*/
package jalview.bin;
+import java.util.Locale;
+
import jalview.analysis.AlignmentUtils;
import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
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.javascript.JSFunctionExec;
import jalview.javascript.JalviewLiteJsApi;
import jalview.javascript.JsCallBack;
+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.applet.Applet;
import java.awt.event.WindowEvent;
import java.io.BufferedReader;
import java.io.IOException;
-import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URL;
+import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
import java.util.StringTokenizer;
* @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";
*
* @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)
{
int apos = -1;
try
{
- apos = new Integer(position).intValue();
+ apos = Integer.valueOf(position).intValue();
apos--;
} catch (NumberFormatException ex)
{
// 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()
{
* @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)
{
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)
{
- 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
{
- to = new Integer(cl.substring(p + 1)).intValue();
+ to = Integer.valueOf(cl.substring(p + 1)).intValue();
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;
}
int r = -1;
try
{
- r = new Integer(cl).intValue();
+ r = Integer.valueOf(cl).intValue();
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
{
- 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);
+ alf.select(sel, csel,
+ 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)
*/
+ @Override
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
- 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 = FileFormats.getInstance().forName(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);
}
- 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)
*/
+ @Override
public void setMouseoverListener(AlignFrame 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;
}
}
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.");
}
*
* @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)
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;
}
}
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.");
}
* @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;
}
}
- jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(
- this, listener, separatorListToArray(modelSet));
+ MouseOverStructureListener mol = new MouseOverStructureListener(this,
+ listener, separatorListToArray(modelSet));
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
.addStructureViewerListener(mol);
* jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
* .AlignFrame, java.lang.String)
*/
+ @Override
public void removeJavascriptListener(AlignFrame 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().");
* @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()
try
{
StructureSelectionManager.getStructureSelectionManager(me)
- .mouseOverStructure(new Integer(pdbResNum).intValue(),
+ .mouseOverStructure(Integer.valueOf(pdbResNum).intValue(),
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)
*/
+ @Override
public void scrollViewToIn(final AlignFrame alf, final String topRow,
final String leftHandColumn)
{
{
try
{
- alf.scrollTo(new Integer(topRow).intValue(), new Integer(
- leftHandColumn).intValue());
+ alf.scrollTo(Integer.valueOf(topRow).intValue(),
+ Integer.valueOf(leftHandColumn).intValue());
} catch (Exception ex)
{
{
try
{
- alf.scrollToRow(new Integer(topRow).intValue());
+ alf.scrollToRow(Integer.valueOf(topRow).intValue());
} catch (Exception ex)
{
{
try
{
- alf.scrollToColumn(new Integer(leftHandColumn).intValue());
+ alf.scrollToColumn(Integer.valueOf(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();
}
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;
{
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();
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
}
else
{
- throw new Error(
- MessageManager
- .getString("error.invalid_separator_parameter"));
+ throw new Error(MessageManager
+ .getString("error.invalid_separator_parameter"));
}
}
int r = 255;
add(launcher);
launcher.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
LoadingThread loader = new LoadingThread(file, file2,
{
// 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 '"
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
* update the protocol state variable for accessing the datasource located
* by file.
*
- * @param file
+ * @param path
* @return possibly updated datasource string
*/
- public String setProtocolState(String file)
+ public String resolveFileProtocol(String path)
{
- if (file.startsWith("PASTE"))
+ /*
+ * is it paste data?
+ */
+ if (path.startsWith("PASTE"))
{
- file = file.substring(5);
- protocol = AppletFormatAdapter.PASTE;
+ protocol = DataSourceType.PASTE;
+ return path.substring(5);
}
- else if (inArchive(file))
+
+ /*
+ * is it a URL?
+ */
+ if (path.indexOf("://") != -1)
{
- protocol = AppletFormatAdapter.CLASSLOADER;
+ protocol = DataSourceType.URL;
+ return path;
}
- else
+
+ /*
+ * 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 = DataSourceType.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))
{
- file = addProtocol(file);
- protocol = AppletFormatAdapter.URL;
+ protocol = DataSourceType.URL;
+ if (debug)
+ {
+ System.err.println("Prepended codebase '" + codeBase
+ + "' to make: '" + withCodeBase + "'");
+ }
+ return withCodeBase;
}
- dbgMsg("Protocol identified as '" + protocol + "'");
- return file;
+
+ /*
+ * try locating by classloader; try this last so files in the directory
+ * are resolved using document base
+ */
+ if (inArchive(path))
+ {
+ protocol = DataSourceType.CLASSLOADER;
+ }
+ return path;
}
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.");
{
return null;
}
- String resolvedFile = setProtocolState(fileParam);
- String format = new IdentifyFile().Identify(resolvedFile, protocol);
- dbgMsg("File identified as '" + format + "'");
+ String resolvedFile = resolveFileProtocol(fileParam);
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();
}
}
* 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">
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 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) };
}
else
{
param = st.nextToken();
- Vector tmp = new Vector();
- Vector tmp2 = new Vector();
+ List<SequenceI> tmp = new ArrayList<>();
+ List<String> tmp2 = new ArrayList<>();
while (st.hasMoreTokens())
{
if (st2.countTokens() > 1)
{
// This is the chain
- tmp2.addElement(st2.nextToken());
+ tmp2.add(st2.nextToken());
seqstring = st2.nextToken();
}
- tmp.addElement(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 = new SequenceI[tmp.size()];
- tmp.copyInto(seqs);
+ seqs = tmp.toArray(new SequenceI[tmp.size()]);
if (tmp2.size() == tmp.size())
{
- chains = new String[tmp2.size()];
- tmp2.copyInto(chains);
+ chains = tmp2.toArray(new String[tmp2.size()]);
}
}
- param = setProtocolState(param);
-
- if (// !jmolAvailable
- // &&
- protocol == AppletFormatAdapter.CLASSLOADER && !useXtrnalSviewer)
- {
- // Re: JAL-357 : the bug isn't a problem if we are using an
- // external viewer!
- // TODO: verify this Re:
- // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
- // This exception preserves the current behaviour where, even if
- // the local pdb file was identified in the class loader
- protocol = AppletFormatAdapter.URL; // this is probably NOT
- // CORRECT!
- param = addProtocol(param); //
- }
-
+ param = resolveFileProtocol(param);
+ // TODO check JAL-357 for files in a jar (CLASSLOADER)
pdb.setFile(param);
if (seqs != null)
if (seqs[i] != null)
{
((Sequence) seqs[i]).addPDBId(pdb);
- StructureSelectionManager.getStructureSelectionManager(
- applet).registerPDBEntry(pdb);
+ StructureSelectionManager
+ .getStructureSelectionManager(applet)
+ .registerPDBEntry(pdb);
}
else
{
{
// 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 + ")");
}
}
}
else
{
- pdbs.addElement(new Object[] { pdb, seqs, chains,
- new String(protocol) });
+ pdbs.addElement(new Object[] { pdb, seqs, chains, protocol });
}
}
}
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];
{
boolean result = false;
String param = applet.getParameter("jnetfile");
+ if (param == null)
+ {
+ // jnet became jpred around 2016
+ param = applet.getParameter("jpredfile");
+ }
if (param != null)
{
try
{
- param = setProtocolState(param);
+ 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.viewport.getAlignment().setupJPredAlignment();
+
alignFrame.alignPanel.fontChanged();
alignFrame.alignPanel.setScrollValues(0, 0);
result = true;
String param = applet.getParameter("annotations");
if (param != null)
{
- param = setProtocolState(param);
+ param = resolveFileProtocol(param);
if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
param, protocol))
}
else
{
- System.err
- .println("Annotations were not added from annotation file '"
+ System.err.println(
+ "Annotations were not added from annotation file '"
+ param + "'");
}
}
param = applet.getParameter("features");
if (param != null)
{
- param = setProtocolState(param);
+ param = resolveFileProtocol(param);
result = alignFrame.parseFeaturesFile(param, protocol);
}
{
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)
{
- 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)
{
try
{
- treeFile = setProtocolState(treeFile);
+ treeFile = resolveFileProtocol(treeFile);
NewickFile fin = new NewickFile(treeFile, protocol);
fin.parse();
return rtn;
} catch (Exception ex)
{
- System.out.println("Exception checking resources: " + f + " "
- + ex);
+ System.out.println("Exception checking resources: " + f + " " + ex);
return false;
}
}
-
- /**
- * If the file is not already in URL format, tries to locate it by resolving
- * as a URL.
- *
- * @param f
- * @return
- */
- String addProtocol(final String f)
- {
- if (f.indexOf("://") != -1)
- {
- // already has URL format
- return f;
- }
-
- /*
- * Try relative to document base
- */
- URL documentBase = getDocumentBase();
- String url = applet.resolveUrlForLocalOrAbsolute(f, documentBase);
- if (urlExists(url))
- {
- if (debug)
- {
- System.err.println("Prepended document base '" + documentBase
- + "' to make: '" + url + "'");
- }
- return url;
- }
-
- /*
- * Try relative to codebase
- */
- URL codeBase = getCodeBase();
- url = applet.resolveUrlForLocalOrAbsolute(f, codeBase);
- if (urlExists(url))
- {
- if (debug)
- {
- System.err.println("Prepended codebase '" + codeBase
- + "' to make: '" + url + "'");
- }
- return url;
- }
-
- return f;
- }
-
- /**
- * Returns true if an input stream can be opened on the specified URL, else
- * false.
- *
- * @param url
- * @return
- */
- private boolean urlExists(String url)
- {
- InputStream is = null;
- try
- {
- is = new URL(url).openStream();
- if (is != null)
- {
- return true;
- }
- } catch (Exception x)
- {
- // ignore
- } finally
- {
- if (is != null)
- {
- try
- {
- is.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- }
- return false;
- }
}
/**
{
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;
}
}
if (debug)
{
- System.err.println("Empty Array from '" + separator
- + "' separated List");
+ System.err.println(
+ "Empty Array from '" + separator + "' separated List");
}
return null;
}
}
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("Returning empty '" + separator
- + "' separated List\n");
+ System.err.println(
+ "Returning empty '" + separator + "' separated List\n");
}
return "" + separator;
}
*
* @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
*/
+ @Override
public String getFeatureGroups()
{
- String lst = arrayToSeparatorList(getDefaultTargetFrame()
- .getFeatureGroups());
+ String lst = arrayToSeparatorList(
+ getDefaultTargetFrame().getFeatureGroups());
return lst;
}
* 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()
- .getFeatureGroupsOfState(visible));
+ return arrayToSeparatorList(
+ getDefaultTargetFrame().getFeatureGroupsOfState(visible));
}
/*
* 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)
{
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
* @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();
}
- 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)
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);
* @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()
* form a complete URL given a path to a resource and a reference location on
* the same server
*
- * @param url
+ * @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 url, URL localref)
+ private String resolveUrlForLocalOrAbsolute(String targetPath,
+ URL localref)
{
- String codebase = localref.toString();
- if (url.indexOf("/") == 0)
+ String resolvedPath = "";
+ if (targetPath.startsWith("/"))
{
+ String codebase = localref.toString();
String localfile = localref.getFile();
- url = codebase.substring(0, codebase.length() - localfile.length())
- + url;
+ 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
{
- url = localref + url;
+ resolvedPath = directoryPath + targetPath;
}
if (debug)
{
- System.err.println("URL: " + localref.toString());
- System.err.println("URL.getFile: " + localref.getFile());
- System.err.println("URL.getPath: " + localref.getPath());
- System.err.println("URL.getQuery: " + localref.getQuery());
- System.err.println("returning " + url);
+ System.err.println(
+ "resolveUrlForLocalOrAbsolute returning " + resolvedPath);
}
- return url;
+ return resolvedPath;
}
/**
// form valid URL
// Should really use docbase, not codebase.
URL prepend;
- url = resolveUrlForLocalOrAbsolute(
- url,
- prepend = getDefaultParameter("resolvetocodebase", false) ? getDocumentBase()
- : getCodeBase());
+ url = 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
git://source.jalview.org / jalview.git / blobdiff