--- /dev/null
+package jalview.api;
+
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.NewickFile;
+
+import java.io.IOException;
+import java.net.URL;
+
+public interface JalviewApp
+{
+ public String getParameter(String name);
+
+ public boolean getDefaultParameter(String name, boolean def);
+
+ public URL getDocumentBase();
+
+ public URL getCodeBase();
+
+ public void setAlignPdbStructures(boolean defaultParameter);
+
+ public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
+ String[] chains, DataSourceType protocol);
+
+ public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
+ String[][] chains, String[] protocols);
+
+ public void updateForLoader();
+
+ public AlignViewportI getViewport();
+
+ public void setFeatureGroupState(String[] groups, boolean state);
+
+ public boolean parseFeaturesFile(String param, DataSourceType protocol);
+
+ public void newFeatureSettings();
+
+ public boolean loadScoreFile(String sScoreFile) throws IOException;
+
+ public void loadTree(NewickFile fin, String treeFile) throws IOException;
+
+}
};
/** Default file is ~/.jalview_properties */
- // BH 2019.05.07 note: Instances of Jalview will share this file.
- static String propertiesFile;
+ private String propertiesFile;
/**
* flag to possibly allow properties to be written to a property file
*/
public static String getProperty(String key)
{
- return getInstance().getPropertyImpl(key);
- }
-
- private String getPropertyImpl(String key)
- {
- String prop = applicationProperties.getProperty(key);
- if (prop == null && Platform.isJS())
- {
- prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
- + "_" + JS_PROPERTY_PREFIX + key);
- }
- return prop;
+ return getInstance().applicationProperties.getProperty(key);
}
/**
*/
package jalview.bin;
+import jalview.api.AlignViewportI;
+import jalview.api.JalviewApp;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.Preferences;
import jalview.gui.PromptUserConfig;
import jalview.io.AppletFormatAdapter;
import jalview.io.BioJsHTMLOutput;
private AlignFrame currentAlignFrame;
+ public boolean isJavaAppletTag;
+
+ public String appletResourcePath;
+
public static AlignFrame getCurrentAlignFrame()
{
return getInstance().currentAlignFrame;
String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
Cache.loadProperties(usrPropsFile);
- if (usrPropsFile != null)
+ if (Platform.isJS())
{
+ isJavaAppletTag = aparser.isApplet();
+ if (isJavaAppletTag)
+ {
+ Preferences.setAppletDefaults();
+ Cache.loadProperties(usrPropsFile); // again, because we
+ // might be changing defaults here?
+ }
System.out.println(
- "CMD [-props " + usrPropsFile + "] executed successfully!");
+ "<Applet> found: " + aparser.getValue("Info.j2sAppletID"));
+ appletResourcePath = aparser.getValue("Info.resourcePath");
}
-
- if (!Platform.isJS())
+ else
/**
* Java only
*
* @j2sIgnore
*/
{
+ if (usrPropsFile != null)
+ {
+ System.out.println(
+ "CMD [-props " + usrPropsFile + "] executed successfully!");
+ }
+
if (aparser.contains("help") || aparser.contains("h"))
{
showUsage();
+ "] executed successfully!");
groovyscript = null;
}
- String imageName = "unnamed.png";
- while (aparser.getSize() > 1)
+
+ if (isJavaAppletTag)
+ {
+ loadAppletParams(aparser, af);
+ }
+ else
{
- // PNG filename
- // SVG filename
- // HTML filename
- // biojsmsa filename
- String outputFormat = aparser.nextValue();
- file = aparser.nextValue();
-
- if (outputFormat.equalsIgnoreCase("png"))
- {
- af.createPNG(new File(file));
- imageName = (new File(file)).getName();
- System.out.println("Creating PNG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("svg"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
- af.createSVG(imageFile);
- System.out.println("Creating SVG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("html"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
- HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.exportHTML(file);
- System.out.println("Creating HTML image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("biojsmsa"))
+ String imageName = "unnamed.png";
+ while (aparser.getSize() > 1)
{
- if (file == null)
+ // PNG filename
+ // SVG filename
+ // HTML filename
+ // biojsmsa filename
+ String outputFormat = aparser.nextValue();
+ file = aparser.nextValue();
+
+ if (outputFormat.equalsIgnoreCase("png"))
{
- System.err.println("The output html file must not be null");
- return;
+ af.createPNG(new File(file));
+ imageName = (new File(file)).getName();
+ System.out.println("Creating PNG image: " + file);
+ continue;
}
- try
+ else if (outputFormat.equalsIgnoreCase("svg"))
{
- BioJsHTMLOutput.refreshVersionInfo(
- BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
- } catch (URISyntaxException e)
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ af.createSVG(imageFile);
+ System.out.println("Creating SVG image: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("html"))
{
- e.printStackTrace();
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(file);
+
+ System.out.println("Creating HTML image: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("biojsmsa"))
+ {
+ if (file == null)
+ {
+ System.err.println("The output html file must not be null");
+ return;
+ }
+ try
+ {
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(file);
+ System.out.println(
+ "Creating BioJS MSA Viwer HTML file: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("imgMap"))
+ {
+ af.createImageMap(new File(file), imageName);
+ System.out.println("Creating image map: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("eps"))
+ {
+ File outputFile = new File(file);
+ System.out.println(
+ "Creating EPS file: " + outputFile.getAbsolutePath());
+ af.createEPS(outputFile);
+ continue;
+ }
+
+ af.saveAlignment(file, format);
+ if (af.isSaveAlignmentSuccessful())
+ {
+ System.out.println("Written alignment in " + format
+ + " format to " + file);
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in "
+ + format + " format!!");
}
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
- bjs.exportHTML(file);
- System.out
- .println("Creating BioJS MSA Viwer HTML file: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("imgMap"))
- {
- af.createImageMap(new File(file), imageName);
- System.out.println("Creating image map: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("eps"))
- {
- File outputFile = new File(file);
- System.out.println(
- "Creating EPS file: " + outputFile.getAbsolutePath());
- af.createEPS(outputFile);
- continue;
- }
- af.saveAlignment(file, format);
- if (af.isSaveAlignmentSuccessful())
- {
- System.out.println("Written alignment in " + format
- + " format to " + file);
}
- else
+
+ while (aparser.getSize() > 0)
{
- System.out.println("Error writing file " + file + " in "
- + format + " format!!");
+ System.out.println("Unknown arg: " + aparser.nextValue());
}
-
- }
-
- while (aparser.getSize() > 0)
- {
- System.out.println("Unknown arg: " + aparser.nextValue());
}
}
}
}
}
+ /**
+ * Get the SwingJS applet ID and combine that with the frameType
+ *
+ * @param frameType
+ * "alignment", "desktop", etc., or null
+ * @return
+ */
+ public static String getAppID(String frameType)
+ {
+ String id = Cache.getProperty("Info.j2sAppletID");
+ if (id == null)
+ {
+ id = "jalview";
+ }
+ return id + (frameType == null ? "" : "-" + frameType);
+ }
+
+ private void loadAppletParams(ArgsParser aparser, AlignFrame af)
+ {
+ Jalview me = this;
+ JalviewApp app = new JalviewApp()
+ {
+
+
+ @Override
+ public String getParameter(String name)
+ {
+ return aparser.getAppletValue(name, null);
+ }
+
+ @Override
+ public boolean getDefaultParameter(String name, boolean def)
+ {
+ String stn;
+ return ((stn = getParameter(name)) == null ? def
+ : "true".equalsIgnoreCase(stn));
+ }
+
+ @Override
+ public URL getDocumentBase()
+ {
+ return Platform.getDocumentBase();
+ }
+
+ @Override
+ public URL getCodeBase()
+ {
+ return Platform.getCodeBase();
+ }
+
+ @Override
+ public AlignViewportI getViewport()
+ {
+ return Jalview.getCurrentAlignFrame().getViewport();
+ }
+
+ @Override
+ public boolean loadScoreFile(String sScoreFile) throws IOException
+ {
+ Jalview.getCurrentAlignFrame().loadJalviewDataFile(sScoreFile, null,
+ null, null);
+ return true;
+ }
+
+ @Override
+ public boolean parseFeaturesFile(String filename,
+ DataSourceType protocol)
+ {
+ return af.parseFeaturesFile(filename, protocol);
+ }
+
+ @Override
+ public void loadTree(NewickFile fin, String treeFile)
+ throws IOException
+ {
+ // n/a -- already done
+ }
+
+ @Override
+ public void setAlignPdbStructures(boolean defaultParameter)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
+ String[] chains, DataSourceType protocol)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
+ String[][] chains, String[] protocols)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void updateForLoader()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setFeatureGroupState(String[] groups, boolean state)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void newFeatureSettings()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ };
+
+ new JalviewAppLoader(true).load(app);
+
+ }
+
}
--- /dev/null
+package jalview.bin;
+
+import jalview.api.JalviewApp;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
+import jalview.io.DataSourceType;
+import jalview.io.JPredFile;
+import jalview.io.JnetAnnotationMaker;
+import jalview.io.NewickFile;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.HttpUtils;
+import jalview.util.MessageManager;
+
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+/**
+ * A class to load parameters for either JalviewLite or Jalview
+ *
+ * @author hansonr
+ *
+ */
+public class JalviewAppLoader
+{
+
+ private JalviewApp app;
+
+ private boolean debug;
+
+ private String separator;
+
+ public JalviewAppLoader(boolean debug)
+ {
+ this.debug = debug;
+ }
+
+ public void load(JalviewApp app)
+ {
+
+ this.app = app;
+
+ String sep = app.getParameter("separator");
+ if (sep != null)
+ {
+ if (sep.length() > 0)
+ {
+ separator = sep;
+ }
+ else
+ {
+ throw new Error(MessageManager
+ .getString("error.invalid_separator_parameter"));
+ }
+ }
+
+ loadTree();
+ loadScoreFile();
+ loadFeatures();
+ loadAnnotations();
+ loadJnetFile();
+ loadPdbFiles();
+ }
+
+ /**
+ * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
+ * else false.
+ *
+ * @param loaderFrame
+ * @return
+ */
+ protected boolean loadPdbFiles()
+ {
+ boolean result = false;
+ /*
+ * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
+ * related to JAL-434
+ */
+
+ boolean doAlign = app.getDefaultParameter("alignpdbfiles", false);
+ app.setAlignPdbStructures(doAlign);
+ /*
+ * <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<Object[]> pdbs = new Vector<>();
+ // create a lazy matcher if we're asked to
+ jalview.analysis.SequenceIdMatcher matcher = (app
+ .getDefaultParameter("relaxedidmatch", false))
+ ? new jalview.analysis.SequenceIdMatcher(
+ app.getViewport().getAlignment()
+ .getSequencesArray())
+ : null;
+
+ String param;
+ do
+ {
+ if (pdbFileCount > 0)
+ {
+ param = app.getParameter("PDBFILE" + pdbFileCount);
+ }
+ else
+ {
+ param = app.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 = app.getParameter("PDBSEQ");
+ if (sequence != null)
+ {
+ seqs = new SequenceI[] { matcher == null
+ ? (Sequence) app.getViewport().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) app.getViewport().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()]);
+ }
+ }
+ ret[0] = param;
+ DataSourceType protocol = resolveFileProtocol(app,
+ ret);
+ // TODO check JAL-357 for files in a jar (CLASSLOADER)
+ pdb.setFile(ret[0]);
+
+ if (seqs != null)
+ {
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i] != null)
+ {
+ ((Sequence) seqs[i]).addPDBId(pdb);
+ StructureSelectionManager
+ .getStructureSelectionManager(
+ (StructureSelectionManagerProvider) app)
+ .registerPDBEntry(pdb);
+ }
+ else
+ {
+ if (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 (doAlign)
+ {
+ pdbs.addElement(new Object[] { pdb, seqs, chains, protocol });
+ }
+ else
+ {
+ app.newStructureView(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 = pdbs.elementAt(pdbsi);
+ pdb[pdbsi] = (PDBEntry) o[0];
+ seqs[pdbsi] = (SequenceI[]) o[1];
+ chains[pdbsi] = (String[]) o[2];
+ protocols[pdbsi] = (String) o[3];
+ }
+ app.alignedStructureView(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()
+ {
+ boolean result = false;
+ String param = app.getParameter("jnetfile");
+ if (param == null)
+ {
+ // jnet became jpred around 2016
+ param = app.getParameter("jpredfile");
+ }
+ if (param != null)
+ {
+ try
+ {
+ ret[0] = param;
+ DataSourceType protocol = resolveFileProtocol(app,
+ ret);
+ JPredFile predictions = new JPredFile(ret[0], protocol);
+ JnetAnnotationMaker.add_annotation(predictions,
+ app.getViewport().getAlignment(), 0, false);
+ // false == do not add sequence profile from concise output
+ app.getViewport().getAlignment().setupJPredAlignment();
+ app.updateForLoader();
+ 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()
+ {
+ boolean result = false;
+ String param = app.getParameter("annotations");
+ if (param != null)
+ {
+ ret[0] = param;
+ DataSourceType protocol = resolveFileProtocol(app,
+ ret);
+ param = ret[0];
+ if (new AnnotationFile().annotateAlignmentView(app.getViewport(),
+ param, protocol))
+ {
+ app.updateForLoader();
+ 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()
+ {
+ 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 = app.getParameter("hidefeaturegroups");
+ if (param != null)
+ {
+ app.setFeatureGroupState(
+ separatorListToArray(param, separator), false);
+ // app.setFeatureGroupStateOn(newAlignFrame, param, false);
+ }
+ // show specific groups
+ param = app.getParameter("showfeaturegroups");
+ if (param != null)
+ {
+ app.setFeatureGroupState(separatorListToArray(param, separator),
+ true);
+ // app.setFeatureGroupStateOn(newAlignFrame, param, true);
+ }
+ // and now load features
+ param = app.getParameter("features");
+ if (param != null)
+ {
+ ret[0] = param;
+ DataSourceType protocol = resolveFileProtocol(app,
+ ret);
+
+ result = app.parseFeaturesFile(param, protocol);
+ }
+
+ param = app.getParameter("showFeatureSettings");
+ if (param != null && param.equalsIgnoreCase("true"))
+ {
+ app.newFeatureSettings();
+ }
+ return result;
+ }
+
+ /**
+ * Load a score file if specified by parameter. Returns true if file was
+ * loaded, else false.
+ *
+ * @param loaderFrame
+ */
+ protected boolean loadScoreFile()
+ {
+ boolean result = false;
+ String sScoreFile = app.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 = app.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;
+ }
+
+ String[] ret = new String[1];
+ /**
+ * Load a tree for the alignment if specified by parameter. Returns true if a
+ * tree was loaded, else false.
+ *
+ * @param loaderFrame
+ * @return
+ */
+ protected boolean loadTree()
+ {
+ boolean result = false;
+ String treeFile = app.getParameter("tree");
+ if (treeFile == null)
+ {
+ treeFile = app.getParameter("treeFile");
+ }
+
+ if (treeFile != null)
+ {
+ try
+ {
+ ret[0] = treeFile;
+ NewickFile fin = new NewickFile(treeFile,
+ resolveFileProtocol(app, ret));
+ fin.parse();
+
+ if (fin.getTree() != null)
+ {
+ app.loadTree(fin, ret[0]);
+ result = true;
+ if (debug)
+ {
+ System.out.println("Successfully imported tree.");
+ }
+ }
+ else
+ {
+ if (debug)
+ {
+ System.out.println("Tree parameter did not resolve to a valid tree.");
+ }
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ return result;
+ }
+
+ /**
+ * 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
+ */
+ public static 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 (JalviewLite.debug)
+ {
+ System.err.println(
+ "resolveUrlForLocalOrAbsolute returning " + resolvedPath);
+ }
+ return resolvedPath;
+ }
+
+ /**
+ * 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;
+ }
+ Vector<String> 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] = 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;
+ }
+
+ public static DataSourceType resolveFileProtocol(JalviewApp app,
+ String[] retPath)
+ {
+ String path = retPath[0];
+ /*
+ * is it paste data?
+ */
+ if (path.startsWith("PASTE"))
+ {
+ retPath[0] = path.substring(5);
+ return DataSourceType.PASTE;
+ }
+
+ /*
+ * is it a URL?
+ */
+ if (path.indexOf("://") >= 0)
+ {
+ return DataSourceType.URL;
+ }
+
+ /*
+ * try relative to document root
+ */
+ URL documentBase = app.getDocumentBase();
+ String withDocBase = resolveUrlForLocalOrAbsolute(path,
+ documentBase);
+ if (HttpUtils.isValidUrl(withDocBase))
+ {
+ // if (debug)
+ // {
+ // System.err.println("Prepended document base '" + documentBase
+ // + "' to make: '" + withDocBase + "'");
+ // }
+ retPath[0] = withDocBase;
+ return DataSourceType.URL;
+ }
+
+ /*
+ * try relative to codebase (if different to document base)
+ */
+ URL codeBase = app.getCodeBase();
+ String withCodeBase = resolveUrlForLocalOrAbsolute(path,
+ codeBase);
+ if (!withCodeBase.equals(withDocBase)
+ && HttpUtils.isValidUrl(withCodeBase))
+ {
+ // if (debug)
+ // {
+ // System.err.println("Prepended codebase '" + codeBase
+ // + "' to make: '" + withCodeBase + "'");
+ // }
+ retPath[0] = withCodeBase;
+ return DataSourceType.URL;
+ }
+
+ /*
+ * try locating by classloader; try this last so files in the directory
+ * are resolved using document base
+ */
+ if (inArchive(app.getClass(), path))
+ {
+ return DataSourceType.CLASSLOADER;
+ }
+ return null;
+ }
+
+ /**
+ * Discovers whether the given file is in the Applet Archive
+ *
+ * @param f
+ * String
+ * @return boolean
+ */
+ private static boolean inArchive(Class<?> c, String f)
+ {
+ // This might throw a security exception in certain browsers
+ // Netscape Communicator for instance.
+ try
+ {
+ boolean rtn = (c.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;
+ }
+ }
+
+}
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)
@Test(groups = "Functional")
public void testSeparatorListToArray()
{
- assertNull(JalviewLite.separatorListToArray(null, "|"));
- assertNull(JalviewLite.separatorListToArray("", "|"));
- assertNull(JalviewLite.separatorListToArray("|", "|"));
- assertNull(JalviewLite.separatorListToArray("abc", "abc"));
+ assertNull(JalviewAppLoader.separatorListToArray(null, "|"));
+ assertNull(JalviewAppLoader.separatorListToArray("", "|"));
+ assertNull(JalviewAppLoader.separatorListToArray("|", "|"));
+ assertNull(JalviewAppLoader.separatorListToArray("abc", "abc"));
- String[] array = JalviewLite.separatorListToArray("abc|def|ghi|", "|");
+ String[] array = JalviewAppLoader.separatorListToArray("abc|def|ghi|", "|");
assertEquals(3, array.length);
assertEquals("abc", array[0]);
assertEquals("def", array[1]);
assertEquals("ghi", array[2]);
assertEquals("[abc]",
- Arrays.toString(JalviewLite.separatorListToArray("abc|", "|")));
- assertEquals("[abc]", Arrays.toString(JalviewLite.separatorListToArray(
+ Arrays.toString(JalviewAppLoader.separatorListToArray("abc|", "|")));
+ assertEquals("[abc]", Arrays.toString(JalviewAppLoader.separatorListToArray(
"abcxy", "xy")));
// these fail:
git://source.jalview.org / jalview.git / commitdiff