/*
- * 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.
*
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
import jalview.io.FileParse;
import jalview.io.IdentifyFile;
import jalview.io.JPredFile;
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 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;
*
* @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)
*/
+ @Override
public String getSelectedSequencesFrom(AlignFrame alf)
{
return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
* .AlignFrame, java.lang.String)
*/
+ @Override
public String getSelectedSequencesFrom(AlignFrame alf, String sep)
{
StringBuffer result = new StringBuffer("");
* @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)
*/
+ @Override
public void highlightIn(final AlignFrame alf, final String sequenceId,
final String position, final String alignedPosition)
{
* @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)
*/
+ @Override
public void selectIn(AlignFrame 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)
*/
+ @Override
public void selectIn(final AlignFrame alf, String sequenceIds,
String columns, String sep)
{
SequenceI rs = sel.getSequenceAt(0);
start = rs.findIndex(start);
end = rs.findIndex(end);
- if (csel != null)
+ List<Integer> cs = new ArrayList<Integer>(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);
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.
* String, java.lang.String)
*/
+ @Override
public String getSelectedSequencesAsAlignment(String format, String suffix)
{
return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview
* .appletgui.AlignFrame, java.lang.String, java.lang.String)
*/
+ @Override
public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, String suffix)
{
try
{
+ FileFormatI theFormat = FileFormat.valueOf(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
- String reply = new AppletFormatAdapter().formatSequences(format,
+ String reply = new AppletFormatAdapter().formatSequences(theFormat,
new Alignment(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
* )
*/
+ @Override
public String getAlignmentOrderFrom(AlignFrame alf)
{
return getAlignmentOrderFrom(alf, separator);
* jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
+ @Override
public String getAlignmentOrderFrom(AlignFrame alf, String sep)
{
AlignmentI alorder = alf.getAlignViewport().getAlignment();
* @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)
*/
+ @Override
public String orderAlignmentBy(AlignFrame alf, String order,
String undoName, String sep)
{
*
* @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)
*/
+ @Override
public String getAlignmentFrom(AlignFrame 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)
*/
+ @Override
public String getAlignmentFrom(AlignFrame alf, String format,
String suffix)
{
{
boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
- String reply = new AppletFormatAdapter().formatSequences(format,
+ FileFormatI theFormat = FileFormat.valueOf(format);
+ String reply = new AppletFormatAdapter().formatSequences(theFormat,
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)
*/
+ @Override
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.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
+ 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)
*/
+ @Override
public boolean loadFeaturesFrom(AlignFrame alf, String features,
boolean autoenabledisplay)
{
- return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE,
+ return 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)
*/
+ @Override
public String getFeaturesFrom(AlignFrame alf, String format)
{
return alf.outputFeatures(false, format);
*
* @see jalview.bin.JalviewLiteJsApi#getAnnotation()
*/
+ @Override
public String getAnnotation()
{
return getAnnotationFrom(getDefaultTargetFrame());
* jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
* )
*/
+ @Override
public String getAnnotationFrom(AlignFrame alf)
{
return 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)
*/
+ @Override
public AlignFrame newViewFrom(AlignFrame alf)
{
return alf.newView(null);
* @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
* java.lang.String)
*/
+ @Override
public AlignFrame newViewFrom(AlignFrame alf, String name)
{
return 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);
* jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
+ @Override
public void setMouseoverListener(AlignFrame af, String listener)
{
if (listener != null)
*
* @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)
*/
+ @Override
public void setSelectionListener(AlignFrame af, String listener)
{
if (listener != null)
* @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
* java.lang.String)
*/
+ @Override
public void setStructureListener(String listener, String modelSet)
{
if (listener != null)
* jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
* .AlignFrame, java.lang.String)
*/
+ @Override
public void removeJavascriptListener(AlignFrame af, String listener)
{
if (listener != null)
}
}
+ @Override
public void stop()
{
System.err.println("Applet " + getName() + " stop().");
tidyUp();
}
+ @Override
public void destroy()
{
System.err.println("Applet " + getName() + " destroy().");
* @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,
* java.lang.String, java.lang.String)
*/
+ @Override
public void mouseOverStructure(final String pdbResNum,
final String chain, final String pdbfile)
{
* 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)
{
add(launcher);
launcher.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
LoadingThread loader = new LoadingThread(file, file2,
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)
{
private boolean running = false;
+ @Override
public void run()
{
if (running || checkedForJmol)
/**
* State variable: protocol for access to file source
*/
- String protocol;
+ DataSourceType protocol;
String _file; // alignment file or URL spec
*/
if (path.startsWith("PASTE"))
{
- protocol = AppletFormatAdapter.PASTE;
+ protocol = DataSourceType.PASTE;
return path.substring(5);
}
*/
if (path.indexOf("://") != -1)
{
- protocol = AppletFormatAdapter.URL;
+ protocol = DataSourceType.URL;
return path;
}
System.err.println("Prepended document base '" + documentBase
+ "' to make: '" + withDocBase + "'");
}
- protocol = AppletFormatAdapter.URL;
+ protocol = DataSourceType.URL;
return withDocBase;
}
if (!withCodeBase.equals(withDocBase)
&& HttpUtils.isValidUrl(withCodeBase))
{
- protocol = AppletFormatAdapter.URL;
+ protocol = DataSourceType.URL;
if (debug)
{
System.err.println("Prepended codebase '" + codeBase
*/
if (inArchive(path))
{
- protocol = AppletFormatAdapter.CLASSLOADER;
+ protocol = DataSourceType.CLASSLOADER;
}
return path;
}
applet = _applet;
}
+ @Override
public void run()
{
LoadJmolThread jmolchecker = new LoadJmolThread();
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
}
else
{
- pdbs.addElement(new Object[] { pdb, seqs, chains,
- new String(protocol) });
+ pdbs.addElement(new Object[] { pdb, seqs, chains, protocol });
}
}
}
{
boolean result = false;
String param = applet.getParameter("jnetfile");
+ if (param == null)
+ {
+ // jnet became jpred around 2016
+ param = applet.getParameter("jpredfile");
+ }
if (param != null)
{
try
*
* @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
*/
+ @Override
public String getFeatureGroups()
{
String lst = arrayToSeparatorList(getDefaultTargetFrame()
* jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
* )
*/
+ @Override
public String getFeatureGroupsOn(AlignFrame alf)
{
String lst = arrayToSeparatorList(alf.getFeatureGroups());
*
* @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
*/
+ @Override
public String getFeatureGroupsOfState(boolean visible)
{
return arrayToSeparatorList(getDefaultTargetFrame()
* jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
* .AlignFrame, boolean)
*/
+ @Override
public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
{
return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
* @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
* AlignFrame, java.lang.String, boolean)
*/
+ @Override
public void setFeatureGroupStateOn(final AlignFrame alf,
final String groups, boolean state)
{
* @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)
* @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)
{
return alignPdbStructures;
}
+ @Override
public void start()
{
// callInitCallback();
* @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);
{
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()