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JAL-3253-applet JAL-3424 headless fix for Windows
author
hansonr
<hansonr@STO24954W.ad.stolaf.edu>
Tue, 27 Aug 2019 23:25:22 +0000
(18:25 -0500)
committer
hansonr
<hansonr@STO24954W.ad.stolaf.edu>
Tue, 27 Aug 2019 23:25:22 +0000
(18:25 -0500)
14 files changed:
src/jalview/bin/Jalview.java
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src/jalview/gui/AlignViewport.java
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src/jalview/gui/AssociatePdbFileWithSeq.java
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src/jalview/gui/CrossRefAction.java
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src/jalview/gui/Desktop.java
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src/jalview/gui/SplitFrame.java
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src/jalview/gui/VamsasApplication.java
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src/jalview/io/FileLoader.java
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src/jalview/io/VamsasAppDatastore.java
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src/jalview/io/vamsas/Sequencemapping.java
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src/jalview/project/Jalview2XML.java
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test-bh.png
[new file with mode: 0644]
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test/jalview/bin/CommandLineOperations.java
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test/jalview/gui/AlignViewportTest.java
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diff --git
a/src/jalview/bin/Jalview.java
b/src/jalview/bin/Jalview.java
index
2efa0fb
..
b149911
100755
(executable)
--- a/
src/jalview/bin/Jalview.java
+++ b/
src/jalview/bin/Jalview.java
@@
-305,6
+305,15
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
Cache.loadProperties(usrPropsFile);
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;
+ }
+
if (isJS)
{
isJavaAppletTag = aparser.isApplet();
if (isJS)
{
isJavaAppletTag = aparser.isApplet();
@@
-336,13
+345,7
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
showUsage();
System.exit(0);
}
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!
// anything else!
@@
-398,7
+401,7
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
try
{
try
{
- if (Platform.isWin())
+ if (!isJS && Platform.isWin())
{
UIManager.setLookAndFeel(
headless ? "javax.swing.plaf.metal.MetalLookAndFeel"
{
UIManager.setLookAndFeel(
headless ? "javax.swing.plaf.metal.MetalLookAndFeel"
@@
-855,12
+858,12
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
+ "] executed successfully!");
groovyscript = null;
}
+ "] executed successfully!");
groovyscript = null;
}
- checkOutputFile(aparser, af, format);
while (aparser.getSize() > 0)
{
System.out.println("Unknown arg: " + aparser.nextValue());
}
}
while (aparser.getSize() > 0)
{
System.out.println("Unknown arg: " + aparser.nextValue());
}
}
+ checkOutputFile(aparser, af, format);
}
}
AlignFrame startUpAlframe = null;
}
}
AlignFrame startUpAlframe = null;
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
eb9c180
..
fb3ec3a
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-391,7
+391,7
@@
public class AlignViewport extends AlignmentViewport
*/
if (align != null)
{
*/
if (align != null)
{
- Desktop.getInstance().getStructureSelectionManager()
+ Desktop.getStructureSelectionManager()
.registerMappings(align.getCodonFrames());
}
.registerMappings(align.getCodonFrames());
}
@@
-412,7
+412,7
@@
public class AlignViewport extends AlignmentViewport
List<AlignedCodonFrame> mappings = al.getCodonFrames();
if (mappings != null)
{
List<AlignedCodonFrame> mappings = al.getCodonFrames();
if (mappings != null)
{
- StructureSelectionManager ssm = Desktop.getInstance()
+ StructureSelectionManager ssm = Desktop
.getStructureSelectionManager();
for (AlignedCodonFrame acf : mappings)
{
.getStructureSelectionManager();
for (AlignedCodonFrame acf : mappings)
{
@@
-538,7
+538,7
@@
public class AlignViewport extends AlignmentViewport
@Override
public void sendSelection()
{
@Override
public void sendSelection()
{
- Desktop.getInstance().getStructureSelectionManager().sendSelection(
+ Desktop.getStructureSelectionManager().sendSelection(
new SequenceGroup(getSelectionGroup()),
new ColumnSelection(getColumnSelection()),
new HiddenColumns(getAlignment().getHiddenColumns()), this);
new SequenceGroup(getSelectionGroup()),
new ColumnSelection(getColumnSelection()),
new HiddenColumns(getAlignment().getHiddenColumns()), this);
@@
-582,7
+582,7
@@
public class AlignViewport extends AlignmentViewport
@Override
public StructureSelectionManager getStructureSelectionManager()
{
@Override
public StructureSelectionManager getStructureSelectionManager()
{
- return Desktop.getInstance().getStructureSelectionManager();
+ return Desktop.getStructureSelectionManager();
}
@Override
}
@Override
diff --git
a/src/jalview/gui/AssociatePdbFileWithSeq.java
b/src/jalview/gui/AssociatePdbFileWithSeq.java
index
b81c344
..
1f540da
100644
(file)
--- a/
src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/
src/jalview/gui/AssociatePdbFileWithSeq.java
@@
-61,7
+61,7
@@
public class AssociatePdbFileWithSeq
{
PDBEntry entry = new PDBEntry();
StructureFile pdbfile = null;
{
PDBEntry entry = new PDBEntry();
StructureFile pdbfile = null;
- pdbfile = Desktop.getInstance().getStructureSelectionManager()
+ pdbfile = Desktop.getStructureSelectionManager()
.setMapping(false, new SequenceI[]
{ sequence }, null, fileName, type);
if (pdbfile == null)
.setMapping(false, new SequenceI[]
{ sequence }, null, fileName, type);
if (pdbfile == null)
diff --git
a/src/jalview/gui/CrossRefAction.java
b/src/jalview/gui/CrossRefAction.java
index
2ee741b
..
f607686
100644
(file)
--- a/
src/jalview/gui/CrossRefAction.java
+++ b/
src/jalview/gui/CrossRefAction.java
@@
-440,7
+440,7
@@
public class CrossRefAction implements Runnable
* register any new mappings for sequence mouseover etc
* (will not duplicate any previously registered mappings)
*/
* register any new mappings for sequence mouseover etc
* (will not duplicate any previously registered mappings)
*/
- Desktop.getInstance().getStructureSelectionManager()
+ Desktop.getStructureSelectionManager()
.registerMappings(dataset.getCodonFrames());
if (copyAlignment.getHeight() <= 0)
.registerMappings(dataset.getCodonFrames());
if (copyAlignment.getHeight() <= 0)
diff --git
a/src/jalview/gui/Desktop.java
b/src/jalview/gui/Desktop.java
index
a58e22a
..
ace7529
100644
(file)
--- a/
src/jalview/gui/Desktop.java
+++ b/
src/jalview/gui/Desktop.java
@@
-909,7
+909,7
@@
public class Desktop extends GDesktop
// A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
// IF JALVIEW IS RUNNING HEADLESS
// ///////////////////////////////////////////////
// A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
// IF JALVIEW IS RUNNING HEADLESS
// ///////////////////////////////////////////////
- if (Desktop.getInstance().instanceOnly || Jalview.isHeadlessMode())
+ if (Jalview.isHeadlessMode() || Desktop.getInstance().instanceOnly)
{
return;
}
{
return;
}
diff --git
a/src/jalview/gui/SplitFrame.java
b/src/jalview/gui/SplitFrame.java
index
8bfa428
..
253b02c
100644
(file)
--- a/
src/jalview/gui/SplitFrame.java
+++ b/
src/jalview/gui/SplitFrame.java
@@
-149,7
+149,7
@@
public class SplitFrame extends GSplitFrame implements SplitContainerI
{
// TODO if CommandListener is only ever 1:1 for complementary views,
// may change broadcast pattern to direct messaging (more efficient)
{
// TODO if CommandListener is only ever 1:1 for complementary views,
// may change broadcast pattern to direct messaging (more efficient)
- final StructureSelectionManager ssm = Desktop.getInstance()
+ final StructureSelectionManager ssm = Desktop
.getStructureSelectionManager();
ssm.addCommandListener(((AlignFrame) getTopFrame()).getViewport());
ssm.addCommandListener(((AlignFrame) getBottomFrame()).getViewport());
.getStructureSelectionManager();
ssm.addCommandListener(((AlignFrame) getTopFrame()).getViewport());
ssm.addCommandListener(((AlignFrame) getBottomFrame()).getViewport());
@@
-555,7
+555,7
@@
public class SplitFrame extends GSplitFrame implements SplitContainerI
*/
adjustLayout();
*/
adjustLayout();
- final StructureSelectionManager ssm = Desktop.getInstance()
+ final StructureSelectionManager ssm = Desktop
.getStructureSelectionManager();
ssm.addCommandListener(newTopPanel.av);
ssm.addCommandListener(newBottomPanel.av);
.getStructureSelectionManager();
ssm.addCommandListener(newTopPanel.av);
ssm.addCommandListener(newBottomPanel.av);
diff --git
a/src/jalview/gui/VamsasApplication.java
b/src/jalview/gui/VamsasApplication.java
index
4404a8d
..
ef814d3
100644
(file)
--- a/
src/jalview/gui/VamsasApplication.java
+++ b/
src/jalview/gui/VamsasApplication.java
@@
-762,7
+762,7
@@
public class VamsasApplication implements SelectionSource, VamsasSource
try
{
IPickManager pm = vclient.getPickManager();
try
{
IPickManager pm = vclient.getPickManager();
- StructureSelectionManager ssm = Desktop.getInstance()
+ StructureSelectionManager ssm = Desktop
.getStructureSelectionManager();
VamsasApplication me = this;
pm.registerMessageHandler(new IMessageHandler()
.getStructureSelectionManager();
VamsasApplication me = this;
pm.registerMessageHandler(new IMessageHandler()
diff --git
a/src/jalview/io/FileLoader.java
b/src/jalview/io/FileLoader.java
index
c3afe1f
..
3585c93
100755
(executable)
--- a/
src/jalview/io/FileLoader.java
+++ b/
src/jalview/io/FileLoader.java
@@
-421,7
+421,7
@@
public class FileLoader implements Runnable
{
// register PDB entries with desktop's structure selection
// manager
{
// register PDB entries with desktop's structure selection
// manager
- Desktop.getInstance().getStructureSelectionManager()
+ Desktop.getStructureSelectionManager()
.registerPDBEntry(pdbe);
}
}
.registerPDBEntry(pdbe);
}
}
diff --git
a/src/jalview/io/VamsasAppDatastore.java
b/src/jalview/io/VamsasAppDatastore.java
index
1f2f0fb
..
84d31f0
100644
(file)
--- a/
src/jalview/io/VamsasAppDatastore.java
+++ b/
src/jalview/io/VamsasAppDatastore.java
@@
-1476,7
+1476,7
@@
public class VamsasAppDatastore
// active
if (mappings != null)
{
// active
if (mappings != null)
{
- Desktop.getInstance().getStructureSelectionManager()
+ Desktop.getStructureSelectionManager()
.registerMappings(mappings);
}
}
.registerMappings(mappings);
}
}
diff --git
a/src/jalview/io/vamsas/Sequencemapping.java
b/src/jalview/io/vamsas/Sequencemapping.java
index
47cceb7
..
542bd3f
100644
(file)
--- a/
src/jalview/io/vamsas/Sequencemapping.java
+++ b/
src/jalview/io/vamsas/Sequencemapping.java
@@
-369,7
+369,7
@@
public class Sequencemapping extends Rangetype
acf.addMap(from, to, mapping);
}
bindjvvobj(mapping, sequenceMapping);
acf.addMap(from, to, mapping);
}
bindjvvobj(mapping, sequenceMapping);
- Desktop.getInstance().getStructureSelectionManager()
+ Desktop.getStructureSelectionManager()
.registerMapping(acf);
// Try to link up any conjugate database references in the two sequences
// matchConjugateDBRefs(from, to, mapping);
.registerMapping(acf);
// Try to link up any conjugate database references in the two sequences
// matchConjugateDBRefs(from, to, mapping);
diff --git
a/src/jalview/project/Jalview2XML.java
b/src/jalview/project/Jalview2XML.java
index
c28f24d
..
1a25270
100644
(file)
--- a/
src/jalview/project/Jalview2XML.java
+++ b/
src/jalview/project/Jalview2XML.java
@@
-3020,7
+3020,7
@@
public class Jalview2XML
{
if (ds.getCodonFrames() != null)
{
{
if (ds.getCodonFrames() != null)
{
- Desktop.getInstance().getStructureSelectionManager()
+ Desktop.getStructureSelectionManager()
.registerMappings(ds.getCodonFrames());
}
}
.registerMappings(ds.getCodonFrames());
}
}
@@
-3658,7
+3658,7
@@
public class Jalview2XML
{
entry.setProperty(prop.getName(), prop.getValue());
}
{
entry.setProperty(prop.getName(), prop.getValue());
}
- Desktop.getInstance().getStructureSelectionManager()
+ Desktop.getStructureSelectionManager()
.registerPDBEntry(entry);
// adds PDBEntry to datasequence's set (since Jalview 2.10)
if (al.getSequenceAt(i).getDatasetSequence() != null)
.registerPDBEntry(entry);
// adds PDBEntry to datasequence's set (since Jalview 2.10)
if (al.getSequenceAt(i).getDatasetSequence() != null)
diff --git a/test-bh.png
b/test-bh.png
new file mode 100644
(file)
index 0000000..
9373554
Binary files /dev/null and b/test-bh.png differ
diff --git
a/test/jalview/bin/CommandLineOperations.java
b/test/jalview/bin/CommandLineOperations.java
index
c7b1d53
..
eaa395e
100644
(file)
--- a/
test/jalview/bin/CommandLineOperations.java
+++ b/
test/jalview/bin/CommandLineOperations.java
@@
-196,6
+196,7
@@
public class CommandLineOperations
String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/testProps.jvprops -colour zappo "
+ "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
+ "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/testProps.jvprops -colour zappo "
+ "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
+ "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
+ System.out.println("CommandLine test " + ++ntest);
Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
String ln = null;
while ((ln = worker.getOutputReader().readLine()) != null)
Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
String ln = null;
while ((ln = worker.getOutputReader().readLine()) != null)
@@
-207,8
+208,11
@@
public class CommandLineOperations
{
System.err.println(ln);
}
{
System.err.println(ln);
}
+
}
}
+ int ntest = 0;
+
@BeforeTest(alwaysRun = true)
public void setUpForCommandLineInputOperations() throws IOException
{
@BeforeTest(alwaysRun = true)
public void setUpForCommandLineInputOperations() throws IOException
{
@@
-248,7
+252,7
@@
public class CommandLineOperations
int timeout)
{
String cmd = harg + type + " " + fileName;
int timeout)
{
String cmd = harg + type + " " + fileName;
- // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
+ System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
File file = new File(fileName);
file.deleteOnExit();
Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
File file = new File(fileName);
file.deleteOnExit();
Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
diff --git
a/test/jalview/gui/AlignViewportTest.java
b/test/jalview/gui/AlignViewportTest.java
index
ff8b19c
..
4db0df2
100644
(file)
--- a/
test/jalview/gui/AlignViewportTest.java
+++ b/
test/jalview/gui/AlignViewportTest.java
@@
-79,7
+79,7
@@
public class AlignViewportTest
/*
* remove any sequence mappings left lying around by other tests
*/
/*
* remove any sequence mappings left lying around by other tests
*/
- Desktop.getInstance().getStructureSelectionManager().resetAll();
+ Desktop.getStructureSelectionManager().resetAll();
}
@BeforeMethod(alwaysRun = true)
}
@BeforeMethod(alwaysRun = true)