//The following public methods maybe called
//externally, eg via javascript in HTML page
/**
- * @return list of selected sequences separated by "¬"
+ * @return String list of selected sequence IDs, each terminated by "¬" (¬)
*/
public String getSelectedSequences()
{
return getSelectedSequencesFrom(getDefaultTargetFrame());
}
+ /**
+ * @param sep separator string or null for default
+ * @return String list of selected sequence IDs, each terminated by sep or ("¬" as default)
+ */
+ public String getSelectedSequences(String sep)
+ {
+ return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
+ }
+ /**
+ * @param alf alignframe containing selection
+ * @return String list of selected sequence IDs, each terminated by "¬"
+ *
+ */
public String getSelectedSequencesFrom(AlignFrame alf)
{
+ return getSelectedSequencesFrom(alf, "¬");
+ }
+ /**
+ * get list of selected sequence IDs separated by given separator
+ * @param alf window containing selection
+ * @param sep separator string to use - default is "¬"
+ * @return String list of selected sequence IDs, each terminated by the given separator
+ */
+ public String getSelectedSequencesFrom(AlignFrame alf, String sep)
+ {
StringBuffer result = new StringBuffer("");
-
+ if (sep==null || sep.length()==0)
+ {
+ sep = "¬";
+ }
if (alf.viewport.getSelectionGroup() != null)
{
SequenceI[] seqs = alf.viewport.getSelectionGroup().
for (int i = 0; i < seqs.length; i++)
{
- result.append(seqs[i].getName() + "¬");
+ result.append(seqs[i].getName());
+ result.append(sep);
}
}
return result.toString();
}
-
+
+ /**
+ * get sequences selected in current alignFrame and return their alignment in format 'format' either with or without suffix
+ * @param alf - where selection is
+ * @param format - format of alignment file
+ * @param suffix - "true" to append /start-end string to each sequence ID
+ * @return selected sequences as flat file or empty string if there was no current selection
+ */
+ public String getSelectedSequencesAsAlignment(String format, String suffix) {
+ return getSelectedSequencesAsAlignmentFrom(currentAlignFrame, format, suffix);
+ }
+
+ /**
+ * get sequences selected in alf and return their alignment in format 'format' either with or without suffix
+ * @param alf - where selection is
+ * @param format - format of alignment file
+ * @param suffix - "true" to append /start-end string to each sequence ID
+ * @return selected sequences as flat file or empty string if there was no current selection
+ */
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, String suffix)
+ {
+ try
+ {
+ boolean seqlimits = suffix.equalsIgnoreCase("true");
+ if (alf.viewport.getSelectionGroup()!=null)
+ {
+ String reply = new AppletFormatAdapter().formatSequences(format,
+ new Alignment(alf.viewport.getSelectionAsNewSequence()), seqlimits);
+ return reply;
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return "Error retrieving alignment in " + format + " format. ";
+ }
+ return "";
+ }
+
public String getAlignment(String format)
{
return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
class LoadingThread
extends Thread
{
- String file;
+ /**
+ * State variable: File source
+ */
+ String file;
+ /**
+ * State variable: protocol for access to file source
+ */
String protocol;
+ /**
+ * State variable: format of file source
+ */
String format;
JalviewLite applet;
-
- public LoadingThread(String _file,
- JalviewLite _applet)
+ private void dbgMsg(String msg)
{
if (applet.debug)
{
- System.err.println("Loading thread started with:\n>>file\n"+_file+">>endfile");
+ System.err.println(msg);
}
- file = _file;
+ }
+ /**
+ * update the protocol state variable for accessing the datasource
+ * located by file.
+ * @param file
+ * @return possibly updated datasource string
+ */
+ public String setProtocolState(String file)
+ {
if (file.startsWith("PASTE"))
{
file = file.substring(5);
file = addProtocol(file);
protocol = AppletFormatAdapter.URL;
}
- if (applet.debug)
- {
- System.err.println("Protocol identified as '"+protocol+"'");
- }
+ dbgMsg("Protocol identified as '"+protocol+"'");
+ return file;
+ }
+ public LoadingThread(String _file,
+ JalviewLite _applet)
+ {
+ dbgMsg("Loading thread started with:\n>>file\n"+_file+">>endfile");
+ file = setProtocolState(_file);
+
format = new jalview.io.IdentifyFile().Identify(file, protocol);
- if (applet.debug)
- {
- System.err.println("File identified as '"+format+"'");
- }
+ dbgMsg("File identified as '"+format+"'");
applet = _applet;
}
private void startLoading()
{
+ dbgMsg("Loading started.");
Alignment al = null;
try
{
}
catch (java.io.IOException ex)
{
+ dbgMsg("File load exception.");
ex.printStackTrace();
}
if ( (al != null) && (al.getHeight() > 0))
{
+ dbgMsg("Successfully loaded file.");
initialAlignFrame = new AlignFrame(al,
applet,
file,
{
try
{
- if (inArchive(treeFile))
+ treeFile = setProtocolState(treeFile);
+ /*if (inArchive(treeFile))
{
protocol = AppletFormatAdapter.CLASSLOADER;
}
protocol = AppletFormatAdapter.URL;
treeFile = addProtocol(treeFile);
}
-
+ */
jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
protocol);
if (fin.getTree() != null)
{
currentAlignFrame.loadTree(fin, treeFile);
+ dbgMsg("Successfuly imported tree.");
+ } else {
+ dbgMsg("Tree parameter did not resolve to a valid tree.");
}
}
catch (Exception ex)
String param = getParameter("features");
if (param != null)
{
- if (!inArchive(param))
- {
- param = addProtocol(param);
- }
-
+ param = setProtocolState(param);
+
currentAlignFrame.parseFeaturesFile(param, protocol);
}
param = getParameter("annotations");
if (param != null)
- {
- if (!inArchive(param))
- {
- param = addProtocol(param);
- }
-
- new AnnotationFile().readAnnotationFile(
+ {
+ param = setProtocolState(param);
+
+ if (new AnnotationFile().readAnnotationFile(
currentAlignFrame.viewport.getAlignment(),
param,
- protocol);
-
- currentAlignFrame.alignPanel.fontChanged();
- currentAlignFrame.alignPanel.setScrollValues(0, 0);
+ protocol))
+ {
+ currentAlignFrame.alignPanel.fontChanged();
+ currentAlignFrame.alignPanel.setScrollValues(0, 0);
+ } else {
+ System.err.println("Annotations were not added from annotation file '"+param+"'");
+ }
}
{
try
{
- if (inArchive(param))
- {
- protocol = AppletFormatAdapter.CLASSLOADER;
- }
- else
- {
- protocol = AppletFormatAdapter.URL;
- param = addProtocol(param);
- }
-
+ param = setProtocolState(param);
jalview.io.JPredFile predictions = new jalview.io.JPredFile(
param, protocol);
- new JnetAnnotationMaker().add_annotation(predictions,
+ JnetAnnotationMaker.add_annotation(predictions,
currentAlignFrame.viewport.getAlignment(),
- 0, false); // do not add sequence profile from concise output
+ 0, false); // false==do not add sequence profile from concise output
currentAlignFrame.alignPanel.fontChanged();
currentAlignFrame.alignPanel.setScrollValues(0, 0);
}
tmp2.copyInto(chains);
}
}
-
- if (inArchive(param) && !jmolAvailable)
+ param = setProtocolState(param);
+
+ if (!jmolAvailable && protocol==AppletFormatAdapter.CLASSLOADER)
{
- protocol = AppletFormatAdapter.CLASSLOADER;
- }
- else
- {
- protocol = AppletFormatAdapter.URL;
- param = addProtocol(param);
+ // TODO: pass PDB file in classloader on to Jmol
+ // 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); //
}
pdb.setFile(param);
{
for (int i = 0; i < seqs.length; i++)
{
- ( (Sequence) seqs[i]).addPDBId(pdb);
+ if (seqs[i]!=null)
+ {
+ ( (Sequence) seqs[i]).addPDBId(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 (jmolAvailable)
//Netscape Communicator for instance.
try
{
- return (getClass().getResourceAsStream("/" + file) != null);
+ boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
+ if (debug)
+ { System.err.println("Resource '"+file+"' was "+(rtn ? "" : "not") +" located by classloader.");
+ }
+ return rtn;
}
catch (Exception ex)
{
if (file.indexOf("://") == -1)
{
file = getCodeBase() + file;
+ if (debug)
+ {
+ System.err.println("Prepended codebase for resource: '"+file+"'");
+ }
}
return file;
git://source.jalview.org / jalview.git / blobdiff