import jalview.javascript.MouseOverStructureListener;
import jalview.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import java.applet.Applet;
import java.awt.event.WindowAdapter;
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;
*
* @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)
{
if (csel != null)
{
List<Integer> cs = csel.getSelected();
+ // note - the following actually clears cs as well, since
+ // csel.getSelected returns a reference. Need to check if we need to
+ // have a concurrentModification exception thrown here
csel.clear();
for (Integer selectedCol : cs)
{
* 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)
{
*
* @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)
{
*
* @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(),
*
* @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)
{
*
* @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,
+ String format = new IdentifyFile().identify(text,
AppletFormatAdapter.PASTE);
try
{
*
* @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)
* 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;
+ return path.substring(5);
}
- else if (inArchive(file))
+
+ /*
+ * is it a URL?
+ */
+ if (path.indexOf("://") != -1)
{
- protocol = AppletFormatAdapter.CLASSLOADER;
+ protocol = AppletFormatAdapter.URL;
+ return path;
}
- else
+
+ /*
+ * try relative to document root
+ */
+ URL documentBase = getDocumentBase();
+ String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase);
+ if (HttpUtils.isValidUrl(withDocBase))
{
- file = addProtocol(file);
+ 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;
}
- dbgMsg("Protocol identified as '" + protocol + "'");
- return file;
+ return path;
}
public LoadingThread(String file, String file2, JalviewLite _applet)
applet = _applet;
}
+ @Override
public void run()
{
LoadJmolThread jmolchecker = new LoadJmolThread();
{
return null;
}
- String resolvedFile = setProtocolState(fileParam);
- String format = new IdentifyFile().Identify(resolvedFile, protocol);
+ String resolvedFile = resolveFileProtocol(fileParam);
+ String format = new IdentifyFile().identify(resolvedFile, protocol);
dbgMsg("File identified as '" + format + "'");
AlignmentI al = null;
try
else
{
param = st.nextToken();
- Vector tmp = new Vector();
- Vector tmp2 = new Vector();
+ List<SequenceI> tmp = new ArrayList<SequenceI>();
+ List<String> tmp2 = new ArrayList<String>();
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
+ 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)
{
try
{
- param = setProtocolState(param);
+ param = resolveFileProtocol(param);
JPredFile predictions = new JPredFile(param, protocol);
JnetAnnotationMaker.add_annotation(predictions,
alignFrame.viewport.getAlignment(), 0, false);
String param = applet.getParameter("annotations");
if (param != null)
{
- param = setProtocolState(param);
+ param = resolveFileProtocol(param);
if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
param, protocol))
param = applet.getParameter("features");
if (param != null)
{
- param = setProtocolState(param);
+ param = resolveFileProtocol(param);
result = alignFrame.parseFeaturesFile(param, protocol);
}
{
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();
- System.err.println("Trying documentbase: " + documentBase);
- String url = applet.resolveUrlForLocalOrAbsolute(f, documentBase);
- if (urlExists(url))
- {
- if (true/* debug */)
- {
- System.err.println("Prepended document base '" + documentBase
- + "' to make: '" + url + "'");
- }
- return url;
- }
-
- /*
- * Try relative to codebase
- */
- URL codeBase = getCodeBase();
- System.err.println("Trying codebase: " + codeBase);
- url = applet.resolveUrlForLocalOrAbsolute(f, codeBase);
- if (urlExists(url))
- {
- if (true/* 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;
- }
}
/**
*
* @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);
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.
if (targetPath.startsWith("/"))
{
/*
- * construct absolute URL to a file on the server
+ * 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;
+ // String localfile = localref.getFile();
+ // resolvedPath = urlPath.substring(0,
+ // urlPath.length() - localfile.length())
+ // + targetPath;
+ resolvedPath = directoryPath + targetPath.substring(1);
}
else
{
git://source.jalview.org / jalview.git / blobdiff