/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * 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.
*
package jalview.bin;
import jalview.analysis.AlignmentUtils;
+import jalview.api.AlignFrameI;
+import jalview.api.AlignViewportI;
+import jalview.api.JalviewApp;
import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
import jalview.appletgui.AlignViewport;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
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.JnetAnnotationMaker;
import jalview.io.NewickFile;
import jalview.javascript.JSFunctionExec;
import jalview.javascript.JalviewLiteJsApi;
import jalview.javascript.JsCallBack;
import jalview.javascript.MouseOverStructureListener;
+import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
-import jalview.util.HttpUtils;
+import jalview.structure.VamsasSource;
+import jalview.util.ColorUtils;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.applet.Applet;
import java.awt.Button;
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.util.Hashtable;
import java.util.List;
-import java.util.StringTokenizer;
import java.util.Vector;
import netscape.javascript.JSObject;
* @author $author$
* @version $Revision: 1.92 $
*/
-public class JalviewLite extends Applet implements
- StructureSelectionManagerProvider, JalviewLiteJsApi
+@SuppressWarnings("serial")
+public class JalviewLite extends Applet
+ implements StructureSelectionManagerProvider, JalviewLiteJsApi,
+ JalviewApp
{
+ public JalviewLite()
+ {
+ appLoader = new JalviewAppLoader(debug);
+ }
private static final String TRUE = "true";
private static final String FALSE = "false";
return StructureSelectionManager.getStructureSelectionManager(this);
}
+ @Override
+ public StructureSelectionManagerProvider getStructureSelectionManagerProvider()
+ {
+ return this;
+ }
+
// /////////////////////////////////////////
// The following public methods may be called
// externally, eg via javascript in HTML page
*
* @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
*/
+ @Override
public String getSelectedSequences()
{
return getSelectedSequencesFrom(getDefaultTargetFrame());
*
* @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
*/
+ @Override
public String getSelectedSequences(String sep)
{
return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
* .AlignFrame)
*/
- public String getSelectedSequencesFrom(AlignFrame alf)
+ @Override
+ public String getSelectedSequencesFrom(AlignFrameI alf)
{
return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
}
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
* .AlignFrame, java.lang.String)
*/
- public String getSelectedSequencesFrom(AlignFrame alf, String sep)
+ @Override
+ public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
{
StringBuffer result = new StringBuffer("");
if (sep == null || sep.length() == 0)
{
sep = separator; // "+0x00AC;
}
- if (alf.viewport.getSelectionGroup() != null)
+ if (((AlignFrame) alf).viewport.getSelectionGroup() != null)
{
- SequenceI[] seqs = alf.viewport.getSelectionGroup()
- .getSequencesInOrder(alf.viewport.getAlignment());
+ SequenceI[] seqs = ((AlignFrame) alf).viewport.getSelectionGroup()
+ .getSequencesInOrder(
+ ((AlignFrame) alf).viewport.getAlignment());
for (int i = 0; i < seqs.length; i++)
{
* @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
* java.lang.String, java.lang.String)
*/
+ @Override
public void highlight(String sequenceId, String position,
String alignedPosition)
{
* @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String, java.lang.String)
*/
- public void highlightIn(final AlignFrame alf, final String sequenceId,
+ @Override
+ public void highlightIn(final AlignFrameI alf, final String sequenceId,
final String position, final String alignedPosition)
{
// TODO: could try to highlight in all alignments if alf==null
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
- alf.viewport.getAlignment().getSequencesArray());
+ ((AlignFrame) alf).viewport.getAlignment().getSequencesArray());
final SequenceI sq = matcher.findIdMatch(sequenceId);
if (sq != null)
{
final StructureSelectionManagerProvider me = this;
final int pos = apos;
// use vamsas listener to broadcast to all listeners in scope
- if (alignedPosition != null
- && (alignedPosition.trim().length() == 0 || alignedPosition
- .toLowerCase().indexOf("false") > -1))
+ if (alignedPosition != null && (alignedPosition.trim().length() == 0
+ || alignedPosition.toLowerCase().indexOf("false") > -1))
{
java.awt.EventQueue.invokeLater(new Runnable()
{
* @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
* java.lang.String)
*/
+ @Override
public void select(String sequenceIds, String columns)
{
selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
* @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);
* @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String)
*/
- public void selectIn(AlignFrame alf, String sequenceIds, String columns)
+ @Override
+ public void selectIn(AlignFrameI alf, String sequenceIds, String columns)
{
selectIn(alf, sequenceIds, columns, separator);
}
* @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String, java.lang.String)
*/
- public void selectIn(final AlignFrame alf, String sequenceIds,
+ @Override
+ public void selectIn(final AlignFrameI alf, String sequenceIds,
String columns, String sep)
{
if (sep == null || sep.length() == 0)
}
}
// deparse fields
- String[] ids = separatorListToArray(sequenceIds, sep);
- String[] cols = separatorListToArray(columns, sep);
+ String[] ids = JalviewAppLoader.separatorListToArray(sequenceIds, sep);
+ String[] cols = JalviewAppLoader.separatorListToArray(columns, sep);
final SequenceGroup sel = new SequenceGroup();
final ColumnSelection csel = new ColumnSelection();
- AlignmentI al = alf.viewport.getAlignment();
+ AlignmentI al = ((AlignFrame) alf).viewport.getAlignment();
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
- alf.viewport.getAlignment().getSequencesArray());
+ ((AlignFrame) alf).viewport.getAlignment().getSequencesArray());
int start = 0, end = al.getWidth(), alw = al.getWidth();
boolean seqsfound = true;
if (ids != null && ids.length > 0)
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;
}
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;
}
}
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;
}
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);
@Override
public void run()
{
- alf.select(sel, csel);
+ ((AlignFrame) alf).select(sel, csel, ((AlignFrame) alf)
+ .getAlignViewport().getAlignment().getHiddenColumns());
}
});
}
* 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);
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview
* .appletgui.AlignFrame, java.lang.String, java.lang.String)
*/
- public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
+ @Override
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
String format, String suffix)
{
try
{
+ FileFormatI theFormat = FileFormats.getInstance().forName(format);
boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
- if (alf.viewport.getSelectionGroup() != null)
+ if (((AlignFrame) 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,
- new Alignment(alf.viewport.getSelectionAsNewSequence()),
+ String reply = new AppletFormatAdapter().formatSequences(theFormat,
+ new Alignment(((AlignFrame) alf).viewport
+ .getSelectionAsNewSequence()),
seqlimits);
return reply;
}
- } catch (Exception ex)
+ } catch (IllegalArgumentException ex)
{
ex.printStackTrace();
- return "Error retrieving alignment in " + format + " format. ";
+ return "Error retrieving alignment, possibly invalid format specifier: "
+ + format;
}
return "";
}
*
* @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
*/
+ @Override
public String getAlignmentOrder()
{
return getAlignmentOrderFrom(getDefaultTargetFrame());
* jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
* )
*/
- public String getAlignmentOrderFrom(AlignFrame alf)
+ @Override
+ public String getAlignmentOrderFrom(AlignFrameI alf)
{
return getAlignmentOrderFrom(alf, separator);
}
* jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
- public String getAlignmentOrderFrom(AlignFrame alf, String sep)
+ @Override
+ public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
{
- AlignmentI alorder = alf.getAlignViewport().getAlignment();
+ AlignmentI alorder = ((AlignFrame) alf).getAlignViewport()
+ .getAlignment();
String[] order = new String[alorder.getHeight()];
for (int i = 0; i < order.length; i++)
{
* @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
* java.lang.String)
*/
+ @Override
public String orderBy(String order, String undoName)
{
return orderBy(order, undoName, separator);
* @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);
* jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String, java.lang.String)
*/
- public String orderAlignmentBy(AlignFrame alf, String order,
+ @Override
+ public String orderAlignmentBy(AlignFrameI alf, String order,
String undoName, String sep)
{
- String[] ids = separatorListToArray(order, sep);
+ String[] ids = JalviewAppLoader.separatorListToArray(order, sep);
SequenceI[] sqs = null;
if (ids != null && ids.length > 0)
{
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
- alf.viewport.getAlignment().getSequencesArray());
+ ((AlignFrame) alf).viewport.getAlignment()
+ .getSequencesArray());
int s = 0;
sqs = new SequenceI[ids.length];
for (int i = 0; i < ids.length; i++)
final String _undoName = undoName;
// TODO: deal with synchronization here: cannot raise any events until after
// this has returned.
- return alf.sortBy(aorder, _undoName) ? TRUE : "";
+ return ((AlignFrame) alf).sortBy(aorder, _undoName) ? TRUE : "";
}
/*
*
* @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)
*/
+ @Override
public String getAlignment(String format)
{
return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE);
* jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
* java.lang.String)
*/
- public String getAlignmentFrom(AlignFrame alf, String format)
+ @Override
+ public String getAlignmentFrom(AlignFrameI alf, String format)
{
return getAlignmentFrom(alf, format, TRUE);
}
* @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
* java.lang.String)
*/
+ @Override
public String getAlignment(String format, String suffix)
{
return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
* jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String)
*/
- public String getAlignmentFrom(AlignFrame alf, String format,
+ @Override
+ public String getAlignmentFrom(AlignFrameI alf, String format,
String suffix)
{
try
{
boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
- String reply = new AppletFormatAdapter().formatSequences(format,
- alf.viewport.getAlignment(), seqlimits);
+ FileFormatI theFormat = FileFormats.getInstance().forName(format);
+ String reply = new AppletFormatAdapter().formatSequences(theFormat,
+ ((AlignFrame) alf).viewport.getAlignment(), seqlimits);
return reply;
- } catch (Exception ex)
+ } catch (IllegalArgumentException ex)
{
ex.printStackTrace();
- return "Error retrieving alignment in " + format + " format. ";
+ return "Error retrieving alignment, possibly invalid format specifier: "
+ + format;
}
}
*
* @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
*/
+ @Override
public void loadAnnotation(String annotation)
{
loadAnnotationFrom(getDefaultTargetFrame(), annotation);
* jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
- public void loadAnnotationFrom(AlignFrame alf, String annotation)
+ @Override
+ public void loadAnnotationFrom(AlignFrameI alf, String annotation)
{
- if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
- annotation, AppletFormatAdapter.PASTE))
+ if (new AnnotationFile().annotateAlignmentView(
+ ((AlignFrame) alf).getAlignViewport(),
+ annotation, DataSourceType.PASTE))
{
- alf.alignPanel.fontChanged();
- alf.alignPanel.setScrollValues(0, 0);
+ ((AlignFrame) alf).alignPanel.fontChanged();
+ ((AlignFrame) alf).alignPanel.setScrollValues(0, 0);
}
else
{
- alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
+ ((AlignFrame) alf).parseFeaturesFile(annotation,
+ DataSourceType.PASTE);
}
}
*
* @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
*/
+ @Override
public void loadFeatures(String features, boolean autoenabledisplay)
{
loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
* jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
- public boolean loadFeaturesFrom(AlignFrame alf, String features,
+ @Override
+ public boolean loadFeaturesFrom(AlignFrameI alf, String features,
boolean autoenabledisplay)
{
- return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE,
+ return ((AlignFrame) alf).parseFeaturesFile(features,
+ DataSourceType.PASTE,
autoenabledisplay);
}
*
* @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
*/
+ @Override
public String getFeatures(String format)
{
return getFeaturesFrom(getDefaultTargetFrame(), format);
* jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
* java.lang.String)
*/
- public String getFeaturesFrom(AlignFrame alf, String format)
+ @Override
+ public String getFeaturesFrom(AlignFrameI alf, String format)
{
- return alf.outputFeatures(false, format);
+ return ((AlignFrame) alf).outputFeatures(false, format);
}
/*
*
* @see jalview.bin.JalviewLiteJsApi#getAnnotation()
*/
+ @Override
public String getAnnotation()
{
return getAnnotationFrom(getDefaultTargetFrame());
* jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
* )
*/
- public String getAnnotationFrom(AlignFrame alf)
+ @Override
+ public String getAnnotationFrom(AlignFrameI alf)
{
- return alf.outputAnnotations(false);
+ return ((AlignFrame) alf).outputAnnotations(false);
}
/*
*
* @see jalview.bin.JalviewLiteJsApi#newView()
*/
+ @Override
public AlignFrame newView()
{
return newViewFrom(getDefaultTargetFrame());
*
* @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
*/
+ @Override
public AlignFrame newView(String name)
{
return newViewFrom(getDefaultTargetFrame(), name);
*
* @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
*/
- public AlignFrame newViewFrom(AlignFrame alf)
+ @Override
+ public AlignFrame newViewFrom(AlignFrameI alf)
{
- return alf.newView(null);
+ return ((AlignFrame) alf).newView(null);
}
/*
* @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
* java.lang.String)
*/
- public AlignFrame newViewFrom(AlignFrame alf, String name)
+ @Override
+ public AlignFrame newViewFrom(AlignFrameI alf, String name)
{
- return alf.newView(name);
+ return ((AlignFrame) alf).newView(name);
}
/*
* @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
* java.lang.String)
*/
+ @Override
public AlignFrame loadAlignment(String text, String title)
{
AlignmentI al = null;
- String format = new IdentifyFile().Identify(text,
- AppletFormatAdapter.PASTE);
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);
}
- } catch (java.io.IOException ex)
+ } catch (IOException ex)
{
ex.printStackTrace();
}
*
* @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
*/
+ @Override
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)
* jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
- public void setMouseoverListener(AlignFrame af, String listener)
+ @Override
+ public void setMouseoverListener(AlignFrameI af, String listener)
{
if (listener != null)
{
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;
}
}
jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
- this, af, listener);
+ this, (AlignFrame) af, listener, debug);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
.addStructureViewerListener(mol);
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 "
+ + ((AlignFrame) af).getAlignViewport()
+ .getSequenceSetId()));
System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
*
* @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)
*/
+ @Override
public void setSelectionListener(String listener)
{
setSelectionListener(null, listener);
* jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
- public void setSelectionListener(AlignFrame af, String listener)
+ @Override
+ public void setSelectionListener(AlignFrameI af, String listener)
{
if (listener != null)
{
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;
}
}
jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
- this, af, listener);
+ this, (AlignFrame) af, listener, debug);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
.addSelectionListener(mol);
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 "
+ + ((AlignFrame) af).getAlignViewport()
+ .getSequenceSetId()));
System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
* @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
* java.lang.String)
*/
+ @Override
public void setStructureListener(String listener, String modelSet)
{
if (listener != null)
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;
}
}
MouseOverStructureListener mol = new MouseOverStructureListener(this,
- listener, separatorListToArray(modelSet));
+ listener, separatorListToArray(modelSet), debug);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
.addStructureViewerListener(mol);
* jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
* .AlignFrame, java.lang.String)
*/
- public void removeJavascriptListener(AlignFrame af, String listener)
+ @Override
+ public void removeJavascriptListener(AlignFrameI af, String listener)
{
if (listener != null)
{
{
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--;
}
}
+ @Override
public void stop()
{
System.err.println("Applet " + getName() + " stop().");
tidyUp();
}
+ @Override
public void destroy()
{
System.err.println("Applet " + getName() + " destroy().");
}
if (jsFunctionExec != null)
{
- jsFunctionExec.stopQueue();
- jsFunctionExec.jvlite = null;
+ jsFunctionExec.tidyUp();
+ jsFunctionExec = null;
}
initialAlignFrame = null;
- jsFunctionExec = null;
javascriptListeners = null;
StructureSelectionManager.release(this);
}
* @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()
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)
{
* jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String)
*/
- public void scrollViewToIn(final AlignFrame alf, final String topRow,
+ @Override
+ public void scrollViewToIn(final AlignFrameI alf, final String topRow,
final String leftHandColumn)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
try
{
- alf.scrollTo(new Integer(topRow).intValue(), new Integer(
- leftHandColumn).intValue());
+ ((AlignFrame) alf).scrollTo(new Integer(topRow).intValue(),
+ new Integer(leftHandColumn).intValue());
} catch (Exception ex)
{
* .AlignFrame, java.lang.String)
*/
@Override
- public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
+ public void scrollViewToRowIn(final AlignFrameI alf, final String topRow)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
try
{
- alf.scrollToRow(new Integer(topRow).intValue());
+ ((AlignFrame) alf).scrollToRow(new Integer(topRow).intValue());
} catch (Exception ex)
{
* .AlignFrame, java.lang.String)
*/
@Override
- public void scrollViewToColumnIn(final AlignFrame alf,
+ public void scrollViewToColumnIn(final AlignFrameI alf,
final String leftHandColumn)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
try
{
- alf.scrollToColumn(new Integer(leftHandColumn).intValue());
+ ((AlignFrame) alf)
+ .scrollToColumn(new Integer(leftHandColumn).intValue());
} catch (Exception ex)
{
- System.err
- .println("Couldn't parse integer arguments (leftHandColumn='"
+ System.err.println(
+ "Couldn't parse integer arguments (leftHandColumn='"
+ leftHandColumn + "')");
ex.printStackTrace();
}
boolean embedded = false;
- private boolean checkForJmol = true;
+ boolean checkForJmol = true;
- private boolean checkedForJmol = false; // ensure we don't check for jmol
+ boolean checkedForJmol = false; // ensure we don't check for jmol
// every time the app is re-inited
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;
+ public JalviewAppLoader appLoader;
+
+ public AlignFrame loaderFrame;
+
public static boolean debug = false;
static String builddate = null, version = null, installation = null;
{
try
{
- BufferedReader reader = new BufferedReader(new InputStreamReader(
- url.openStream()));
+ BufferedReader reader = new BufferedReader(
+ new InputStreamReader(url.openStream()));
String line;
while ((line = reader.readLine()) != null)
{
} 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();
}
else
{
- throw new Error(
- MessageManager
- .getString("error.invalid_separator_parameter"));
+ throw new Error(MessageManager
+ .getString("error.invalid_separator_parameter"));
}
}
+
+ // Background color
+
int r = 255;
int g = 255;
int b = 255;
b = 255;
}
}
+ setBackground(new Color(r, g, b));
+
param = getParameter("label");
if (param != null)
{
launcher.setLabel(param);
}
- setBackground(new Color(r, g, b));
-
file = getParameter("file");
if (file == null)
{
- // Maybe the sequences are added as parameters
- StringBuffer data = new StringBuffer("PASTE");
- int i = 1;
- while ((file = getParameter("sequence" + i)) != null)
- {
- data.append(file.toString() + "\n");
- i++;
- }
- if (data.length() > 5)
- {
- file = data.toString();
- }
+ file = appLoader.getPastedSequence(this);
}
if (getDefaultParameter("enableSplitFrame", true))
{
file2 = getParameter("file2");
}
- embedded = TRUE.equalsIgnoreCase(getParameter("embedded"));
+ embedded = (TRUE.equalsIgnoreCase(getParameter("embedded"))
+ || file != null
+ && FALSE.equalsIgnoreCase(getParameter("showbutton")));
if (embedded)
{
- LoadingThread loader = new LoadingThread(file, file2, this);
- loader.start();
- }
- else if (file != null)
- {
- /*
- * Start the applet immediately or show a button to start it
- */
- if (FALSE.equalsIgnoreCase(getParameter("showbutton")))
- {
- LoadingThread loader = new LoadingThread(file, file2, this);
- loader.start();
- }
- else
- {
- add(launcher);
- launcher.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- LoadingThread loader = new LoadingThread(file, file2,
- JalviewLite.this);
- loader.start();
- }
- });
- }
+ startLoading();
}
- else
+ else if (file == null)
{
// jalview initialisation with no alignment. loadAlignment() method can
// still be called to open new alignments.
fileFound = false;
callInitCallback();
}
+ else
+ {
+ add(launcher);
+ launcher.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ startLoading();
+ }
+ });
+ }
+ }
+
+ protected void startLoading()
+ {
+ LoadingThread loader = new LoadingThread(file, file2, this);
+ loader.start();
}
private void initLiveConnect()
}
}
- private void callInitCallback()
+ void callInitCallback()
{
String initjscallback = getParameter("oninit");
if (initjscallback == null)
try
{
// do onInit with the JS executor thread
- new JSFunctionExec(this).executeJavascriptFunction(true,
- initjscallback, null, "Calling oninit callback '"
- + initjscallback + "'.");
+ new JSFunctionExec(this, debug).executeJavascriptFunction(true,
+ initjscallback, null,
+ "Calling oninit callback '" + initjscallback + "'.");
} catch (Exception e)
{
System.err.println("Exception when executing _oninit callback '"
frame.setTitle(title);
frame.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent e)
{
if (frame instanceof AlignFrame)
frame.dispose();
}
+ @Override
public void windowActivated(WindowEvent e)
{
if (frame instanceof AlignFrame)
* @param g
* graphics context
*/
+ @Override
public void paint(Graphics g)
{
if (!fileFound)
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)
{
private boolean running = false;
+ @Override
public void run()
{
if (running || checkedForJmol)
}
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)
{
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;
/**
* State variable: protocol for access to file source
*/
- String protocol;
+ DataSourceType protocol;
String _file; // alignment file or URL spec
JalviewLite applet;
- private void dbgMsg(String msg)
+ public void dbgMsg(String msg)
{
if (JalviewLite.debug)
{
*/
public String resolveFileProtocol(String path)
{
- /*
- * is it paste data?
- */
- if (path.startsWith("PASTE"))
- {
- protocol = AppletFormatAdapter.PASTE;
- return path.substring(5);
- }
-
- /*
- * is it a URL?
- */
- if (path.indexOf("://") != -1)
- {
- protocol = AppletFormatAdapter.URL;
- return path;
- }
-
- /*
- * try relative to document root
- */
- URL documentBase = getDocumentBase();
- String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase);
- if (HttpUtils.isValidUrl(withDocBase))
- {
- if (debug)
- {
- System.err.println("Prepended document base '" + documentBase
- + "' to make: '" + withDocBase + "'");
- }
- protocol = AppletFormatAdapter.URL;
- return withDocBase;
- }
-
- /*
- * try relative to codebase (if different to document base)
- */
- URL codeBase = getCodeBase();
- String withCodeBase = applet.resolveUrlForLocalOrAbsolute(path,
- codeBase);
- if (!withCodeBase.equals(withDocBase)
- && HttpUtils.isValidUrl(withCodeBase))
- {
- protocol = AppletFormatAdapter.URL;
- if (debug)
- {
- System.err.println("Prepended codebase '" + codeBase
- + "' to make: '" + withCodeBase + "'");
- }
- return withCodeBase;
- }
- /*
- * try locating by classloader; try this last so files in the directory
- * are resolved using document base
- */
- if (inArchive(path))
- {
- protocol = AppletFormatAdapter.CLASSLOADER;
- }
- return path;
+ String[] ret = new String[] { path };
+ protocol = JalviewAppLoader.resolveFileProtocol(applet, ret);
+ return ret[0];
}
public LoadingThread(String file, String file2, JalviewLite _applet)
applet = _applet;
}
+ @Override
public void run()
{
LoadJmolThread jmolchecker = new LoadJmolThread();
*/
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.");
if (newAlignFrame != null)
{
addToDisplay(newAlignFrame, newAlignFrame2);
- loadTree(newAlignFrame);
-
- loadScoreFile(newAlignFrame);
-
- loadFeatures(newAlignFrame);
-
- loadAnnotations(newAlignFrame);
-
- loadJnetFile(newAlignFrame);
-
- loadPdbFiles(newAlignFrame);
+ applet.loaderFrame = newAlignFrame;
+ appLoader.load(applet);
}
else
{
fileFound = false;
applet.remove(launcher);
applet.repaint();
+ callInitCallback();
}
- callInitCallback();
}
/**
return null;
}
String resolvedFile = resolveFileProtocol(fileParam);
- String format = new IdentifyFile().Identify(resolvedFile, protocol);
- dbgMsg("File identified as '" + format + "'");
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))
// 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(
- "label.successfully_loaded_file",
- new Object[] { resolvedFile }));
+ "label.successfully_loaded_file", new Object[]
+ { resolvedFile }));
return newAlignFrame;
}
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();
}
}
return null;
}
- /**
- * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
- * else false.
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadPdbFiles(AlignFrame alignFrame)
- {
- boolean result = false;
- /*
- * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
- * related to JAL-434
- */
-
- 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="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
- *
- * <param name="PDBfile3" value="1q0o Q45135_9MICO">
- */
+ }
- int pdbFileCount = 0;
- // Accumulate pdbs here if they are heading for the same view (if
- // alignPdbStructures is true)
- Vector pdbs = new Vector();
- // create a lazy matcher if we're asked to
- jalview.analysis.SequenceIdMatcher matcher = (applet
- .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
- alignFrame.getAlignViewport().getAlignment()
- .getSequencesArray()) : null;
+ /**
+ * @return the default alignFrame acted on by the public applet methods. May
+ * return null with an error message on System.err indicating the
+ * fact.
+ */
+ public AlignFrame getDefaultTargetFrame()
+ {
+ if (currentAlignFrame != null)
+ {
+ return currentAlignFrame;
+ }
+ if (initialAlignFrame != null)
+ {
+ return initialAlignFrame;
+ }
+ System.err.println(
+ "Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
+ return null;
+ }
- String param;
- do
- {
- if (pdbFileCount > 0)
- {
- param = applet.getParameter("PDBFILE" + pdbFileCount);
- }
- else
- {
- param = applet.getParameter("PDBFILE");
- }
+ /**
+ * separator used for separatorList
+ */
+ protected String separator = "" + ((char) 0x00AC); // the default used to be
+ // '|' but many sequence
+ // IDS include pipes.
- if (param != null)
- {
- PDBEntry pdb = new PDBEntry();
+ /**
+ * set to enable the URL based javascript execution mechanism
+ */
+ private boolean jsfallbackEnabled = false;
- String seqstring;
- SequenceI[] seqs = null;
- String[] chains = null;
+ /**
+ * parse the string into a list
+ *
+ * @param list
+ * @return elements separated by separator
+ */
+ @Override
+ public String[] separatorListToArray(String list)
+ {
+ return JalviewAppLoader.separatorListToArray(list, separator);
+ }
- StringTokenizer st = new StringTokenizer(param, " ");
+ /**
+ * concatenate the list with separator
+ *
+ * @param list
+ * @return concatenated string
+ */
+ @Override
+ public String arrayToSeparatorList(String[] list)
+ {
+ return JalviewAppLoader.arrayToSeparatorList(list, separator);
+ }
- if (st.countTokens() < 2)
- {
- String sequence = applet.getParameter("PDBSEQ");
- if (sequence != null)
- {
- seqs = new SequenceI[] { matcher == null ? (Sequence) alignFrame
- .getAlignViewport().getAlignment().findName(sequence)
- : matcher.findIdMatch(sequence) };
- }
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
+ */
+ @Override
+ public String getFeatureGroups()
+ {
+ String lst = arrayToSeparatorList(
+ getDefaultTargetFrame().getFeatureGroups());
+ return lst;
+ }
- }
- else
- {
- param = st.nextToken();
- List<SequenceI> tmp = new ArrayList<SequenceI>();
- List<String> tmp2 = new ArrayList<String>();
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
+ * )
+ */
+ @Override
+ public String getFeatureGroupsOn(AlignFrameI alf)
+ {
+ String lst = arrayToSeparatorList(
+ ((AlignFrame) alf).getFeatureGroups());
+ return lst;
+ }
- while (st.hasMoreTokens())
- {
- seqstring = st.nextToken();
- StringTokenizer st2 = new StringTokenizer(seqstring, "=");
- if (st2.countTokens() > 1)
- {
- // This is the chain
- tmp2.add(st2.nextToken());
- seqstring = st2.nextToken();
- }
- tmp.add(matcher == null ? (Sequence) alignFrame
- .getAlignViewport().getAlignment()
- .findName(seqstring) : matcher.findIdMatch(seqstring));
- }
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
+ */
+ @Override
+ public String getFeatureGroupsOfState(boolean visible)
+ {
+ return arrayToSeparatorList(
+ getDefaultTargetFrame().getFeatureGroupsOfState(visible));
+ }
- seqs = tmp.toArray(new SequenceI[tmp.size()]);
- if (tmp2.size() == tmp.size())
- {
- chains = tmp2.toArray(new String[tmp2.size()]);
- }
- }
- param = resolveFileProtocol(param);
- // TODO check JAL-357 for files in a jar (CLASSLOADER)
- pdb.setFile(param);
-
- if (seqs != null)
- {
- for (int i = 0; i < seqs.length; i++)
- {
- if (seqs[i] != null)
- {
- ((Sequence) seqs[i]).addPDBId(pdb);
- StructureSelectionManager.getStructureSelectionManager(
- applet).registerPDBEntry(pdb);
- }
- else
- {
- if (JalviewLite.debug)
- {
- // 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 "
- + i + ")");
- }
- }
- }
-
- if (!alignPdbStructures)
- {
- alignFrame.newStructureView(applet, pdb, seqs, chains,
- protocol);
- }
- else
- {
- pdbs.addElement(new Object[] { pdb, seqs, chains,
- new String(protocol) });
- }
- }
- }
-
- pdbFileCount++;
- } while (param != null || pdbFileCount < 10);
- if (pdbs.size() > 0)
- {
- SequenceI[][] seqs = new SequenceI[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++)
- {
- Object[] o = (Object[]) pdbs.elementAt(pdbsi);
- pdb[pdbsi] = (PDBEntry) o[0];
- seqs[pdbsi] = (SequenceI[]) o[1];
- chains[pdbsi] = (String[]) o[2];
- protocols[pdbsi] = (String) o[3];
- }
- alignFrame.alignedStructureView(applet, pdb, seqs, chains,
- protocols);
- result = true;
- }
- return result;
- }
-
- /**
- * Load in a Jnetfile if specified by parameter. Returns true if loaded,
- * else false.
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadJnetFile(AlignFrame alignFrame)
- {
- boolean result = false;
- String param = applet.getParameter("jnetfile");
- if (param != null)
- {
- try
- {
- param = resolveFileProtocol(param);
- JPredFile predictions = new JPredFile(param, protocol);
- 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.alignPanel.fontChanged();
- alignFrame.alignPanel.setScrollValues(0, 0);
- result = true;
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- return result;
- }
-
- /**
- * Load annotations if specified by parameter. Returns true if loaded, else
- * false.
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadAnnotations(AlignFrame alignFrame)
- {
- boolean result = false;
- String param = applet.getParameter("annotations");
- if (param != null)
- {
- param = resolveFileProtocol(param);
-
- if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
- param, protocol))
- {
- alignFrame.alignPanel.fontChanged();
- alignFrame.alignPanel.setScrollValues(0, 0);
- result = true;
- }
- else
- {
- System.err
- .println("Annotations were not added from annotation file '"
- + param + "'");
- }
- }
- return result;
- }
-
- /**
- * Load features file and view settings as specified by parameters. Returns
- * true if features were loaded, else false.
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadFeatures(AlignFrame alignFrame)
- {
- boolean result = false;
- // ///////////////////////////
- // modify display of features
- // we do this before any features have been loaded, ensuring any hidden
- // groups are hidden when features first displayed
- //
- // hide specific groups
- //
- String param = applet.getParameter("hidefeaturegroups");
- if (param != null)
- {
- alignFrame.setFeatureGroupState(separatorListToArray(param), false);
- // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
- }
- // show specific groups
- param = applet.getParameter("showfeaturegroups");
- if (param != null)
- {
- alignFrame.setFeatureGroupState(separatorListToArray(param), true);
- // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
- }
- // and now load features
- param = applet.getParameter("features");
- if (param != null)
- {
- param = resolveFileProtocol(param);
-
- result = alignFrame.parseFeaturesFile(param, protocol);
- }
-
- param = applet.getParameter("showFeatureSettings");
- if (param != null && param.equalsIgnoreCase(TRUE))
- {
- alignFrame.viewport.setShowSequenceFeatures(true);
- new FeatureSettings(alignFrame.alignPanel);
- }
- return result;
- }
-
- /**
- * Load a score file if specified by parameter. Returns true if file was
- * loaded, else false.
- *
- * @param alignFrame
- */
- protected boolean loadScoreFile(AlignFrame alignFrame)
- {
- boolean result = false;
- String sScoreFile = applet.getParameter("scoreFile");
- if (sScoreFile != null && !"".equals(sScoreFile))
- {
- try
- {
- if (debug)
- {
- System.err
- .println("Attempting to load T-COFFEE score file from the scoreFile parameter");
- }
- result = alignFrame.loadScoreFile(sScoreFile);
- if (!result)
- {
- System.err
- .println("Failed to parse T-COFFEE parameter as a valid score file ('"
- + sScoreFile + "')");
- }
- } catch (Exception e)
- {
- System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
- sScoreFile, e.getMessage());
- }
- }
- return result;
- }
-
- /**
- * Load a tree for the alignment if specified by parameter. Returns true if
- * a tree was loaded, else false.
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadTree(AlignFrame alignFrame)
- {
- boolean result = false;
- String treeFile = applet.getParameter("tree");
- if (treeFile == null)
- {
- treeFile = applet.getParameter("treeFile");
- }
-
- if (treeFile != null)
- {
- try
- {
- treeFile = resolveFileProtocol(treeFile);
- NewickFile fin = new NewickFile(treeFile, protocol);
- fin.parse();
-
- if (fin.getTree() != null)
- {
- alignFrame.loadTree(fin, treeFile);
- result = true;
- dbgMsg("Successfully imported tree.");
- }
- else
- {
- dbgMsg("Tree parameter did not resolve to a valid tree.");
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- return result;
- }
-
- /**
- * Discovers whether the given file is in the Applet Archive
- *
- * @param f
- * String
- * @return boolean
- */
- boolean inArchive(String f)
- {
- // This might throw a security exception in certain browsers
- // Netscape Communicator for instance.
- try
- {
- boolean rtn = (getClass().getResourceAsStream("/" + f) != null);
- if (debug)
- {
- System.err.println("Resource '" + f + "' was "
- + (rtn ? "" : "not ") + "located by classloader.");
- }
- return rtn;
- } catch (Exception ex)
- {
- System.out.println("Exception checking resources: " + f + " " + ex);
- return false;
- }
- }
- }
-
- /**
- * @return the default alignFrame acted on by the public applet methods. May
- * return null with an error message on System.err indicating the
- * fact.
- */
- public AlignFrame getDefaultTargetFrame()
- {
- if (currentAlignFrame != null)
- {
- return currentAlignFrame;
- }
- if (initialAlignFrame != null)
- {
- return initialAlignFrame;
- }
- System.err
- .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
- return null;
- }
-
- /**
- * separator used for separatorList
- */
- protected String separator = "" + ((char) 0x00AC); // the default used to be
- // '|' but many sequence
- // IDS include pipes.
-
- /**
- * set to enable the URL based javascript execution mechanism
- */
- public boolean jsfallbackEnabled = false;
-
- /**
- * parse the string into a list
- *
- * @param list
- * @return elements separated by separator
- */
- public String[] separatorListToArray(String list)
- {
- return separatorListToArray(list, separator);
- }
-
- /**
- * parse the string into a list
- *
- * @param list
- * @param separator
- * @return elements separated by separator
- */
- public static String[] separatorListToArray(String list, String separator)
- {
- // TODO use StringUtils version (slightly different...)
- int seplen = separator.length();
- if (list == null || list.equals("") || list.equals(separator))
- {
- return null;
- }
- java.util.Vector jv = new Vector();
- int cp = 0, pos;
- while ((pos = list.indexOf(separator, cp)) > cp)
- {
- jv.addElement(list.substring(cp, pos));
- cp = pos + seplen;
- }
- if (cp < list.length())
- {
- String c = list.substring(cp);
- if (!c.equals(separator))
- {
- jv.addElement(c);
- }
- }
- if (jv.size() > 0)
- {
- String[] v = new String[jv.size()];
- for (int i = 0; i < v.length; i++)
- {
- v[i] = (String) jv.elementAt(i);
- }
- jv.removeAllElements();
- if (debug)
- {
- System.err.println("Array from '" + separator
- + "' separated List:\n" + v.length);
- for (int i = 0; i < v.length; i++)
- {
- System.err.println("item " + i + " '" + v[i] + "'");
- }
- }
- return v;
- }
- if (debug)
- {
- System.err.println("Empty Array from '" + separator
- + "' separated List");
- }
- return null;
- }
-
- /**
- * concatenate the list with separator
- *
- * @param list
- * @return concatenated string
- */
- public String arrayToSeparatorList(String[] list)
- {
- return arrayToSeparatorList(list, separator);
- }
-
- /**
- * concatenate the list with separator
- *
- * @param list
- * @param separator
- * @return concatenated string
- */
- public static String arrayToSeparatorList(String[] list, String separator)
- {
- // TODO use StringUtils version
- StringBuffer v = new StringBuffer();
- if (list != null && list.length > 0)
- {
- for (int i = 0, iSize = list.length; i < iSize; i++)
- {
- if (list[i] != null)
- {
- if (i > 0)
- {
- v.append(separator);
- }
- v.append(list[i]);
- }
- }
- if (debug)
- {
- System.err.println("Returning '" + separator
- + "' separated List:\n");
- System.err.println(v);
- }
- return v.toString();
- }
- if (debug)
- {
- System.err.println("Returning empty '" + separator
- + "' separated List\n");
- }
- return "" + separator;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
- */
- public String getFeatureGroups()
- {
- String lst = arrayToSeparatorList(getDefaultTargetFrame()
- .getFeatureGroups());
- return lst;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
- * )
- */
- public String getFeatureGroupsOn(AlignFrame alf)
- {
- String lst = arrayToSeparatorList(alf.getFeatureGroups());
- return lst;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
- */
- public String getFeatureGroupsOfState(boolean visible)
- {
- return arrayToSeparatorList(getDefaultTargetFrame()
- .getFeatureGroupsOfState(visible));
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
- * .AlignFrame, boolean)
- */
- public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
- {
- return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
- }
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
+ * .AlignFrame, boolean)
+ */
+ @Override
+ public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
+ {
+ return arrayToSeparatorList(
+ ((AlignFrame) alf).getFeatureGroupsOfState(visible));
+ }
/*
* (non-Javadoc)
* @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
* AlignFrame, java.lang.String, boolean)
*/
- public void setFeatureGroupStateOn(final AlignFrame alf,
+ @Override
+ public void setFeatureGroupStateOn(final AlignFrameI alf,
final String groups, boolean state)
{
final boolean st = state;// !(state==null || state.equals("") ||
@Override
public void run()
{
- alf.setFeatureGroupState(separatorListToArray(groups), st);
+ ((AlignFrame) alf)
+ .setFeatureGroupState(separatorListToArray(groups), st);
}
});
}
* @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
* boolean)
*/
+ @Override
public void setFeatureGroupState(String groups, boolean state)
{
setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
*
* @see jalview.bin.JalviewLiteJsApi#getSeparator()
*/
+ @Override
public String getSeparator()
{
return separator;
*
* @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
*/
+ @Override
public void setSeparator(String separator)
{
if (separator == null || separator.length() < 1)
* the value to return otherwise
* @return true or false
*/
+ @Override
public boolean getDefaultParameter(String name, boolean def)
{
String stn;
* @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String, java.lang.String)
*/
- public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
+ @Override
+ public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
String pdbEntryString, String pdbFile)
{
- return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
+ return ((AlignFrame) alFrame).addPdbFile(sequenceId, pdbEntryString,
+ pdbFile);
}
- protected void setAlignPdbStructures(boolean alignPdbStructures)
+ @Override
+ public void setAlignPdbStructures(boolean alignPdbStructures)
{
this.alignPdbStructures = alignPdbStructures;
}
return alignPdbStructures;
}
+ @Override
public void start()
{
// callInitCallback();
}
- private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();
+ private Hashtable<String, int[]> 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)
- {
- Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
- if (msgset == null)
- {
- msgset = new Hashtable<String, String[]>();
- jsmessages.put(messageclass, msgset);
- }
- msgset.put(viewId, colcommands);
- long[] l = new long[colcommands.length];
- for (int i = 0; i < colcommands.length; i++)
- {
- l[i] = colcommands[i].hashCode();
- }
- jshashes.put(messageclass + "|" + viewId, l);
- }
- /*
- * (non-Javadoc)
- *
- * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
- * java.lang.String)
- */
- public String getJsMessage(String messageclass, String viewId)
+ @Override
+ public Hashtable<String, int[]> getJSHashes()
{
- Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
- if (msgset != null)
- {
- String[] msgs = msgset.get(viewId);
- if (msgs != null)
- {
- for (int i = 0; i < msgs.length; i++)
- {
- if (msgs[i] != null)
- {
- String m = msgs[i];
- msgs[i] = null;
- return m;
- }
- }
- }
- }
- return "";
+ return jshashes;
}
- public boolean isJsMessageSetChanged(String string, String string2,
- String[] colcommands)
+ @Override
+ public Hashtable<String, Hashtable<String, String[]>> getJSMessages()
{
- long[] l = jshashes.get(string + "|" + string2);
- if (l == null && colcommands != null)
- {
- return true;
- }
- for (int i = 0; i < colcommands.length; i++)
- {
- if (l[i] != colcommands[i].hashCode())
- {
- return true;
- }
- }
- return false;
+ return jsmessages;
}
- private Vector jsExecQueue = new Vector();
+ private Vector<Runnable> jsExecQueue = new Vector<>();
- public Vector getJsExecQueue()
+ @Override
+ public Vector<Runnable> getJsExecQueue(JSFunctionExec exec)
{
+ jsFunctionExec = exec;
return jsExecQueue;
}
- public void setExecutor(JSFunctionExec jsFunctionExec2)
- {
- jsFunctionExec = jsFunctionExec2;
- }
+ // public void setExecutor(JSFunctionExec jsFunctionExec2)
+ // {
+ // jsFunctionExec = jsFunctionExec2;
+ // }
/**
* return the given colour value parameter or the given default if parameter
{
return defcolour;
}
- Color col = jalview.schemes.ColourSchemeProperty
- .getAWTColorFromName(colprop);
+ Color col = ColorUtils.parseColourString(colprop);
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;
-
}
public void openJalviewHelpUrl()
}
/**
- * form a complete URL given a path to a resource and a reference location on
- * the same server
- *
- * @param targetPath
- * - an absolute path on the same server as localref or a document
- * located relative to localref
- * @param localref
- * - a URL on the same server as url
- * @return a complete URL for the resource located by url
- */
- private String resolveUrlForLocalOrAbsolute(String targetPath,
- 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.
- * www.jalview.org/examples/index.html#applets?a=b is trimmed to
- * www.jalview.org/examples/
- */
- String urlPath = localref.toString();
- String directoryPath = urlPath;
- int lastSeparator = directoryPath.lastIndexOf("/");
- if (lastSeparator > 0)
- {
- directoryPath = directoryPath.substring(0, lastSeparator + 1);
- }
-
- if (targetPath.startsWith("/"))
- {
- /*
- * construct absolute URL to a file on the server - this is not allowed?
- */
- // String localfile = localref.getFile();
- // resolvedPath = urlPath.substring(0,
- // urlPath.length() - localfile.length())
- // + targetPath;
- resolvedPath = directoryPath + targetPath.substring(1);
- }
- else
- {
- resolvedPath = directoryPath + targetPath;
- }
- if (debug)
- {
- System.err.println("resolveUrlForLocalOrAbsolute returning "
- + resolvedPath);
- }
- return resolvedPath;
- }
-
- /**
* open a URL in the browser - resolving it according to relative refs and
* coping with javascript: protocol if necessary.
*
// form valid URL
// Should really use docbase, not codebase.
URL prepend;
- url = resolveUrlForLocalOrAbsolute(
- url,
- prepend = getDefaultParameter("resolvetocodebase", false) ? getCodeBase()
+ url = JalviewAppLoader.resolveUrlForLocalOrAbsolute(url,
+ prepend = getDefaultParameter("resolvetocodebase", false)
+ ? getCodeBase()
: 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
}
}
- /**
- * bind structures in a viewer to any matching sequences in an alignFrame (use
- * sequenceIds to limit scope of search to specific sequences)
- *
- * @param alFrame
- * @param viewer
- * @param sequenceIds
- * @return TODO: consider making an exception structure for indicating when
- * binding fails public SequenceStructureBinding
- * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
- * sequenceIds) {
- *
- * if (sequenceIds != null && sequenceIds.length() > 0) { return
- * alFrame.addStructureViewInstance(viewer,
- * separatorListToArray(sequenceIds)); } else { return
- * alFrame.addStructureViewInstance(viewer, null); } // return null; }
- */
+ @Override
+ public AlignViewportI getViewport()
+ {
+ return loaderFrame.getAlignViewport();
+ }
+
+ @Override
+ public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
+ String[] chains, DataSourceType protocol)
+ {
+ loaderFrame.newStructureView(this, pdb, seqs, chains,
+ protocol);
+ }
+
+ @Override
+ public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
+ String[][] chains, String[] protocols)
+ {
+ loaderFrame.alignedStructureView(this, pdb, seqs, chains, protocols);
+ }
+
+ @Override
+ public void updateForAnnotations()
+ {
+ loaderFrame.alignPanel.fontChanged();
+ loaderFrame.alignPanel.setScrollValues(0, 0);
+ }
+
+ @Override
+ public void setFeatureGroupState(String[] groups, boolean state)
+ {
+ loaderFrame.setFeatureGroupState(groups, state);
+ }
+
+ @Override
+ public boolean parseFeaturesFile(String param, DataSourceType protocol)
+ {
+ return loaderFrame.parseFeaturesFile(param, protocol);
+ }
+
+ @Override
+ public void newFeatureSettings()
+ {
+ getViewport().setShowSequenceFeatures(true);
+ new FeatureSettings(loaderFrame.alignPanel);
+ }
+
+ @Override
+ public boolean loadScoreFile(String sScoreFile) throws IOException
+ {
+ return loaderFrame.loadScoreFile(sScoreFile);
+ }
+
+ @Override
+ public void loadTree(NewickFile tree, String treeFile) throws IOException
+ {
+ loaderFrame.loadTree(tree, treeFile);
+ }
+
+ @Override
+ public boolean isJsfallbackEnabled()
+ {
+ return jsfallbackEnabled;
+ }
+
+ @Override
+ public JSObject getJSObject()
+ {
+ return JSObject.getWindow(this);
+ }
+
+ @Override
+ public void updateColoursFromMouseOver(Object source,
+ MouseOverStructureListener listener)
+ {
+ }
+
+ @Override
+ public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel,
+ HiddenColumns hidden, SelectionSource source, Object alignFrame)
+ {
+ // System.err.println("Testing selection event relay to
+ // jsfunction:"+_listener);
+ String setid = "";
+ AlignFrame src = (AlignFrame) alignFrame;
+ if (source != null)
+ {
+ if (source instanceof jalview.appletgui.AlignViewport
+ && ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame.viewport == source)
+ {
+ // should be valid if it just generated an event!
+ src = ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame;
+
+ }
+ }
+ String[] seqs = new String[] {};
+ String[] cols = new String[] {};
+ int strt = 0, end = (src == null) ? -1
+ : src.alignPanel.av.getAlignment().getWidth();
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ seqs = new String[seqsel.getSize()];
+ for (int i = 0; i < seqs.length; i++)
+ {
+ seqs[i] = seqsel.getSequenceAt(i).getName();
+ }
+ if (strt < seqsel.getStartRes())
+ {
+ strt = seqsel.getStartRes();
+ }
+ if (end == -1 || end > seqsel.getEndRes())
+ {
+ end = seqsel.getEndRes();
+ }
+ }
+ if (colsel != null && !colsel.isEmpty())
+ {
+ if (end == -1)
+ {
+ end = colsel.getMax() + 1;
+ }
+ cols = new String[colsel.getSelected().size()];
+ for (int i = 0; i < cols.length; i++)
+ {
+ cols[i] = "" + (1 + colsel.getSelected().get(i).intValue());
+ }
+ }
+ else
+ {
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ // send a valid range, otherwise we send the empty selection
+ cols = new String[2];
+ cols[0] = "" + (1 + strt) + "-" + (1 + end);
+ }
+ }
+ return new Object[]
+ { src, setid, arrayToSeparatorList(seqs), arrayToSeparatorList(cols) };
+ }
+
+ @Override
+ public String getJsMessage(String messageclass, String viewId)
+ {
+ return JSFunctionExec.getJsMessage(messageclass, viewId, this);
+ }
+
+ @Override
+ public Object getFrameForSource(VamsasSource source)
+ {
+ if (source != null)
+ {
+ if (source instanceof jalview.appletgui.AlignViewport
+ && ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame.viewport == source)
+ {
+ // should be valid if it just generated an event!
+ return ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame;
+
+ }
+ // TODO: ensure that if '_af' is specified along with a handler
+ // function, then only events from that alignFrame are sent to that
+ // function
+ }
+ return null;
+ }
+
+ @Override
+ public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp)
+ {
+ return new jalview.appletgui.FeatureRenderer((AlignmentViewport) vp);
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignment(String format,
+ boolean suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ String format, boolean suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ // /**
+ // * bind structures in a viewer to any matching sequences in an alignFrame
+ // (use
+ // * sequenceIds to limit scope of search to specific sequences)
+ // *
+ // * @param alFrame
+ // * @param viewer
+ // * @param sequenceIds
+ // * @return TODO: consider making an exception structure for indicating when
+ // * binding fails public SequenceStructureBinding
+ // * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
+ // * sequenceIds) {
+ // *
+ // * if (sequenceIds != null && sequenceIds.length() > 0) { return
+ // * alFrame.addStructureViewInstance(viewer,
+ // * separatorListToArray(sequenceIds)); } else { return
+ // * alFrame.addStructureViewInstance(viewer, null); } // return null; }
+ // */
}
git://source.jalview.org / jalview.git / blobdiff