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JAL-1807 explicit imports (jalview.bin)
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 10 Jul 2015 05:12:47 +0000
(06:12 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 10 Jul 2015 05:12:47 +0000
(06:12 +0100)
src/jalview/bin/Cache.java
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src/jalview/bin/Jalview.java
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src/jalview/bin/JalviewLite.java
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src/jalview/bin/JalviewLiteURLRetrieve.java
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diff --git
a/src/jalview/bin/Cache.java
b/src/jalview/bin/Cache.java
index
10aba00
..
4ed6e1a
100755
(executable)
--- a/
src/jalview/bin/Cache.java
+++ b/
src/jalview/bin/Cache.java
@@
-20,6
+20,12
@@
*/
package jalview.bin;
*/
package jalview.bin;
+import jalview.gui.UserDefinedColours;
+import jalview.io.PIRFile;
+import jalview.jbgui.GDesktop;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
+import jalview.util.Format;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
@@
-253,7
+259,7
@@
public class Cache
// log output
Logger laxis = Logger.getLogger("org.apache.axis");
Logger lcastor = Logger.getLogger("org.exolab.castor");
// log output
Logger laxis = Logger.getLogger("org.apache.axis");
Logger lcastor = Logger.getLogger("org.exolab.castor");
- jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
+ Cache.log = Logger.getLogger("jalview.bin.Jalview");
laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
Level.INFO.toString())));
laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
Level.INFO.toString())));
@@
-265,13
+271,13
@@
public class Cache
// lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
// lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
// Level.INFO.toString())));
// lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
// lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
// Level.INFO.toString())));
- jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
+ Cache.log.setLevel(Level.toLevel(Cache.getDefault(
"logs.Jalview.level", Level.INFO.toString())));
// laxis.addAppender(ap);
// lcastor.addAppender(ap);
"logs.Jalview.level", Level.INFO.toString())));
// laxis.addAppender(ap);
// lcastor.addAppender(ap);
- // jalview.bin.Cache.log.addAppender(ap);
+ // Cache.log.addAppender(ap);
// Tell the user that debug is enabled
// Tell the user that debug is enabled
- jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
+ Cache.log.debug("Jalview Debugging Output Follows.");
} catch (Exception ex)
{
System.err.println("Problems initializing the log4j system\n");
} catch (Exception ex)
{
System.err.println("Problems initializing the log4j system\n");
@@
-470,9
+476,9
@@
public class Cache
setProperty("VERSION", codeVersion);
// LOAD USERDEFINED COLOURS
setProperty("VERSION", codeVersion);
// LOAD USERDEFINED COLOURS
- jalview.gui.UserDefinedColours
+ UserDefinedColours
.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
- jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
+ PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
false);
}
false);
}
@@
-608,10
+614,10
@@
public class Cache
{
try
{
{
try
{
- if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
+ if (GDesktop.class.getClassLoader().loadClass(
"uk.ac.vamsas.client.VorbaId") != null)
{
"uk.ac.vamsas.client.VorbaId") != null)
{
- jalview.bin.Cache.log
+ Cache.log
.debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
vamsasJarsArePresent = 1;
Logger lvclient = Logger.getLogger("uk.ac.vamsas");
.debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
vamsasJarsArePresent = 1;
Logger lvclient = Logger.getLogger("uk.ac.vamsas");
@@
-625,7
+631,7
@@
public class Cache
} catch (Exception e)
{
vamsasJarsArePresent = 0;
} catch (Exception e)
{
vamsasJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Vamsas Classes are not present");
+ Cache.log.debug("Vamsas Classes are not present");
}
}
return (vamsasJarsArePresent > 0);
}
}
return (vamsasJarsArePresent > 0);
@@
-650,7
+656,7
@@
public class Cache
if (Cache.class.getClassLoader().loadClass(
"groovy.lang.GroovyObject") != null)
{
if (Cache.class.getClassLoader().loadClass(
"groovy.lang.GroovyObject") != null)
{
- jalview.bin.Cache.log
+ Cache.log
.debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
groovyJarsArePresent = 1;
Logger lgclient = Logger.getLogger("groovy");
.debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
groovyJarsArePresent = 1;
Logger lgclient = Logger.getLogger("groovy");
@@
-664,11
+670,11
@@
public class Cache
} catch (Error e)
{
groovyJarsArePresent = 0;
} catch (Error e)
{
groovyJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
+ Cache.log.debug("Groovy Classes are not present", e);
} catch (Exception e)
{
groovyJarsArePresent = 0;
} catch (Exception e)
{
groovyJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Groovy Classes are not present");
+ Cache.log.debug("Groovy Classes are not present");
}
}
return (groovyJarsArePresent > 0);
}
}
return (groovyJarsArePresent > 0);
@@
-723,9
+729,9
@@
public class Cache
new Object[]
{
"Jalview Desktop",
new Object[]
{
"Jalview Desktop",
- (vrs = jalview.bin.Cache.getProperty("VERSION")
+ (vrs = Cache.getProperty("VERSION")
+ "_"
+ "_"
- + jalview.bin.Cache.getDefault("BUILD_DATE",
+ + Cache.getDefault("BUILD_DATE",
"unknown")), "UA-9060947-1" });
jgoogleanalyticstracker.getMethod("trackAsynchronously",
new Class[]
"unknown")), "UA-9060947-1" });
jgoogleanalyticstracker.getMethod("trackAsynchronously",
new Class[]
@@
-811,13
+817,12
@@
public class Cache
{
return defcolour;
}
{
return defcolour;
}
- Color col = jalview.schemes.ColourSchemeProperty
- .getAWTColorFromName(colprop);
+ Color col = ColourSchemeProperty.getAWTColorFromName(colprop);
if (col == null)
{
try
{
if (col == null)
{
try
{
- col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
+ col = new UserColourScheme(colprop).findColour('A');
} catch (Exception ex)
{
log.warn("Couldn't parse '" + colprop + "' as a colour for "
} catch (Exception ex)
{
log.warn("Couldn't parse '" + colprop + "' as a colour for "
@@
-836,7
+841,7
@@
public class Cache
*/
public static void setColourProperty(String property, Color colour)
{
*/
public static void setColourProperty(String property, Color colour)
{
- setProperty(property, jalview.util.Format.getHexString(colour));
+ setProperty(property, Format.getHexString(colour));
}
public static final DateFormat date_format = SimpleDateFormat
}
public static final DateFormat date_format = SimpleDateFormat
diff --git
a/src/jalview/bin/Jalview.java
b/src/jalview/bin/Jalview.java
index
f6d0099
..
8669a96
100755
(executable)
--- a/
src/jalview/bin/Jalview.java
+++ b/
src/jalview/bin/Jalview.java
@@
-22,8
+22,17
@@
package jalview.bin;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.PromptUserConfig;
+import jalview.io.AppletFormatAdapter;
import jalview.io.BioJsHTMLOutput;
import jalview.io.BioJsHTMLOutput;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
import jalview.io.HtmlSvgOutput;
import jalview.io.HtmlSvgOutput;
+import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
@@
-231,7
+240,7
@@
public class Jalview
}
String file = null, protocol = null, format = null, data = null;
}
String file = null, protocol = null, format = null, data = null;
- jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless);
+ FileLoader fileLoader = new FileLoader(!headless);
Vector getFeatures = null; // vector of das source nicknames to fetch
// features from
// loading is done.
Vector getFeatures = null; // vector of das source nicknames to fetch
// features from
// loading is done.
@@
-262,13
+271,13
@@
public class Jalview
{
try
{
{
try
{
- String viprotocol = jalview.io.AppletFormatAdapter
+ String viprotocol = AppletFormatAdapter
.checkProtocol(vamsasImport);
.checkProtocol(vamsasImport);
- if (viprotocol == jalview.io.FormatAdapter.FILE)
+ if (viprotocol == FormatAdapter.FILE)
{
inSession = desktop.vamsasImport(new File(vamsasImport));
}
{
inSession = desktop.vamsasImport(new File(vamsasImport));
}
- else if (viprotocol == jalview.io.FormatAdapter.URL)
+ else if (viprotocol == FormatAdapter.URL)
{
inSession = desktop.vamsasImport(new URL(vamsasImport));
}
{
inSession = desktop.vamsasImport(new URL(vamsasImport));
}
@@
-354,9
+363,9
@@
public class Jalview
}
}
}
}
- protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);
+ protocol = AppletFormatAdapter.checkProtocol(file);
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ format = new IdentifyFile().Identify(file, protocol);
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
@@
-372,12
+381,12
@@
public class Jalview
{
data.replaceAll("%20", " ");
{
data.replaceAll("%20", " ");
- jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
+ ColourSchemeI cs = ColourSchemeProperty
.getColour(af.getViewport().getAlignment(), data);
if (cs == null)
{
.getColour(af.getViewport().getAlignment(), data);
if (cs == null)
{
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+ UserColourScheme ucs = new UserColourScheme(
"white");
ucs.parseAppletParameter(data);
cs = ucs;
"white");
ucs.parseAppletParameter(data);
cs = ucs;
@@
-392,14
+401,14
@@
public class Jalview
if (data != null)
{
af.parseFeaturesFile(data,
if (data != null)
{
af.parseFeaturesFile(data,
- jalview.io.AppletFormatAdapter.checkProtocol(data));
+ AppletFormatAdapter.checkProtocol(data));
System.out.println("Added " + data);
}
data = aparser.getValue("features", true);
if (data != null)
{
af.parseFeaturesFile(data,
System.out.println("Added " + data);
}
data = aparser.getValue("features", true);
if (data != null)
{
af.parseFeaturesFile(data,
- jalview.io.AppletFormatAdapter.checkProtocol(data));
+ AppletFormatAdapter.checkProtocol(data));
System.out.println("Added " + data);
}
System.out.println("Added " + data);
}
@@
-425,11
+434,11
@@
public class Jalview
data = aparser.getValue("tree", true);
if (data != null)
{
data = aparser.getValue("tree", true);
if (data != null)
{
- jalview.io.NewickFile fin = null;
+ NewickFile fin = null;
try
{
try
{
- fin = new jalview.io.NewickFile(data,
- jalview.io.AppletFormatAdapter.checkProtocol(data));
+ fin = new NewickFile(data,
+ AppletFormatAdapter.checkProtocol(data));
if (fin != null)
{
af.getViewport().setCurrentTree(
if (fin != null)
{
af.getViewport().setCurrentTree(
@@
-470,7
+479,7
@@
public class Jalview
{
// Execute the groovy script after we've done all the rendering stuff
// and before any images or figures are generated.
{
// Execute the groovy script after we've done all the rendering stuff
// and before any images or figures are generated.
- if (jalview.bin.Cache.groovyJarsPresent())
+ if (Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
executeGroovyScript(groovyscript, new Object[]
{
System.out.println("Executing script " + groovyscript);
executeGroovyScript(groovyscript, new Object[]
@@
-553,11
+562,11
@@
public class Jalview
// ////////////////////
if (!headless && file == null && vamsasImport == null
// ////////////////////
if (!headless && file == null && vamsasImport == null
- && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+ && Cache.getDefault("SHOW_STARTUP_FILE", true))
{
{
- file = jalview.bin.Cache.getDefault(
+ file = Cache.getDefault(
"STARTUP_FILE",
"STARTUP_FILE",
- jalview.bin.Cache.getDefault("www.jalview.org",
+ Cache.getDefault("www.jalview.org",
"http://www.jalview.org")
+ "/examples/exampleFile_2_7.jar");
if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar"))
"http://www.jalview.org")
+ "/examples/exampleFile_2_7.jar");
if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar"))
@@
-565,7
+574,7
@@
public class Jalview
// hardwire upgrade of the startup file
file.replace("_2_3.jar", "_2_7.jar");
// and remove the stale setting
// hardwire upgrade of the startup file
file.replace("_2_3.jar", "_2_7.jar");
// and remove the stale setting
- jalview.bin.Cache.removeProperty("STARTUP_FILE");
+ Cache.removeProperty("STARTUP_FILE");
}
protocol = "File";
}
protocol = "File";
@@
-581,7
+590,7
@@
public class Jalview
}
else
{
}
else
{
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ format = new IdentifyFile().Identify(file, protocol);
}
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
}
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
@@
-603,7
+612,7
@@
public class Jalview
// Once all other stuff is done, execute any groovy scripts (in order)
if (groovyscript != null)
{
// Once all other stuff is done, execute any groovy scripts (in order)
if (groovyscript != null)
{
- if (jalview.bin.Cache.groovyJarsPresent())
+ if (Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
executeGroovyScript(groovyscript, new Object[]
{
System.out.println("Executing script " + groovyscript);
executeGroovyScript(groovyscript, new Object[]
@@
-673,7
+682,7
@@
public class Jalview
/**
* start a User Config prompt asking if we can log usage statistics.
*/
/**
* start a User Config prompt asking if we can log usage statistics.
*/
- jalview.gui.PromptUserConfig prompter = new jalview.gui.PromptUserConfig(
+ PromptUserConfig prompter = new PromptUserConfig(
desktop.desktop,
"USAGESTATS",
"Jalview Usage Statistics",
desktop.desktop,
"USAGESTATS",
"Jalview Usage Statistics",
diff --git
a/src/jalview/bin/JalviewLite.java
b/src/jalview/bin/JalviewLite.java
index
ae5c63f
..
5d1f0b0
100644
(file)
--- a/
src/jalview/bin/JalviewLite.java
+++ b/
src/jalview/bin/JalviewLite.java
@@
-20,6
+20,7
@@
*/
package jalview.bin;
*/
package jalview.bin;
+import jalview.analysis.SequenceIdMatcher;
import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
import jalview.appletgui.AlignViewport;
import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
import jalview.appletgui.AlignViewport;
@@
-44,6
+45,11
@@
import jalview.io.NewickFile;
import jalview.javascript.JSFunctionExec;
import jalview.javascript.JalviewLiteJsApi;
import jalview.javascript.JsCallBack;
import jalview.javascript.JSFunctionExec;
import jalview.javascript.JalviewLiteJsApi;
import jalview.javascript.JsCallBack;
+import jalview.javascript.JsSelectionSender;
+import jalview.javascript.MouseOverListener;
+import jalview.javascript.MouseOverStructureListener;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
import jalview.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
@@
-178,7
+184,7
@@
public class JalviewLite extends Applet implements
final String position, final String alignedPosition)
{
// TODO: could try to highlight in all alignments if alf==null
final String position, final String alignedPosition)
{
// TODO: could try to highlight in all alignments if alf==null
- jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ SequenceIdMatcher matcher = new SequenceIdMatcher(
alf.viewport.getAlignment().getSequencesArray());
final SequenceI sq = matcher.findIdMatch(sequenceId);
if (sq != null)
alf.viewport.getAlignment().getSequencesArray());
final SequenceI sq = matcher.findIdMatch(sequenceId);
if (sq != null)
@@
-284,7
+290,7
@@
public class JalviewLite extends Applet implements
final SequenceGroup sel = new SequenceGroup();
final ColumnSelection csel = new ColumnSelection();
AlignmentI al = alf.viewport.getAlignment();
final SequenceGroup sel = new SequenceGroup();
final ColumnSelection csel = new ColumnSelection();
AlignmentI al = alf.viewport.getAlignment();
- jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ SequenceIdMatcher matcher = new SequenceIdMatcher(
alf.viewport.getAlignment().getSequencesArray());
int start = 0, end = al.getWidth(), alw = al.getWidth();
boolean seqsfound = true;
alf.viewport.getAlignment().getSequencesArray());
int start = 0, end = al.getWidth(), alw = al.getWidth();
boolean seqsfound = true;
@@
-598,7
+604,7
@@
public class JalviewLite extends Applet implements
SequenceI[] sqs = null;
if (ids != null && ids.length > 0)
{
SequenceI[] sqs = null;
if (ids != null && ids.length > 0)
{
- jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ SequenceIdMatcher matcher = new SequenceIdMatcher(
alf.viewport.getAlignment().getSequencesArray());
int s = 0;
sqs = new SequenceI[ids.length];
alf.viewport.getAlignment().getSequencesArray());
int s = 0;
sqs = new SequenceI[ids.length];
@@
-876,7
+882,7
@@
public class JalviewLite extends Applet implements
setMouseoverListener(currentAlignFrame, listener);
}
setMouseoverListener(currentAlignFrame, listener);
}
- private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();
+ private Vector<JSFunctionExec> javascriptListeners = new Vector<JSFunctionExec>();
/*
* (non-Javadoc)
/*
* (non-Javadoc)
@@
-897,7
+903,7
@@
public class JalviewLite extends Applet implements
return;
}
}
return;
}
}
- jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
+ MouseOverListener mol = new MouseOverListener(
this, af, listener);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
this, af, listener);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
@@
-941,8
+947,7
@@
public class JalviewLite extends Applet implements
return;
}
}
return;
}
}
- jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
- this, af, listener);
+ JsSelectionSender mol = new JsSelectionSender(this, af, listener);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
.addSelectionListener(mol);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
.addSelectionListener(mol);
@@
-974,7
+979,7
@@
public class JalviewLite extends Applet implements
return;
}
}
return;
}
}
- jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(
+ MouseOverStructureListener mol = new MouseOverStructureListener(
this, listener, separatorListToArray(modelSet));
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
this, listener, separatorListToArray(modelSet));
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
@@
-1071,8
+1076,7
@@
public class JalviewLite extends Applet implements
{
while (javascriptListeners.size() > 0)
{
{
while (javascriptListeners.size() > 0)
{
- jalview.javascript.JSFunctionExec mol = javascriptListeners
- .elementAt(0);
+ JSFunctionExec mol = javascriptListeners.elementAt(0);
javascriptListeners.removeElement(mol);
if (mol instanceof SelectionListener)
{
javascriptListeners.removeElement(mol);
if (mol instanceof SelectionListener)
{
@@
-1098,7
+1102,7
@@
public class JalviewLite extends Applet implements
StructureSelectionManager.release(this);
}
StructureSelectionManager.release(this);
}
- private jalview.javascript.JSFunctionExec jsFunctionExec;
+ private JSFunctionExec jsFunctionExec;
/*
* (non-Javadoc)
/*
* (non-Javadoc)
@@
-1996,8
+2000,8
@@
public class JalviewLite extends Applet implements
// alignPdbStructures is true)
Vector pdbs = new Vector();
// create a lazy matcher if we're asked to
// alignPdbStructures is true)
Vector pdbs = new Vector();
// create a lazy matcher if we're asked to
- jalview.analysis.SequenceIdMatcher matcher = (applet
- .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
+ SequenceIdMatcher matcher = (applet.getDefaultParameter(
+ "relaxedidmatch", false)) ? new SequenceIdMatcher(
alignFrame.getAlignViewport().getAlignment()
.getSequencesArray()) : null;
alignFrame.getAlignViewport().getAlignment()
.getSequencesArray()) : null;
@@
-2853,13
+2857,12
@@
public class JalviewLite extends Applet implements
{
return defcolour;
}
{
return defcolour;
}
- Color col = jalview.schemes.ColourSchemeProperty
- .getAWTColorFromName(colprop);
+ Color col = ColourSchemeProperty.getAWTColorFromName(colprop);
if (col == null)
{
try
{
if (col == null)
{
try
{
- col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
+ col = new UserColourScheme(colprop).findColour('A');
} catch (Exception ex)
{
System.err.println("Couldn't parse '" + colprop
} catch (Exception ex)
{
System.err.println("Couldn't parse '" + colprop
diff --git
a/src/jalview/bin/JalviewLiteURLRetrieve.java
b/src/jalview/bin/JalviewLiteURLRetrieve.java
index
6be1016
..
f84cd07
100644
(file)
--- a/
src/jalview/bin/JalviewLiteURLRetrieve.java
+++ b/
src/jalview/bin/JalviewLiteURLRetrieve.java
@@
-23,6
+23,7
@@
package jalview.bin;
import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
+import jalview.io.IdentifyFile;
import java.applet.Applet;
import java.io.InputStream;
import java.applet.Applet;
import java.io.InputStream;
@@
-113,7
+114,7
@@
public class JalviewLiteURLRetrieve extends Applet
String format = getParameter("format");
if (format == null || format.length() == 0)
{
String format = getParameter("format");
if (format == null || format.length() == 0)
{
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ format = new IdentifyFile().Identify(file, protocol);
System.out.println("Format is " + format);
}
else
System.out.println("Format is " + format);
}
else