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JAL-1551 formatting
author
Jim Procter
<jprocter@issues.jalview.org>
Mon, 4 Apr 2016 14:49:02 +0000
(15:49 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Mon, 4 Apr 2016 14:49:02 +0000
(15:49 +0100)
src/jalview/bin/JalviewLite.java
patch
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blob
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history
diff --git
a/src/jalview/bin/JalviewLite.java
b/src/jalview/bin/JalviewLite.java
index
095cfd3
..
13e4b7e
100644
(file)
--- a/
src/jalview/bin/JalviewLite.java
+++ b/
src/jalview/bin/JalviewLite.java
@@
-100,6
+100,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
*/
*
* @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
*/
+ @Override
public String getSelectedSequences()
{
return getSelectedSequencesFrom(getDefaultTargetFrame());
public String getSelectedSequences()
{
return getSelectedSequencesFrom(getDefaultTargetFrame());
@@
-110,6
+111,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
*/
*
* @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
*/
+ @Override
public String getSelectedSequences(String sep)
{
return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
public String getSelectedSequences(String sep)
{
return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
@@
-122,6
+124,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
* .AlignFrame)
*/
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
* .AlignFrame)
*/
+ @Override
public String getSelectedSequencesFrom(AlignFrame alf)
{
return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
public String getSelectedSequencesFrom(AlignFrame alf)
{
return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
@@
-134,6
+137,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
* .AlignFrame, java.lang.String)
*/
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
* .AlignFrame, java.lang.String)
*/
+ @Override
public String getSelectedSequencesFrom(AlignFrame alf, String sep)
{
StringBuffer result = new StringBuffer("");
public String getSelectedSequencesFrom(AlignFrame alf, String sep)
{
StringBuffer result = new StringBuffer("");
@@
-162,6
+166,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
* java.lang.String, java.lang.String)
*/
* @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
* java.lang.String, java.lang.String)
*/
+ @Override
public void highlight(String sequenceId, String position,
String alignedPosition)
{
public void highlight(String sequenceId, String position,
String alignedPosition)
{
@@
-175,6
+180,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String, java.lang.String)
*/
* @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String, java.lang.String)
*/
+ @Override
public void highlightIn(final AlignFrame alf, final String sequenceId,
final String position, final String alignedPosition)
{
public void highlightIn(final AlignFrame alf, final String sequenceId,
final String position, final String alignedPosition)
{
@@
-231,6
+237,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
* java.lang.String)
*/
* @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
* java.lang.String)
*/
+ @Override
public void select(String sequenceIds, String columns)
{
selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
public void select(String sequenceIds, String columns)
{
selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
@@
-242,6
+249,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
* java.lang.String, java.lang.String)
*/
* @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
* java.lang.String, java.lang.String)
*/
+ @Override
public void select(String sequenceIds, String columns, String sep)
{
selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);
public void select(String sequenceIds, String columns, String sep)
{
selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);
@@
-253,6
+261,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String)
*/
* @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String)
*/
+ @Override
public void selectIn(AlignFrame alf, String sequenceIds, String columns)
{
selectIn(alf, sequenceIds, columns, separator);
public void selectIn(AlignFrame alf, String sequenceIds, String columns)
{
selectIn(alf, sequenceIds, columns, separator);
@@
-264,6
+273,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String, java.lang.String)
*/
* @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String, java.lang.String)
*/
+ @Override
public void selectIn(final AlignFrame alf, String sequenceIds,
String columns, String sep)
{
public void selectIn(final AlignFrame alf, String sequenceIds,
String columns, String sep)
{
@@
-489,6
+499,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.
* String, java.lang.String)
*/
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.
* String, java.lang.String)
*/
+ @Override
public String getSelectedSequencesAsAlignment(String format, String suffix)
{
return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
public String getSelectedSequencesAsAlignment(String format, String suffix)
{
return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
@@
-502,6
+513,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview
* .appletgui.AlignFrame, java.lang.String, java.lang.String)
*/
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview
* .appletgui.AlignFrame, java.lang.String, java.lang.String)
*/
+ @Override
public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, String suffix)
{
public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, String suffix)
{
@@
-531,6
+543,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
*/
*
* @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
*/
+ @Override
public String getAlignmentOrder()
{
return getAlignmentOrderFrom(getDefaultTargetFrame());
public String getAlignmentOrder()
{
return getAlignmentOrderFrom(getDefaultTargetFrame());
@@
-543,6
+556,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
* )
*/
* jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
* )
*/
+ @Override
public String getAlignmentOrderFrom(AlignFrame alf)
{
return getAlignmentOrderFrom(alf, separator);
public String getAlignmentOrderFrom(AlignFrame alf)
{
return getAlignmentOrderFrom(alf, separator);
@@
-555,6
+569,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
* jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
+ @Override
public String getAlignmentOrderFrom(AlignFrame alf, String sep)
{
AlignmentI alorder = alf.getAlignViewport().getAlignment();
public String getAlignmentOrderFrom(AlignFrame alf, String sep)
{
AlignmentI alorder = alf.getAlignViewport().getAlignment();
@@
-572,6
+587,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
* java.lang.String)
*/
* @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
* java.lang.String)
*/
+ @Override
public String orderBy(String order, String undoName)
{
return orderBy(order, undoName, separator);
public String orderBy(String order, String undoName)
{
return orderBy(order, undoName, separator);
@@
-583,6
+599,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
* java.lang.String, java.lang.String)
*/
* @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
* java.lang.String, java.lang.String)
*/
+ @Override
public String orderBy(String order, String undoName, String sep)
{
return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
public String orderBy(String order, String undoName, String sep)
{
return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
@@
-595,6
+612,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String, java.lang.String)
*/
* jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String, java.lang.String)
*/
+ @Override
public String orderAlignmentBy(AlignFrame alf, String order,
String undoName, String sep)
{
public String orderAlignmentBy(AlignFrame alf, String order,
String undoName, String sep)
{
@@
-651,6
+669,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)
*/
*
* @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)
*/
+ @Override
public String getAlignment(String format)
{
return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE);
public String getAlignment(String format)
{
return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE);
@@
-663,6
+682,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
* java.lang.String)
*/
* jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
* java.lang.String)
*/
+ @Override
public String getAlignmentFrom(AlignFrame alf, String format)
{
return getAlignmentFrom(alf, format, TRUE);
public String getAlignmentFrom(AlignFrame alf, String format)
{
return getAlignmentFrom(alf, format, TRUE);
@@
-674,6
+694,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
* java.lang.String)
*/
* @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
* java.lang.String)
*/
+ @Override
public String getAlignment(String format, String suffix)
{
return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
public String getAlignment(String format, String suffix)
{
return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
@@
-686,6
+707,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String)
*/
* jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String)
*/
+ @Override
public String getAlignmentFrom(AlignFrame alf, String format,
String suffix)
{
public String getAlignmentFrom(AlignFrame alf, String format,
String suffix)
{
@@
-708,6
+730,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
*/
*
* @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
*/
+ @Override
public void loadAnnotation(String annotation)
{
loadAnnotationFrom(getDefaultTargetFrame(), annotation);
public void loadAnnotation(String annotation)
{
loadAnnotationFrom(getDefaultTargetFrame(), annotation);
@@
-720,6
+743,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
* jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
+ @Override
public void loadAnnotationFrom(AlignFrame alf, String annotation)
{
if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
public void loadAnnotationFrom(AlignFrame alf, String annotation)
{
if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
@@
-739,6
+763,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
*/
*
* @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
*/
+ @Override
public void loadFeatures(String features, boolean autoenabledisplay)
{
loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
public void loadFeatures(String features, boolean autoenabledisplay)
{
loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
@@
-751,6
+776,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
* jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
+ @Override
public boolean loadFeaturesFrom(AlignFrame alf, String features,
boolean autoenabledisplay)
{
public boolean loadFeaturesFrom(AlignFrame alf, String features,
boolean autoenabledisplay)
{
@@
-763,6
+789,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
*/
*
* @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
*/
+ @Override
public String getFeatures(String format)
{
return getFeaturesFrom(getDefaultTargetFrame(), format);
public String getFeatures(String format)
{
return getFeaturesFrom(getDefaultTargetFrame(), format);
@@
-775,6
+802,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
* java.lang.String)
*/
* jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
* java.lang.String)
*/
+ @Override
public String getFeaturesFrom(AlignFrame alf, String format)
{
return alf.outputFeatures(false, format);
public String getFeaturesFrom(AlignFrame alf, String format)
{
return alf.outputFeatures(false, format);
@@
-785,6
+813,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#getAnnotation()
*/
*
* @see jalview.bin.JalviewLiteJsApi#getAnnotation()
*/
+ @Override
public String getAnnotation()
{
return getAnnotationFrom(getDefaultTargetFrame());
public String getAnnotation()
{
return getAnnotationFrom(getDefaultTargetFrame());
@@
-797,6
+826,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
* )
*/
* jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
* )
*/
+ @Override
public String getAnnotationFrom(AlignFrame alf)
{
return alf.outputAnnotations(false);
public String getAnnotationFrom(AlignFrame alf)
{
return alf.outputAnnotations(false);
@@
-807,6
+837,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#newView()
*/
*
* @see jalview.bin.JalviewLiteJsApi#newView()
*/
+ @Override
public AlignFrame newView()
{
return newViewFrom(getDefaultTargetFrame());
public AlignFrame newView()
{
return newViewFrom(getDefaultTargetFrame());
@@
-817,6
+848,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
*/
*
* @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
*/
+ @Override
public AlignFrame newView(String name)
{
return newViewFrom(getDefaultTargetFrame(), name);
public AlignFrame newView(String name)
{
return newViewFrom(getDefaultTargetFrame(), name);
@@
-827,6
+859,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
*/
*
* @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
*/
+ @Override
public AlignFrame newViewFrom(AlignFrame alf)
{
return alf.newView(null);
public AlignFrame newViewFrom(AlignFrame alf)
{
return alf.newView(null);
@@
-838,6
+871,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
* java.lang.String)
*/
* @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
* java.lang.String)
*/
+ @Override
public AlignFrame newViewFrom(AlignFrame alf, String name)
{
return alf.newView(name);
public AlignFrame newViewFrom(AlignFrame alf, String name)
{
return alf.newView(name);
@@
-849,6
+883,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
* java.lang.String)
*/
* @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
* java.lang.String)
*/
+ @Override
public AlignFrame loadAlignment(String text, String title)
{
AlignmentI al = null;
public AlignFrame loadAlignment(String text, String title)
{
AlignmentI al = null;
@@
-875,6
+910,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
*/
*
* @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
*/
+ @Override
public void setMouseoverListener(String listener)
{
setMouseoverListener(currentAlignFrame, listener);
public void setMouseoverListener(String listener)
{
setMouseoverListener(currentAlignFrame, listener);
@@
-889,6
+925,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
* jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
+ @Override
public void setMouseoverListener(AlignFrame af, String listener)
{
if (listener != null)
public void setMouseoverListener(AlignFrame af, String listener)
{
if (listener != null)
@@
-921,6
+958,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)
*/
*
* @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)
*/
+ @Override
public void setSelectionListener(String listener)
{
setSelectionListener(null, listener);
public void setSelectionListener(String listener)
{
setSelectionListener(null, listener);
@@
-933,6
+971,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
* jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
+ @Override
public void setSelectionListener(AlignFrame af, String listener)
{
if (listener != null)
public void setSelectionListener(AlignFrame af, String listener)
{
if (listener != null)
@@
-971,6
+1010,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
* java.lang.String)
*/
* @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
* java.lang.String)
*/
+ @Override
public void setStructureListener(String listener, String modelSet)
{
if (listener != null)
public void setStructureListener(String listener, String modelSet)
{
if (listener != null)
@@
-1004,6
+1044,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
* .AlignFrame, java.lang.String)
*/
* jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
* .AlignFrame, java.lang.String)
*/
+ @Override
public void removeJavascriptListener(AlignFrame af, String listener)
{
if (listener != null)
public void removeJavascriptListener(AlignFrame af, String listener)
{
if (listener != null)
@@
-1053,12
+1094,14
@@
public class JalviewLite extends Applet implements
}
}
}
}
+ @Override
public void stop()
{
System.err.println("Applet " + getName() + " stop().");
tidyUp();
}
public void stop()
{
System.err.println("Applet " + getName() + " stop().");
tidyUp();
}
+ @Override
public void destroy()
{
System.err.println("Applet " + getName() + " destroy().");
public void destroy()
{
System.err.println("Applet " + getName() + " destroy().");
@@
-1115,6
+1158,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,
* java.lang.String, java.lang.String)
*/
* @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,
* java.lang.String, java.lang.String)
*/
+ @Override
public void mouseOverStructure(final String pdbResNum,
final String chain, final String pdbfile)
{
public void mouseOverStructure(final String pdbResNum,
final String chain, final String pdbfile)
{
@@
-1152,6
+1196,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String)
*/
* jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String)
*/
+ @Override
public void scrollViewToIn(final AlignFrame alf, final String topRow,
final String leftHandColumn)
{
public void scrollViewToIn(final AlignFrame alf, final String topRow,
final String leftHandColumn)
{
@@
-1491,6
+1536,7
@@
public class JalviewLite extends Applet implements
add(launcher);
launcher.addActionListener(new java.awt.event.ActionListener()
{
add(launcher);
launcher.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
LoadingThread loader = new LoadingThread(file, file2,
public void actionPerformed(ActionEvent e)
{
LoadingThread loader = new LoadingThread(file, file2,
@@
-1613,6
+1659,7
@@
public class JalviewLite extends Applet implements
frame.setTitle(title);
frame.addWindowListener(new WindowAdapter()
{
frame.setTitle(title);
frame.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent e)
{
if (frame instanceof AlignFrame)
public void windowClosing(WindowEvent e)
{
if (frame instanceof AlignFrame)
@@
-1637,6
+1684,7
@@
public class JalviewLite extends Applet implements
frame.dispose();
}
frame.dispose();
}
+ @Override
public void windowActivated(WindowEvent e)
{
if (frame instanceof AlignFrame)
public void windowActivated(WindowEvent e)
{
if (frame instanceof AlignFrame)
@@
-1674,6
+1722,7
@@
public class JalviewLite extends Applet implements
* @param g
* graphics context
*/
* @param g
* graphics context
*/
+ @Override
public void paint(Graphics g)
{
if (!fileFound)
public void paint(Graphics g)
{
if (!fileFound)
@@
-1725,6
+1774,7
@@
public class JalviewLite extends Applet implements
{
private boolean running = false;
{
private boolean running = false;
+ @Override
public void run()
{
if (running || checkedForJmol)
public void run()
{
if (running || checkedForJmol)
@@
-1869,6
+1919,7
@@
public class JalviewLite extends Applet implements
applet = _applet;
}
applet = _applet;
}
+ @Override
public void run()
{
LoadJmolThread jmolchecker = new LoadJmolThread();
public void run()
{
LoadJmolThread jmolchecker = new LoadJmolThread();
@@
-2569,6
+2620,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
*/
*
* @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
*/
+ @Override
public String getFeatureGroups()
{
String lst = arrayToSeparatorList(getDefaultTargetFrame()
public String getFeatureGroups()
{
String lst = arrayToSeparatorList(getDefaultTargetFrame()
@@
-2583,6
+2635,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
* )
*/
* jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
* )
*/
+ @Override
public String getFeatureGroupsOn(AlignFrame alf)
{
String lst = arrayToSeparatorList(alf.getFeatureGroups());
public String getFeatureGroupsOn(AlignFrame alf)
{
String lst = arrayToSeparatorList(alf.getFeatureGroups());
@@
-2594,6
+2647,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
*/
*
* @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
*/
+ @Override
public String getFeatureGroupsOfState(boolean visible)
{
return arrayToSeparatorList(getDefaultTargetFrame()
public String getFeatureGroupsOfState(boolean visible)
{
return arrayToSeparatorList(getDefaultTargetFrame()
@@
-2607,6
+2661,7
@@
public class JalviewLite extends Applet implements
* jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
* .AlignFrame, boolean)
*/
* jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
* .AlignFrame, boolean)
*/
+ @Override
public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
{
return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
{
return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
@@
-2618,6
+2673,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
* AlignFrame, java.lang.String, boolean)
*/
* @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
* AlignFrame, java.lang.String, boolean)
*/
+ @Override
public void setFeatureGroupStateOn(final AlignFrame alf,
final String groups, boolean state)
{
public void setFeatureGroupStateOn(final AlignFrame alf,
final String groups, boolean state)
{
@@
-2639,6
+2695,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
* boolean)
*/
* @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
* boolean)
*/
+ @Override
public void setFeatureGroupState(String groups, boolean state)
{
setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
public void setFeatureGroupState(String groups, boolean state)
{
setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
@@
-2649,6
+2706,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#getSeparator()
*/
*
* @see jalview.bin.JalviewLiteJsApi#getSeparator()
*/
+ @Override
public String getSeparator()
{
return separator;
public String getSeparator()
{
return separator;
@@
-2659,6
+2717,7
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
*/
*
* @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
*/
+ @Override
public void setSeparator(String separator)
{
if (separator == null || separator.length() < 1)
public void setSeparator(String separator)
{
if (separator == null || separator.length() < 1)
@@
-2703,6
+2762,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String, java.lang.String)
*/
* @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String, java.lang.String)
*/
+ @Override
public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
String pdbEntryString, String pdbFile)
{
public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
String pdbEntryString, String pdbFile)
{
@@
-2719,6
+2779,7
@@
public class JalviewLite extends Applet implements
return alignPdbStructures;
}
return alignPdbStructures;
}
+ @Override
public void start()
{
// callInitCallback();
public void start()
{
// callInitCallback();
@@
-2752,6
+2813,7
@@
public class JalviewLite extends Applet implements
* @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
* java.lang.String)
*/
* @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
* java.lang.String)
*/
+ @Override
public String getJsMessage(String messageclass, String viewId)
{
Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
public String getJsMessage(String messageclass, String viewId)
{
Hashtable<String, String[]> msgset = jsmessages.get(messageclass);