package jalview.bin;
import jalview.analysis.AlignmentUtils;
+import jalview.api.AlignViewportI;
+import jalview.api.JalviewApp;
import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
import jalview.appletgui.AlignViewport;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
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.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
import jalview.util.ColorUtils;
-import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import java.applet.Applet;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
-import java.util.StringTokenizer;
import java.util.Vector;
import netscape.javascript.JSObject;
* @version $Revision: 1.92 $
*/
public class JalviewLite extends Applet
- implements StructureSelectionManagerProvider, JalviewLiteJsApi
+ implements StructureSelectionManagerProvider, JalviewLiteJsApi,
+ JalviewApp
{
+ public JalviewLite()
+ {
+ appLoader = new JalviewAppLoader(debug);
+ }
private static final String TRUE = "true";
private static final String FALSE = "false";
}
}
// 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();
public String orderAlignmentBy(AlignFrame 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)
{
*/
public boolean useXtrnalSviewer = false;
+ public JalviewAppLoader appLoader;
+
+ public AlignFrame loaderFrame;
+
public static boolean debug = false;
static String builddate = null, version = null, installation = null;
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 = DataSourceType.PASTE;
- return path.substring(5);
- }
-
- /*
- * is it a URL?
- */
- if (path.indexOf("://") != -1)
- {
- protocol = DataSourceType.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 = 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))
- {
- protocol = DataSourceType.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 = DataSourceType.CLASSLOADER;
- }
- return path;
+ String[] ret = new String[] { path };
+ protocol = JalviewAppLoader.resolveFileProtocol(applet, ret);
+ return ret[0];
}
public LoadingThread(String file, String file2, JalviewLite _applet)
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
{
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;
-
- String param;
- do
- {
- if (pdbFileCount > 0)
- {
- param = applet.getParameter("PDBFILE" + pdbFileCount);
- }
- else
- {
- param = applet.getParameter("PDBFILE");
- }
-
- if (param != null)
- {
- PDBEntry pdb = new PDBEntry();
-
- String seqstring;
- SequenceI[] seqs = null;
- String[] chains = null;
-
- StringTokenizer st = new StringTokenizer(param, " ");
-
- 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) };
- }
-
- }
- else
- {
- param = st.nextToken();
- List<SequenceI> tmp = new ArrayList<>();
- List<String> tmp2 = new ArrayList<>();
-
- 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));
- }
-
- 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, 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)
- {
- // jnet became jpred around 2016
- param = applet.getParameter("jpredfile");
- }
- 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
-
- alignFrame.viewport.getAlignment().setupJPredAlignment();
-
- 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;
- }
- }
}
/**
*/
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;
+ return JalviewAppLoader.separatorListToArray(list, separator);
}
/**
* the value to return otherwise
* @return true or false
*/
+ @Override
public boolean getDefaultParameter(String name, boolean def)
{
String stn;
return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
}
- protected void setAlignPdbStructures(boolean alignPdbStructures)
+ @Override
+ public void setAlignPdbStructures(boolean alignPdbStructures)
{
this.alignPdbStructures = alignPdbStructures;
}
}
/**
- * 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,
+ url = JalviewAppLoader.resolveUrlForLocalOrAbsolute(url,
prepend = getDefaultParameter("resolvetocodebase", false)
? getCodeBase()
: getDocumentBase());
}
}
+ @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 updateForLoader()
+ {
+ 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);
+ }
+
/**
* bind structures in a viewer to any matching sequences in an alignFrame (use
* sequenceIds to limit scope of search to specific sequences)
git://source.jalview.org / jalview.git / blobdiff