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JAL-4390 don't output alignment to text panel and stdout when lots of sequences proce...
[jalview.git]
/
src
/
jalview
/
bin
/
JalviewLite.java
diff --git
a/src/jalview/bin/JalviewLite.java
b/src/jalview/bin/JalviewLite.java
index
64cf283
..
7d66f6d
100644
(file)
--- a/
src/jalview/bin/JalviewLite.java
+++ b/
src/jalview/bin/JalviewLite.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,6
+20,8
@@
*/
package jalview.bin;
*/
package jalview.bin;
+import java.util.Locale;
+
import jalview.analysis.AlignmentUtils;
import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
import jalview.analysis.AlignmentUtils;
import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
@@
-37,6
+39,9
@@
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileParse;
import jalview.io.IdentifyFile;
import jalview.io.JPredFile;
import jalview.io.FileParse;
import jalview.io.IdentifyFile;
import jalview.io.JPredFile;
@@
-48,6
+53,7
@@
import jalview.javascript.JsCallBack;
import jalview.javascript.MouseOverStructureListener;
import jalview.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
import jalview.javascript.MouseOverStructureListener;
import jalview.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
+import jalview.util.ColorUtils;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
@@
-63,6
+69,7
@@
import java.awt.event.ActionEvent;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.BufferedReader;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.BufferedReader;
+import java.io.IOException;
import java.io.InputStreamReader;
import java.net.URL;
import java.util.ArrayList;
import java.io.InputStreamReader;
import java.net.URL;
import java.util.ArrayList;
@@
-79,8
+86,8
@@
import netscape.javascript.JSObject;
* @author $author$
* @version $Revision: 1.92 $
*/
* @author $author$
* @version $Revision: 1.92 $
*/
-public class JalviewLite extends Applet implements
- StructureSelectionManagerProvider, JalviewLiteJsApi
+public class JalviewLite extends Applet
+ implements StructureSelectionManagerProvider, JalviewLiteJsApi
{
private static final String TRUE = "true";
{
private static final String TRUE = "true";
@@
-100,6
+107,7
@@
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
+118,7
@@
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
+131,7
@@
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
+144,7
@@
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
+173,7
@@
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
+187,7
@@
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)
{
@@
-187,7
+200,7
@@
public class JalviewLite extends Applet implements
int apos = -1;
try
{
int apos = -1;
try
{
- apos = new Integer(position).intValue();
+ apos = Integer.valueOf(position).intValue();
apos--;
} catch (NumberFormatException ex)
{
apos--;
} catch (NumberFormatException ex)
{
@@
-198,7
+211,7
@@
public class JalviewLite extends Applet implements
// use vamsas listener to broadcast to all listeners in scope
if (alignedPosition != null
&& (alignedPosition.trim().length() == 0 || alignedPosition
// use vamsas listener to broadcast to all listeners in scope
if (alignedPosition != null
&& (alignedPosition.trim().length() == 0 || alignedPosition
- .toLowerCase().indexOf("false") > -1))
+ .toLowerCase(Locale.ROOT).indexOf("false") > -1))
{
java.awt.EventQueue.invokeLater(new Runnable()
{
{
java.awt.EventQueue.invokeLater(new Runnable()
{
@@
-231,6
+244,7
@@
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
+256,7
@@
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
+268,7
@@
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
+280,7
@@
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)
{
@@
-323,23
+340,23
@@
public class JalviewLite extends Applet implements
int from = -1, to = -1;
try
{
int from = -1, to = -1;
try
{
- from = new Integer(cl.substring(0, p)).intValue();
+ from = Integer.valueOf(cl.substring(0, p)).intValue();
from--;
} catch (NumberFormatException ex)
{
from--;
} catch (NumberFormatException ex)
{
- System.err
- .println("ERROR: Couldn't parse first integer in range element column selection string '"
+ System.err.println(
+ "ERROR: Couldn't parse first integer in range element column selection string '"
+ cl + "' - format is 'from-to'");
return;
}
try
{
+ cl + "' - format is 'from-to'");
return;
}
try
{
- to = new Integer(cl.substring(p + 1)).intValue();
+ to = Integer.valueOf(cl.substring(p + 1)).intValue();
to--;
} catch (NumberFormatException ex)
{
to--;
} catch (NumberFormatException ex)
{
- System.err
- .println("ERROR: Couldn't parse second integer in range element column selection string '"
+ System.err.println(
+ "ERROR: Couldn't parse second integer in range element column selection string '"
+ cl + "' - format is 'from-to'");
return;
}
+ cl + "' - format is 'from-to'");
return;
}
@@
-394,19
+411,19
@@
public class JalviewLite extends Applet implements
int r = -1;
try
{
int r = -1;
try
{
- r = new Integer(cl).intValue();
+ r = Integer.valueOf(cl).intValue();
r--;
} catch (NumberFormatException ex)
{
r--;
} catch (NumberFormatException ex)
{
- if (cl.toLowerCase().equals("sequence"))
+ if (cl.toLowerCase(Locale.ROOT).equals("sequence"))
{
// we are in the dataset sequence's coordinate frame.
inseqpos = true;
}
else
{
{
// we are in the dataset sequence's coordinate frame.
inseqpos = true;
}
else
{
- System.err
- .println("ERROR: Couldn't parse integer from point selection element of column selection string '"
+ System.err.println(
+ "ERROR: Couldn't parse integer from point selection element of column selection string '"
+ cl + "'");
return;
}
+ cl + "'");
return;
}
@@
-456,14
+473,11
@@
public class JalviewLite extends Applet implements
SequenceI rs = sel.getSequenceAt(0);
start = rs.findIndex(start);
end = rs.findIndex(end);
SequenceI rs = sel.getSequenceAt(0);
start = rs.findIndex(start);
end = rs.findIndex(end);
- if (csel != null)
+ List<Integer> cs = new ArrayList<>(csel.getSelected());
+ csel.clear();
+ for (Integer selectedCol : cs)
{
{
- List<Integer> cs = csel.getSelected();
- csel.clear();
- for (Integer selectedCol : cs)
- {
- csel.addElement(rs.findIndex(selectedCol));
- }
+ csel.addElement(rs.findIndex(selectedCol));
}
}
sel.setStartRes(start);
}
}
sel.setStartRes(start);
@@
-473,7
+487,8
@@
public class JalviewLite extends Applet implements
@Override
public void run()
{
@Override
public void run()
{
- alf.select(sel, csel);
+ alf.select(sel, csel,
+ alf.getAlignViewport().getAlignment().getHiddenColumns());
}
});
}
}
});
}
@@
-486,7
+501,9
@@
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)
*/
- public String getSelectedSequencesAsAlignment(String format, String suffix)
+ @Override
+ public String getSelectedSequencesAsAlignment(String format,
+ String suffix)
{
return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
format, suffix);
{
return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
format, suffix);
@@
-499,26
+516,29
@@
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)
{
try
{
public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, String suffix)
{
try
{
+ FileFormatI theFormat = FileFormats.getInstance().forName(format);
boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
if (alf.viewport.getSelectionGroup() != null)
{
// JBPNote: getSelectionAsNewSequence behaviour has changed - this
// method now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
if (alf.viewport.getSelectionGroup() != null)
{
// JBPNote: getSelectionAsNewSequence behaviour has changed - this
// method now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
- String reply = new AppletFormatAdapter().formatSequences(format,
+ String reply = new AppletFormatAdapter().formatSequences(theFormat,
new Alignment(alf.viewport.getSelectionAsNewSequence()),
seqlimits);
return reply;
}
new Alignment(alf.viewport.getSelectionAsNewSequence()),
seqlimits);
return reply;
}
- } catch (Exception ex)
+ } catch (IllegalArgumentException ex)
{
ex.printStackTrace();
{
ex.printStackTrace();
- return "Error retrieving alignment in " + format + " format. ";
+ return "Error retrieving alignment, possibly invalid format specifier: "
+ + format;
}
return "";
}
}
return "";
}
@@
-528,6
+548,7
@@
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());
@@
-540,6
+561,7
@@
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);
@@
-552,6
+574,7
@@
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();
@@
-569,6
+592,7
@@
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);
@@
-580,6
+604,7
@@
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);
@@
-592,6
+617,7
@@
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)
{
@@
-648,6
+674,7
@@
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);
@@
-660,6
+687,7
@@
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);
@@
-671,6
+699,7
@@
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);
@@
-683,6
+712,7
@@
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)
{
@@
-690,13
+720,15
@@
public class JalviewLite extends Applet implements
{
boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
{
boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
- String reply = new AppletFormatAdapter().formatSequences(format,
+ FileFormatI theFormat = FileFormats.getInstance().forName(format);
+ String reply = new AppletFormatAdapter().formatSequences(theFormat,
alf.viewport.getAlignment(), seqlimits);
return reply;
alf.viewport.getAlignment(), seqlimits);
return reply;
- } catch (Exception ex)
+ } catch (IllegalArgumentException ex)
{
ex.printStackTrace();
{
ex.printStackTrace();
- return "Error retrieving alignment in " + format + " format. ";
+ return "Error retrieving alignment, possibly invalid format specifier: "
+ + format;
}
}
}
}
@@
-705,6
+737,7
@@
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);
@@
-717,17
+750,18
@@
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(),
- annotation, AppletFormatAdapter.PASTE))
+ annotation, DataSourceType.PASTE))
{
alf.alignPanel.fontChanged();
alf.alignPanel.setScrollValues(0, 0);
}
else
{
{
alf.alignPanel.fontChanged();
alf.alignPanel.setScrollValues(0, 0);
}
else
{
- alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
+ alf.parseFeaturesFile(annotation, DataSourceType.PASTE);
}
}
}
}
@@
-736,6
+770,7
@@
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);
@@
-748,10
+783,11
@@
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)
{
- return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE,
+ return alf.parseFeaturesFile(features, DataSourceType.PASTE,
autoenabledisplay);
}
autoenabledisplay);
}
@@
-760,6
+796,7
@@
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);
@@
-772,6
+809,7
@@
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);
@@
-782,6
+820,7
@@
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());
@@
-794,6
+833,7
@@
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);
@@
-804,6
+844,7
@@
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());
@@
-814,6
+855,7
@@
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);
@@
-824,6
+866,7
@@
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);
@@
-835,6
+878,7
@@
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);
@@
-846,21
+890,22
@@
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;
- String format = new IdentifyFile().Identify(text,
- AppletFormatAdapter.PASTE);
try
{
try
{
- al = new AppletFormatAdapter().readFile(text,
- AppletFormatAdapter.PASTE, format);
+ FileFormatI format = new IdentifyFile().identify(text,
+ DataSourceType.PASTE);
+ al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE,
+ format);
if (al.getHeight() > 0)
{
return new AlignFrame(al, this, title, false);
}
if (al.getHeight() > 0)
{
return new AlignFrame(al, this, title, false);
}
- } catch (java.io.IOException ex)
+ } catch (IOException ex)
{
ex.printStackTrace();
}
{
ex.printStackTrace();
}
@@
-872,12
+917,13
@@
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);
}
- private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();
+ private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<>();
/*
* (non-Javadoc)
/*
* (non-Javadoc)
@@
-886,6
+932,7
@@
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)
@@
-893,8
+940,8
@@
public class JalviewLite extends Applet implements
listener = listener.trim();
if (listener.length() == 0)
{
listener = listener.trim();
if (listener.length() == 0)
{
- System.err
- .println("jalview Javascript error: Ignoring empty function for mouseover listener.");
+ System.err.println(
+ "jalview Javascript error: Ignoring empty function for mouseover listener.");
return;
}
}
return;
}
}
@@
-906,8
+953,9
@@
public class JalviewLite extends Applet implements
if (debug)
{
System.err.println("Added a mouseover listener for "
if (debug)
{
System.err.println("Added a mouseover listener for "
- + ((af == null) ? "All frames" : "Just views for "
- + af.getAlignViewport().getSequenceSetId()));
+ + ((af == null) ? "All frames"
+ : "Just views for "
+ + af.getAlignViewport().getSequenceSetId()));
System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
@@
-918,6
+966,7
@@
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);
@@
-930,6
+979,7
@@
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)
@@
-937,8
+987,8
@@
public class JalviewLite extends Applet implements
listener = listener.trim();
if (listener.length() == 0)
{
listener = listener.trim();
if (listener.length() == 0)
{
- System.err
- .println("jalview Javascript error: Ignoring empty function for selection listener.");
+ System.err.println(
+ "jalview Javascript error: Ignoring empty function for selection listener.");
return;
}
}
return;
}
}
@@
-950,8
+1000,9
@@
public class JalviewLite extends Applet implements
if (debug)
{
System.err.println("Added a selection listener for "
if (debug)
{
System.err.println("Added a selection listener for "
- + ((af == null) ? "All frames" : "Just views for "
- + af.getAlignViewport().getSequenceSetId()));
+ + ((af == null) ? "All frames"
+ : "Just views for "
+ + af.getAlignViewport().getSequenceSetId()));
System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
@@
-968,6
+1019,7
@@
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)
@@
-975,8
+1027,8
@@
public class JalviewLite extends Applet implements
listener = listener.trim();
if (listener.length() == 0)
{
listener = listener.trim();
if (listener.length() == 0)
{
- System.err
- .println("jalview Javascript error: Ignoring empty function for selection listener.");
+ System.err.println(
+ "jalview Javascript error: Ignoring empty function for selection listener.");
return;
}
}
return;
}
}
@@
-1001,6
+1053,7
@@
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)
@@
-1016,9
+1069,8
@@
public class JalviewLite extends Applet implements
{
Object lstn = javascriptListeners.elementAt(ms);
JsCallBack lstner = (JsCallBack) lstn;
{
Object lstn = javascriptListeners.elementAt(ms);
JsCallBack lstner = (JsCallBack) lstn;
- if ((af == null || lstner.getAlignFrame() == af)
- && (listener == null || lstner.getListenerFunction().equals(
- listener)))
+ if ((af == null || lstner.getAlignFrame() == af) && (listener == null
+ || lstner.getListenerFunction().equals(listener)))
{
javascriptListeners.removeElement(lstner);
msSize--;
{
javascriptListeners.removeElement(lstner);
msSize--;
@@
-1050,12
+1102,14
@@
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().");
@@
-1112,8
+1166,9
@@
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)
*/
- public void mouseOverStructure(final String pdbResNum,
- final String chain, final String pdbfile)
+ @Override
+ public void mouseOverStructure(final String pdbResNum, final String chain,
+ final String pdbfile)
{
final StructureSelectionManagerProvider me = this;
java.awt.EventQueue.invokeLater(new Runnable()
{
final StructureSelectionManagerProvider me = this;
java.awt.EventQueue.invokeLater(new Runnable()
@@
-1124,13
+1179,13
@@
public class JalviewLite extends Applet implements
try
{
StructureSelectionManager.getStructureSelectionManager(me)
try
{
StructureSelectionManager.getStructureSelectionManager(me)
- .mouseOverStructure(new Integer(pdbResNum).intValue(),
+ .mouseOverStructure(Integer.valueOf(pdbResNum).intValue(),
chain, pdbfile);
if (debug)
{
chain, pdbfile);
if (debug)
{
- System.err.println("mouseOver for '" + pdbResNum
- + "' in chain '" + chain + "' in structure '" + pdbfile
- + "'");
+ System.err
+ .println("mouseOver for '" + pdbResNum + "' in chain '"
+ + chain + "' in structure '" + pdbfile + "'");
}
} catch (NumberFormatException e)
{
}
} catch (NumberFormatException e)
{
@@
-1149,6
+1204,7
@@
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)
{
@@
-1159,8
+1215,8
@@
public class JalviewLite extends Applet implements
{
try
{
{
try
{
- alf.scrollTo(new Integer(topRow).intValue(), new Integer(
- leftHandColumn).intValue());
+ alf.scrollTo(Integer.valueOf(topRow).intValue(),
+ Integer.valueOf(leftHandColumn).intValue());
} catch (Exception ex)
{
} catch (Exception ex)
{
@@
-1191,7
+1247,7
@@
public class JalviewLite extends Applet implements
{
try
{
{
try
{
- alf.scrollToRow(new Integer(topRow).intValue());
+ alf.scrollToRow(Integer.valueOf(topRow).intValue());
} catch (Exception ex)
{
} catch (Exception ex)
{
@@
-1223,12
+1279,12
@@
public class JalviewLite extends Applet implements
{
try
{
{
try
{
- alf.scrollToColumn(new Integer(leftHandColumn).intValue());
+ alf.scrollToColumn(Integer.valueOf(leftHandColumn).intValue());
} catch (Exception ex)
{
} catch (Exception ex)
{
- System.err
- .println("Couldn't parse integer arguments (leftHandColumn='"
+ System.err.println(
+ "Couldn't parse integer arguments (leftHandColumn='"
+ leftHandColumn + "')");
ex.printStackTrace();
}
+ leftHandColumn + "')");
ex.printStackTrace();
}
@@
-1280,7
+1336,7
@@
public class JalviewLite extends Applet implements
private boolean alignPdbStructures = false;
/**
private boolean alignPdbStructures = false;
/**
- * use an external structure viewer exclusively (no jmols or MCViews will be
+ * use an external structure viewer exclusively (no jmols or mc_views will be
* opened by JalviewLite itself)
*/
public boolean useXtrnalSviewer = false;
* opened by JalviewLite itself)
*/
public boolean useXtrnalSviewer = false;
@@
-1302,8
+1358,8
@@
public class JalviewLite extends Applet implements
{
try
{
{
try
{
- BufferedReader reader = new BufferedReader(new InputStreamReader(
- url.openStream()));
+ BufferedReader reader = new BufferedReader(
+ new InputStreamReader(url.openStream()));
String line;
while ((line = reader.readLine()) != null)
{
String line;
while ((line = reader.readLine()) != null)
{
@@
-1370,8
+1426,8
@@
public class JalviewLite extends Applet implements
} catch (Exception ex)
{
} catch (Exception ex)
{
- System.err
- .println("Warning: No JalviewLite javascript callbacks available.");
+ System.err.println(
+ "Warning: No JalviewLite javascript callbacks available.");
if (debug)
{
ex.printStackTrace();
if (debug)
{
ex.printStackTrace();
@@
-1387,7
+1443,8
@@
public class JalviewLite extends Applet implements
String externalsviewer = getParameter("externalstructureviewer");
if (externalsviewer != null)
{
String externalsviewer = getParameter("externalstructureviewer");
if (externalsviewer != null)
{
- useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE);
+ useXtrnalSviewer = externalsviewer.trim().toLowerCase(Locale.ROOT)
+ .equals(TRUE);
}
/**
* if true disable the check for jmol
}
/**
* if true disable the check for jmol
@@
-1413,9
+1470,8
@@
public class JalviewLite extends Applet implements
}
else
{
}
else
{
- throw new Error(
- MessageManager
- .getString("error.invalid_separator_parameter"));
+ throw new Error(MessageManager
+ .getString("error.invalid_separator_parameter"));
}
}
int r = 255;
}
}
int r = 255;
@@
-1488,6
+1544,7
@@
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,
@@
-1571,8
+1628,8
@@
public class JalviewLite extends Applet implements
{
// do onInit with the JS executor thread
new JSFunctionExec(this).executeJavascriptFunction(true,
{
// do onInit with the JS executor thread
new JSFunctionExec(this).executeJavascriptFunction(true,
- initjscallback, null, "Calling oninit callback '"
- + initjscallback + "'.");
+ initjscallback, null,
+ "Calling oninit callback '" + initjscallback + "'.");
} catch (Exception e)
{
System.err.println("Exception when executing _oninit callback '"
} catch (Exception e)
{
System.err.println("Exception when executing _oninit callback '"
@@
-1610,6
+1667,7
@@
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)
@@
-1634,6
+1692,7
@@
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)
@@
-1671,6
+1730,7
@@
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)
@@
-1680,8
+1740,8
@@
public class JalviewLite extends Applet implements
g.fillRect(0, 0, getSize().width, getSize().height);
g.setColor(Color.red);
g.drawString(
g.fillRect(0, 0, getSize().width, getSize().height);
g.setColor(Color.red);
g.drawString(
- MessageManager.getString("label.jalview_cannot_open_file"),
- 5, 15);
+ MessageManager.getString("label.jalview_cannot_open_file"), 5,
+ 15);
g.drawString("\"" + file + "\"", 5, 30);
}
else if (embedded)
g.drawString("\"" + file + "\"", 5, 30);
}
else if (embedded)
@@
-1722,6
+1782,7
@@
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)
@@
-1740,8
+1801,8
@@
public class JalviewLite extends Applet implements
}
if (!jmolAvailable)
{
}
if (!jmolAvailable)
{
- System.out
- .println("Jmol not available - Using MCview for structures");
+ System.out.println(
+ "Jmol not available - Using mc_view for structures");
}
} catch (java.lang.ClassNotFoundException ex)
{
}
} catch (java.lang.ClassNotFoundException ex)
{
@@
-1752,8
+1813,8
@@
public class JalviewLite extends Applet implements
jmolAvailable = false;
if (debug)
{
jmolAvailable = false;
if (debug)
{
- System.err
- .println("Skipping Jmol check. Will use MCView (probably)");
+ System.err.println(
+ "Skipping Jmol check. Will use mc_view (probably)");
}
}
checkedForJmol = true;
}
}
checkedForJmol = true;
@@
-1771,7
+1832,7
@@
public class JalviewLite extends Applet implements
/**
* State variable: protocol for access to file source
*/
/**
* State variable: protocol for access to file source
*/
- String protocol;
+ DataSourceType protocol;
String _file; // alignment file or URL spec
String _file; // alignment file or URL spec
@@
-1801,7
+1862,7
@@
public class JalviewLite extends Applet implements
*/
if (path.startsWith("PASTE"))
{
*/
if (path.startsWith("PASTE"))
{
- protocol = AppletFormatAdapter.PASTE;
+ protocol = DataSourceType.PASTE;
return path.substring(5);
}
return path.substring(5);
}
@@
-1810,7
+1871,7
@@
public class JalviewLite extends Applet implements
*/
if (path.indexOf("://") != -1)
{
*/
if (path.indexOf("://") != -1)
{
- protocol = AppletFormatAdapter.URL;
+ protocol = DataSourceType.URL;
return path;
}
return path;
}
@@
-1826,7
+1887,7
@@
public class JalviewLite extends Applet implements
System.err.println("Prepended document base '" + documentBase
+ "' to make: '" + withDocBase + "'");
}
System.err.println("Prepended document base '" + documentBase
+ "' to make: '" + withDocBase + "'");
}
- protocol = AppletFormatAdapter.URL;
+ protocol = DataSourceType.URL;
return withDocBase;
}
return withDocBase;
}
@@
-1839,7
+1900,7
@@
public class JalviewLite extends Applet implements
if (!withCodeBase.equals(withDocBase)
&& HttpUtils.isValidUrl(withCodeBase))
{
if (!withCodeBase.equals(withDocBase)
&& HttpUtils.isValidUrl(withCodeBase))
{
- protocol = AppletFormatAdapter.URL;
+ protocol = DataSourceType.URL;
if (debug)
{
System.err.println("Prepended codebase '" + codeBase
if (debug)
{
System.err.println("Prepended codebase '" + codeBase
@@
-1854,7
+1915,7
@@
public class JalviewLite extends Applet implements
*/
if (inArchive(path))
{
*/
if (inArchive(path))
{
- protocol = AppletFormatAdapter.CLASSLOADER;
+ protocol = DataSourceType.CLASSLOADER;
}
return path;
}
}
return path;
}
@@
-1866,6
+1927,7
@@
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();
@@
-1890,7
+1952,8
@@
public class JalviewLite extends Applet implements
*/
private void startLoading()
{
*/
private void startLoading()
{
- dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
+ dbgMsg("Loading thread started with:\n>>file\n" + _file
+ + ">>endfile");
dbgMsg("Loading started.");
dbgMsg("Loading started.");
@@
-1967,11
+2030,12
@@
public class JalviewLite extends Applet implements
return null;
}
String resolvedFile = resolveFileProtocol(fileParam);
return null;
}
String resolvedFile = resolveFileProtocol(fileParam);
- String format = new IdentifyFile().Identify(resolvedFile, protocol);
- dbgMsg("File identified as '" + format + "'");
AlignmentI al = null;
try
{
AlignmentI al = null;
try
{
+ FileFormatI format = new IdentifyFile().identify(resolvedFile,
+ protocol);
+ dbgMsg("File identified as '" + format + "'");
al = new AppletFormatAdapter().readFile(resolvedFile, protocol,
format);
if ((al != null) && (al.getHeight() > 0))
al = new AppletFormatAdapter().readFile(resolvedFile, protocol,
format);
if ((al != null) && (al.getHeight() > 0))
@@
-1988,16
+2052,16
@@
public class JalviewLite extends Applet implements
// update the focus.
currentAlignFrame = newAlignFrame;
// update the focus.
currentAlignFrame = newAlignFrame;
- if (protocol == AppletFormatAdapter.PASTE)
+ if (protocol == DataSourceType.PASTE)
{
{
- newAlignFrame.setTitle(MessageManager.formatMessage(
- "label.sequences_from", new Object[] { applet
- .getDocumentBase().toString() }));
+ newAlignFrame.setTitle(MessageManager
+ .formatMessage("label.sequences_from", new Object[]
+ { applet.getDocumentBase().toString() }));
}
newAlignFrame.statusBar.setText(MessageManager.formatMessage(
}
newAlignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file",
- new Object[] { resolvedFile }));
+ "label.successfully_loaded_file", new Object[]
+ { resolvedFile }));
return newAlignFrame;
}
return newAlignFrame;
}
@@
-2020,8
+2084,8
@@
public class JalviewLite extends Applet implements
dbgMsg(">>>Dump finished.");
} catch (Exception e)
{
dbgMsg(">>>Dump finished.");
} catch (Exception e)
{
- System.err
- .println("Exception when trying to dump the content of the file parameter.");
+ System.err.println(
+ "Exception when trying to dump the content of the file parameter.");
e.printStackTrace();
}
}
e.printStackTrace();
}
}
@@
-2044,8
+2108,8
@@
public class JalviewLite extends Applet implements
* related to JAL-434
*/
* related to JAL-434
*/
- applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
- false));
+ applet.setAlignPdbStructures(
+ getDefaultParameter("alignpdbfiles", false));
/*
* <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
* PDB|1GAQ|1GAQ|C">
/*
* <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
* PDB|1GAQ|1GAQ|C">
@@
-2061,9
+2125,11
@@
public class JalviewLite extends Applet implements
Vector pdbs = new Vector();
// create a lazy matcher if we're asked to
jalview.analysis.SequenceIdMatcher matcher = (applet
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(
- alignFrame.getAlignViewport().getAlignment()
- .getSequencesArray()) : null;
+ .getDefaultParameter("relaxedidmatch", false))
+ ? new jalview.analysis.SequenceIdMatcher(
+ alignFrame.getAlignViewport().getAlignment()
+ .getSequencesArray())
+ : null;
String param;
do
String param;
do
@@
-2092,8
+2158,9
@@
public class JalviewLite extends Applet implements
String sequence = applet.getParameter("PDBSEQ");
if (sequence != null)
{
String sequence = applet.getParameter("PDBSEQ");
if (sequence != null)
{
- seqs = new SequenceI[] { matcher == null ? (Sequence) alignFrame
- .getAlignViewport().getAlignment().findName(sequence)
+ seqs = new SequenceI[] { matcher == null
+ ? (Sequence) alignFrame.getAlignViewport()
+ .getAlignment().findName(sequence)
: matcher.findIdMatch(sequence) };
}
: matcher.findIdMatch(sequence) };
}
@@
-2101,8
+2168,8
@@
public class JalviewLite extends Applet implements
else
{
param = st.nextToken();
else
{
param = st.nextToken();
- List<SequenceI> tmp = new ArrayList<SequenceI>();
- List<String> tmp2 = new ArrayList<String>();
+ List<SequenceI> tmp = new ArrayList<>();
+ List<String> tmp2 = new ArrayList<>();
while (st.hasMoreTokens())
{
while (st.hasMoreTokens())
{
@@
-2114,9
+2181,10
@@
public class JalviewLite extends Applet implements
tmp2.add(st2.nextToken());
seqstring = st2.nextToken();
}
tmp2.add(st2.nextToken());
seqstring = st2.nextToken();
}
- tmp.add(matcher == null ? (Sequence) alignFrame
- .getAlignViewport().getAlignment()
- .findName(seqstring) : matcher.findIdMatch(seqstring));
+ tmp.add(matcher == null
+ ? (Sequence) alignFrame.getAlignViewport()
+ .getAlignment().findName(seqstring)
+ : matcher.findIdMatch(seqstring));
}
seqs = tmp.toArray(new SequenceI[tmp.size()]);
}
seqs = tmp.toArray(new SequenceI[tmp.size()]);
@@
-2136,8
+2204,9
@@
public class JalviewLite extends Applet implements
if (seqs[i] != null)
{
((Sequence) seqs[i]).addPDBId(pdb);
if (seqs[i] != null)
{
((Sequence) seqs[i]).addPDBId(pdb);
- StructureSelectionManager.getStructureSelectionManager(
- applet).registerPDBEntry(pdb);
+ StructureSelectionManager
+ .getStructureSelectionManager(applet)
+ .registerPDBEntry(pdb);
}
else
{
}
else
{
@@
-2145,8
+2214,8
@@
public class JalviewLite extends Applet implements
{
// this may not really be a problem but we give a warning
// anyway
{
// this may not really be a problem but we give a warning
// anyway
- System.err
- .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
+ System.err.println(
+ "Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
+ i + ")");
}
}
+ i + ")");
}
}
@@
-2159,8
+2228,7
@@
public class JalviewLite extends Applet implements
}
else
{
}
else
{
- pdbs.addElement(new Object[] { pdb, seqs, chains,
- new String(protocol) });
+ pdbs.addElement(new Object[] { pdb, seqs, chains, protocol });
}
}
}
}
}
}
@@
-2173,7
+2241,8
@@
public class JalviewLite extends Applet implements
PDBEntry[] pdb = new PDBEntry[pdbs.size()];
String[][] chains = new String[pdbs.size()][];
String[] protocols = new String[pdbs.size()];
PDBEntry[] pdb = new PDBEntry[pdbs.size()];
String[][] chains = new String[pdbs.size()][];
String[] protocols = new String[pdbs.size()];
- for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
+ for (int pdbsi = 0, pdbsiSize = pdbs
+ .size(); pdbsi < pdbsiSize; pdbsi++)
{
Object[] o = (Object[]) pdbs.elementAt(pdbsi);
pdb[pdbsi] = (PDBEntry) o[0];
{
Object[] o = (Object[]) pdbs.elementAt(pdbsi);
pdb[pdbsi] = (PDBEntry) o[0];
@@
-2199,6
+2268,11
@@
public class JalviewLite extends Applet implements
{
boolean result = false;
String param = applet.getParameter("jnetfile");
{
boolean result = false;
String param = applet.getParameter("jnetfile");
+ if (param == null)
+ {
+ // jnet became jpred around 2016
+ param = applet.getParameter("jpredfile");
+ }
if (param != null)
{
try
if (param != null)
{
try
@@
-2208,12
+2282,9
@@
public class JalviewLite extends Applet implements
JnetAnnotationMaker.add_annotation(predictions,
alignFrame.viewport.getAlignment(), 0, false);
// false == do not add sequence profile from concise output
JnetAnnotationMaker.add_annotation(predictions,
alignFrame.viewport.getAlignment(), 0, false);
// false == do not add sequence profile from concise output
- SequenceI repseq = alignFrame.viewport.getAlignment()
- .getSequenceAt(0);
- alignFrame.viewport.getAlignment().setSeqrep(repseq);
- ColumnSelection cs = new ColumnSelection();
- cs.hideInsertionsFor(repseq);
- alignFrame.viewport.setColumnSelection(cs);
+
+ alignFrame.viewport.getAlignment().setupJPredAlignment();
+
alignFrame.alignPanel.fontChanged();
alignFrame.alignPanel.setScrollValues(0, 0);
result = true;
alignFrame.alignPanel.fontChanged();
alignFrame.alignPanel.setScrollValues(0, 0);
result = true;
@@
-2249,8
+2320,8
@@
public class JalviewLite extends Applet implements
}
else
{
}
else
{
- System.err
- .println("Annotations were not added from annotation file '"
+ System.err.println(
+ "Annotations were not added from annotation file '"
+ param + "'");
}
}
+ param + "'");
}
}
@@
-2321,14
+2392,14
@@
public class JalviewLite extends Applet implements
{
if (debug)
{
{
if (debug)
{
- System.err
- .println("Attempting to load T-COFFEE score file from the scoreFile parameter");
+ System.err.println(
+ "Attempting to load T-COFFEE score file from the scoreFile parameter");
}
result = alignFrame.loadScoreFile(sScoreFile);
if (!result)
{
}
result = alignFrame.loadScoreFile(sScoreFile);
if (!result)
{
- System.err
- .println("Failed to parse T-COFFEE parameter as a valid score file ('"
+ System.err.println(
+ "Failed to parse T-COFFEE parameter as a valid score file ('"
+ sScoreFile + "')");
}
} catch (Exception e)
+ sScoreFile + "')");
}
} catch (Exception e)
@@
-2404,8
+2475,7
@@
public class JalviewLite extends Applet implements
return rtn;
} catch (Exception ex)
{
return rtn;
} catch (Exception ex)
{
- System.out.println("Exception checking resources: " + f + " "
- + ex);
+ System.out.println("Exception checking resources: " + f + " " + ex);
return false;
}
}
return false;
}
}
@@
-2426,8
+2496,8
@@
public class JalviewLite extends Applet implements
{
return initialAlignFrame;
}
{
return initialAlignFrame;
}
- System.err
- .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
+ System.err.println(
+ "Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
return null;
}
return null;
}
@@
-2505,8
+2575,8
@@
public class JalviewLite extends Applet implements
}
if (debug)
{
}
if (debug)
{
- System.err.println("Empty Array from '" + separator
- + "' separated List");
+ System.err.println(
+ "Empty Array from '" + separator + "' separated List");
}
return null;
}
}
return null;
}
@@
-2548,16
+2618,16
@@
public class JalviewLite extends Applet implements
}
if (debug)
{
}
if (debug)
{
- System.err.println("Returning '" + separator
- + "' separated List:\n");
+ System.err
+ .println("Returning '" + separator + "' separated List:\n");
System.err.println(v);
}
return v.toString();
}
if (debug)
{
System.err.println(v);
}
return v.toString();
}
if (debug)
{
- System.err.println("Returning empty '" + separator
- + "' separated List\n");
+ System.err.println(
+ "Returning empty '" + separator + "' separated List\n");
}
return "" + separator;
}
}
return "" + separator;
}
@@
-2567,10
+2637,11
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
*/
*
* @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
*/
+ @Override
public String getFeatureGroups()
{
public String getFeatureGroups()
{
- String lst = arrayToSeparatorList(getDefaultTargetFrame()
- .getFeatureGroups());
+ String lst = arrayToSeparatorList(
+ getDefaultTargetFrame().getFeatureGroups());
return lst;
}
return lst;
}
@@
-2581,6
+2652,7
@@
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());
@@
-2592,10
+2664,11
@@
public class JalviewLite extends Applet implements
*
* @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
*/
*
* @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
*/
+ @Override
public String getFeatureGroupsOfState(boolean visible)
{
public String getFeatureGroupsOfState(boolean visible)
{
- return arrayToSeparatorList(getDefaultTargetFrame()
- .getFeatureGroupsOfState(visible));
+ return arrayToSeparatorList(
+ getDefaultTargetFrame().getFeatureGroupsOfState(visible));
}
/*
}
/*
@@
-2605,6
+2678,7
@@
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));
@@
-2616,11
+2690,12
@@
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)
{
final boolean st = state;// !(state==null || state.equals("") ||
public void setFeatureGroupStateOn(final AlignFrame alf,
final String groups, boolean state)
{
final boolean st = state;// !(state==null || state.equals("") ||
- // state.toLowerCase().equals("false"));
+ // state.toLowerCase(Locale.ROOT).equals("false"));
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
@@
-2637,6
+2712,7
@@
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);
@@
-2647,6
+2723,7
@@
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;
@@
-2657,6
+2734,7
@@
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)
@@
-2701,6
+2779,7
@@
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)
{
@@
-2717,14
+2796,15
@@
public class JalviewLite extends Applet implements
return alignPdbStructures;
}
return alignPdbStructures;
}
+ @Override
public void start()
{
// callInitCallback();
}
public void start()
{
// callInitCallback();
}
- private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();
+ private Hashtable<String, long[]> jshashes = new Hashtable<>();
- private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();
+ private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<>();
public void setJsMessageSet(String messageclass, String viewId,
String[] colcommands)
public void setJsMessageSet(String messageclass, String viewId,
String[] colcommands)
@@
-2732,7
+2812,7
@@
public class JalviewLite extends Applet implements
Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
if (msgset == null)
{
Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
if (msgset == null)
{
- msgset = new Hashtable<String, String[]>();
+ msgset = new Hashtable<>();
jsmessages.put(messageclass, msgset);
}
msgset.put(viewId, colcommands);
jsmessages.put(messageclass, msgset);
}
msgset.put(viewId, colcommands);
@@
-2750,6
+2830,7
@@
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);
@@
-2817,22
+2898,13
@@
public class JalviewLite extends Applet implements
{
return defcolour;
}
{
return defcolour;
}
- Color col = jalview.schemes.ColourSchemeProperty
- .getAWTColorFromName(colprop);
+ Color col = ColorUtils.parseColourString(colprop);
if (col == null)
{
if (col == null)
{
- try
- {
- col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
- } catch (Exception ex)
- {
- System.err.println("Couldn't parse '" + colprop
- + "' as a colour for " + colparam);
- col = null;
- }
+ System.err.println("Couldn't parse '" + colprop + "' as a colour for "
+ + colparam);
}
return (col == null) ? defcolour : col;
}
return (col == null) ? defcolour : col;
-
}
public void openJalviewHelpUrl()
}
public void openJalviewHelpUrl()
@@
-2860,6
+2932,14
@@
public class JalviewLite extends Applet implements
URL localref)
{
String resolvedPath = "";
URL localref)
{
String resolvedPath = "";
+ if (targetPath.startsWith("/"))
+ {
+ String codebase = localref.toString();
+ String localfile = localref.getFile();
+ resolvedPath = codebase.substring(0,
+ codebase.length() - localfile.length()) + targetPath;
+ return resolvedPath;
+ }
/*
* get URL path and strip off any trailing file e.g.
/*
* get URL path and strip off any trailing file e.g.
@@
-2891,8
+2971,8
@@
public class JalviewLite extends Applet implements
}
if (debug)
{
}
if (debug)
{
- System.err.println("resolveUrlForLocalOrAbsolute returning "
- + resolvedPath);
+ System.err.println(
+ "resolveUrlForLocalOrAbsolute returning " + resolvedPath);
}
return resolvedPath;
}
}
return resolvedPath;
}
@@
-2914,17
+2994,15
@@
public class JalviewLite extends Applet implements
// form valid URL
// Should really use docbase, not codebase.
URL prepend;
// form valid URL
// Should really use docbase, not codebase.
URL prepend;
- url = resolveUrlForLocalOrAbsolute(
- url,
- prepend = getDefaultParameter("resolvetocodebase", false) ? getCodeBase()
+ url = resolveUrlForLocalOrAbsolute(url,
+ prepend = getDefaultParameter("resolvetocodebase", false)
+ ? getCodeBase()
: getDocumentBase());
if (debug)
{
: getDocumentBase());
if (debug)
{
- System.err
- .println("Show url (prepended "
- + prepend
- + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
- + url);
+ System.err.println("Show url (prepended " + prepend
+ + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
+ + url);
}
}
else
}
}
else