);
+ if (!Jalview.isJS())
+ {
+ exportImageMenu.add(createSVG);
+ }
addSequenceMenu.add(addFromFile);
addSequenceMenu.add(addFromText);
addSequenceMenu.add(addFromURL);
addSequenceMenu.add(addFromFile);
addSequenceMenu.add(addFromText);
addSequenceMenu.add(addFromURL);
diff --git
a/src/jalview/jbgui/GDesktop.java
b/src/jalview/jbgui/GDesktop.java
index
11a558c
..
9ffd701
100755
(executable)
--- a/
src/jalview/jbgui/GDesktop.java
+++ b/
src/jalview/jbgui/GDesktop.java
@@
-21,6
+21,7
@@
package jalview.jbgui;
import jalview.api.AlignmentViewPanel;
package jalview.jbgui;
import jalview.api.AlignmentViewPanel;
+import jalview.bin.Jalview;
import jalview.io.FileFormatException;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.io.FileFormatException;
import jalview.util.MessageManager;
import jalview.util.Platform;
@@
-225,7
+226,7
@@
public class GDesktop extends JFrame
@Override
public void actionPerformed(ActionEvent e)
{
@Override
public void actionPerformed(ActionEvent e)
{
- documentationMenuItem_actionPerformed(e);
+ documentationMenuItem_actionPerformed();
}
});
this.getContentPane().setLayout(flowLayout1);
}
});
this.getContentPane().setLayout(flowLayout1);
@@
-246,7
+247,7
@@
public class GDesktop extends JFrame
@Override
public void actionPerformed(ActionEvent e)
{
@Override
public void actionPerformed(ActionEvent e)
{
- saveState_actionPerformed(e);
+ saveState_actionPerformed();
}
});
loadState.setText(MessageManager.getString("action.load_project"));
}
});
loadState.setText(MessageManager.getString("action.load_project"));
@@
-255,7
+256,7
@@
public class GDesktop extends JFrame
@Override
public void actionPerformed(ActionEvent e)
{
@Override
public void actionPerformed(ActionEvent e)
{
- loadState_actionPerformed(e);
+ loadState_actionPerformed();
}
});
inputMenu.setText(MessageManager.getString("label.input_alignment"));
}
});
inputMenu.setText(MessageManager.getString("label.input_alignment"));
@@
-423,9
+424,12
@@
public class GDesktop extends JFrame
desktopMenubar.add(windowMenu);
FileMenu.add(inputMenu);
FileMenu.add(inputSequence);
desktopMenubar.add(windowMenu);
FileMenu.add(inputMenu);
FileMenu.add(inputSequence);
- FileMenu.addSeparator();
- FileMenu.add(saveState);
- FileMenu.add(loadState);
+ if (!Jalview.isJS())
+ {
+ FileMenu.addSeparator();
+ FileMenu.add(saveState);
+ FileMenu.add(loadState);
+ }
FileMenu.addSeparator();
FileMenu.add(quit);
HelpMenu.add(aboutMenuItem);
FileMenu.addSeparator();
FileMenu.add(quit);
HelpMenu.add(aboutMenuItem);
@@
-437,11
+441,17
@@
public class GDesktop extends JFrame
VamsasMenu.add(vamsasSave);
VamsasMenu.add(vamsasStop);
toolsMenu.add(preferences);
VamsasMenu.add(vamsasSave);
VamsasMenu.add(vamsasStop);
toolsMenu.add(preferences);
- toolsMenu.add(showMemusage);
- toolsMenu.add(showConsole);
+ if (!Jalview.isJS())
+ {
+ toolsMenu.add(showMemusage);
+ toolsMenu.add(showConsole);
+ }
toolsMenu.add(showNews);
toolsMenu.add(showNews);
- toolsMenu.add(garbageCollect);
- toolsMenu.add(groovyShell);
+ if (!Jalview.isJS())
+ {
+ toolsMenu.add(garbageCollect);
+ toolsMenu.add(groovyShell);
+ }
toolsMenu.add(experimentalFeatures);
// toolsMenu.add(snapShotWindow);
inputMenu.add(inputLocalFileMenuItem);
toolsMenu.add(experimentalFeatures);
// toolsMenu.add(snapShotWindow);
inputMenu.add(inputLocalFileMenuItem);
@@
-551,13
+561,7
@@
public class GDesktop extends JFrame
{
}
{
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void documentationMenuItem_actionPerformed(ActionEvent e)
+ protected void documentationMenuItem_actionPerformed()
{
}
{
}
@@
-581,33
+585,11
@@
public class GDesktop extends JFrame
{
}
{
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void saveState_actionPerformed(ActionEvent e)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void loadState_actionPerformed(ActionEvent e)
+ public void saveState_actionPerformed()
{
}
{
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void loadJalviewAlign_actionPerformed(ActionEvent e)
+ public void loadState_actionPerformed()
{
}
{
}
diff --git
a/src/jalview/jbgui/GUserDefinedColours.java
b/src/jalview/jbgui/GUserDefinedColours.java
index
3d7d779
..
1b2b069
100755
(executable)
--- a/
src/jalview/jbgui/GUserDefinedColours.java
+++ b/
src/jalview/jbgui/GUserDefinedColours.java
@@
-20,6
+20,7
@@
*/
package jalview.jbgui;
*/
package jalview.jbgui;
+import jalview.bin.Jalview;
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
@@
-230,7
+231,10
@@
public class GUserDefinedColours extends JPanel
okCancelPanel.add(applyButton);
okCancelPanel.add(okButton);
okCancelPanel.add(cancelButton);
okCancelPanel.add(applyButton);
okCancelPanel.add(okButton);
okCancelPanel.add(cancelButton);
- lowerPanel.add(saveLoadPanel, java.awt.BorderLayout.NORTH);
+ if (!Jalview.isJS())
+ {
+ lowerPanel.add(saveLoadPanel, java.awt.BorderLayout.NORTH);
+ }
lowerPanel.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
namePanel.add(schemeName, java.awt.BorderLayout.CENTER);
lowerPanel.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
namePanel.add(schemeName, java.awt.BorderLayout.CENTER);