--- /dev/null
+package jalview.bin;
+
+import jalview.api.AlignFrameI;
+import jalview.api.JalviewApp;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.Desktop;
+import jalview.io.AnnotationFile;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FeaturesFile;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.IdentifyFile;
+import jalview.io.JPredFile;
+import jalview.io.JnetAnnotationMaker;
+import jalview.io.NewickFile;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.HttpUtils;
+import jalview.util.MessageManager;
+
+import java.awt.EventQueue;
+import java.io.IOException;
+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; // Jalview or JalviewJS or JalviewLite
+
+ private boolean debug;
+
+ String separator = "\u00AC"; // JalviewLite note: the default used to
+ // be '|', but many sequence IDS include
+ // pipes.
+
+ public String getSeparator()
+ {
+ return separator;
+ }
+
+ public void setSeparator(String separator)
+ {
+ this.separator = 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();
+ callInitCallback();
+ }
+
+ /**
+ * 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">
+ */
+
+ // 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;
+
+ int pdbFileCount = 0;
+ 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()]);
+ }
+ }
+ pdb.setId(param);
+ 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.updateForAnnotations();
+ 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.updateForAnnotations();
+ 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(ret[0], 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 (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;
+ }
+ }
+
+ public void callInitCallback()
+ {
+ String initjscallback = app.getParameter("oninit");
+ if (initjscallback == null)
+ {
+ return;
+ }
+ initjscallback = initjscallback.trim();
+ if (initjscallback.length() > 0)
+ {
+ // TODO
+ }
+ }
+
+ /**
+ * read sequence1...sequenceN as a raw alignment
+ *
+ * @param jalviewApp
+ * @return
+ */
+ public String getPastedSequence(JalviewApp jalviewApp)
+ {
+ StringBuffer data = new StringBuffer("PASTE");
+ int i = 1;
+ String file = null;
+ while ((file = app.getParameter("sequence" + i)) != null)
+ {
+ data.append(file.toString() + "\n");
+ i++;
+ }
+ if (data.length() > 5)
+ {
+ file = data.toString();
+ }
+ return file;
+ }
+
+ /**
+ * concatenate the list with separator
+ *
+ * @param list
+ * @param separator
+ * @return concatenated string
+ */
+ public static String arrayToSeparatorList(String[] list, String separator)
+ {
+ // TODO use StringUtils version
+ StringBuffer v = new StringBuffer();
+ if (list != null && list.length > 0)
+ {
+ for (int i = 0, iSize = list.length; i < iSize; i++)
+ {
+ if (list[i] != null)
+ {
+ if (i > 0)
+ {
+ v.append(separator);
+ }
+ v.append(list[i]);
+ }
+ }
+ // if (debug)
+ // {
+ // System.err
+ // .println("Returning '" + separator + "' separated List:\n");
+ // System.err.println(v);
+ // }
+ return v.toString();
+ }
+ // if (debug)
+ // {
+ // System.err.println(
+ // "Returning empty '" + separator + "' separated List\n");
+ // }
+ return "" + separator;
+ }
+
+ public String arrayToSeparatorList(String[] array)
+ {
+ return arrayToSeparatorList(array, separator);
+ }
+
+ public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
+ {
+ StringBuffer result = new StringBuffer("");
+ if (sep == null || sep.length() == 0)
+ {
+ sep = separator; // "+0x00AC;
+ }
+ AlignViewport v = ((AlignFrame) alf).getViewport();
+ if (v.getSelectionGroup() != null)
+ {
+ SequenceI[] seqs = v.getSelectionGroup()
+ .getSequencesInOrder(v.getAlignment());
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ result.append(seqs[i].getName());
+ result.append(sep);
+ }
+ }
+
+ return result.toString();
+ }
+
+ public void setFeatureGroupStateOn(final AlignFrameI alf,
+ final String groups, boolean state)
+ {
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ ((AlignFrame) alf).setFeatureGroupState(
+ separatorListToArray(groups, separator), state);
+ }
+ });
+ }
+
+ public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
+ {
+ return arrayToSeparatorList(
+ ((AlignFrame) alf).getFeatureGroupsOfState(visible));
+ }
+
+ public void scrollViewToIn(final AlignFrameI alf, final String topRow,
+ final String leftHandColumn)
+ {
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ ((AlignFrame) alf).scrollTo(new Integer(topRow).intValue(),
+ new Integer(leftHandColumn).intValue());
+
+ } catch (Exception ex)
+ {
+ System.err.println("Couldn't parse integer arguments (topRow='"
+ + topRow + "' and leftHandColumn='" + leftHandColumn
+ + "')");
+ ex.printStackTrace();
+ }
+ }
+ });
+ }
+
+ public void scrollViewToRowIn(final AlignFrameI alf, final String topRow)
+ {
+
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ ((AlignFrame) alf).scrollToRow(new Integer(topRow).intValue());
+
+ } catch (Exception ex)
+ {
+ System.err.println("Couldn't parse integer arguments (topRow='"
+ + topRow + "')");
+ ex.printStackTrace();
+ }
+
+ }
+ });
+ }
+
+ public void scrollViewToColumnIn(final AlignFrameI alf,
+ final String leftHandColumn)
+ {
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ ((AlignFrame) alf)
+ .scrollToColumn(new Integer(leftHandColumn).intValue());
+
+ } catch (Exception ex)
+ {
+ System.err.println(
+ "Couldn't parse integer arguments (leftHandColumn='"
+ + leftHandColumn + "')");
+ ex.printStackTrace();
+ }
+ }
+ });
+
+ }
+
+ public boolean addPdbFile(AlignFrameI alf, String sequenceId,
+ String pdbEntryString, String pdbFile)
+ {
+ AlignFrame alFrame = (AlignFrame) alf;
+ SequenceI toaddpdb = alFrame.getViewport().getAlignment()
+ .findName(sequenceId);
+ boolean needtoadd = false;
+ if (toaddpdb != null)
+ {
+ Vector<PDBEntry> pdbe = toaddpdb.getAllPDBEntries();
+ PDBEntry pdbentry = null;
+ if (pdbe != null && pdbe.size() > 0)
+ {
+ for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
+ {
+ pdbentry = pdbe.elementAt(pe);
+ if (!pdbentry.getId().equals(pdbEntryString)
+ && !pdbentry.getFile().equals(pdbFile))
+ {
+ pdbentry = null;
+ }
+ else
+ {
+ continue;
+ }
+ }
+ }
+ if (pdbentry == null)
+ {
+ pdbentry = new PDBEntry();
+ pdbentry.setId(pdbEntryString);
+ pdbentry.setFile(pdbFile);
+ needtoadd = true; // add this new entry to sequence.
+ }
+ // resolve data source
+ // TODO: this code should be a refactored to an io package
+ DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
+ FileFormat.PDB);
+ if (protocol == null)
+ {
+ return false;
+ }
+ if (needtoadd)
+ {
+ pdbentry.setProperty("protocol", protocol);
+ toaddpdb.addPDBId(pdbentry);
+ alFrame.alignPanel.getStructureSelectionManager()
+ .registerPDBEntry(pdbentry);
+ }
+ }
+ return true;
+ }
+
+ public AlignFrameI loadAlignment(String text, int width, int height,
+ String title)
+ {
+ AlignmentI al = null;
+
+ try
+ {
+ FileFormatI format = new IdentifyFile().identify(text,
+ DataSourceType.PASTE);
+ al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE,
+ format);
+ if (al.getHeight() > 0)
+ {
+ return new AlignFrame(al, width, height, title);
+ }
+ } catch (IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ return null;
+ }
+
+ public String getFeatureGroupsOn(AlignFrameI alf)
+ {
+ return arrayToSeparatorList(
+ ((AlignFrame) alf).getFeatureGroups());
+ }
+
+ public void highlightIn(final AlignFrameI alf, final String sequenceId,
+ final String position, final String alignedPosition)
+ {
+ // TODO: could try to highlight in all alignments if alf==null
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ ((AlignFrame) alf).getViewport().getAlignment()
+ .getSequencesArray());
+ final SequenceI sq = matcher.findIdMatch(sequenceId);
+ if (sq != null)
+ {
+ int apos = -1;
+ try
+ {
+ apos = new Integer(position).intValue();
+ apos--;
+ } catch (NumberFormatException ex)
+ {
+ return;
+ }
+ final int pos = apos;
+ // use vamsas listener to broadcast to all listeners in scope
+ if (alignedPosition != null && (alignedPosition.trim().length() == 0
+ || alignedPosition.toLowerCase().indexOf("false") > -1))
+ {
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.getInstance())
+ .mouseOverVamsasSequence(sq, sq.findIndex(pos), null);
+ }
+ });
+ }
+ else
+ {
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.getInstance())
+ .mouseOverVamsasSequence(sq, pos, null);
+ }
+ });
+ }
+ }
+ }
+
+ public void selectIn(final AlignFrameI alf, String sequenceIds,
+ String columns, String sep)
+ {
+ if (sep == null || sep.length() == 0)
+ {
+ sep = separator;
+ }
+ else
+ {
+ if (debug)
+ {
+ System.err.println("Selecting region using separator string '"
+ + separator + "'");
+ }
+ }
+ // deparse fields
+ String[] ids = JalviewAppLoader.separatorListToArray(sequenceIds, sep);
+ String[] cols = JalviewAppLoader.separatorListToArray(columns, sep);
+ final SequenceGroup sel = new SequenceGroup();
+ final ColumnSelection csel = new ColumnSelection();
+ AlignmentI al = ((AlignFrame) alf).getViewport().getAlignment();
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ ((AlignFrame) alf).getViewport().getAlignment()
+ .getSequencesArray());
+ int start = 0, end = al.getWidth(), alw = al.getWidth();
+ boolean seqsfound = true;
+ if (ids != null && ids.length > 0)
+ {
+ seqsfound = false;
+ for (int i = 0; i < ids.length; i++)
+ {
+ if (ids[i].trim().length() == 0)
+ {
+ continue;
+ }
+ SequenceI sq = matcher.findIdMatch(ids[i]);
+ if (sq != null)
+ {
+ seqsfound = true;
+ sel.addSequence(sq, false);
+ }
+ }
+ }
+ boolean inseqpos = false;
+ if (cols != null && cols.length > 0)
+ {
+ boolean seset = false;
+ for (int i = 0; i < cols.length; i++)
+ {
+ String cl = cols[i].trim();
+ if (cl.length() == 0)
+ {
+ continue;
+ }
+ int p;
+ if ((p = cl.indexOf("-")) > -1)
+ {
+ int from = -1, to = -1;
+ try
+ {
+ from = new Integer(cl.substring(0, p)).intValue();
+ from--;
+ } catch (NumberFormatException ex)
+ {
+ System.err.println(
+ "ERROR: Couldn't parse first integer in range element column selection string '"
+ + cl + "' - format is 'from-to'");
+ return;
+ }
+ try
+ {
+ to = new Integer(cl.substring(p + 1)).intValue();
+ to--;
+ } catch (NumberFormatException ex)
+ {
+ System.err.println(
+ "ERROR: Couldn't parse second integer in range element column selection string '"
+ + cl + "' - format is 'from-to'");
+ return;
+ }
+ if (from >= 0 && to >= 0)
+ {
+ // valid range
+ if (from < to)
+ {
+ int t = to;
+ to = from;
+ to = t;
+ }
+ if (!seset)
+ {
+ start = from;
+ end = to;
+ seset = true;
+ }
+ else
+ {
+ // comment to prevent range extension
+ if (start > from)
+ {
+ start = from;
+ }
+ if (end < to)
+ {
+ end = to;
+ }
+ }
+ for (int r = from; r <= to; r++)
+ {
+ if (r >= 0 && r < alw)
+ {
+ csel.addElement(r);
+ }
+ }
+ if (debug)
+ {
+ System.err.println("Range '" + cl + "' deparsed as [" + from
+ + "," + to + "]");
+ }
+ }
+ else
+ {
+ System.err.println("ERROR: Invalid Range '" + cl
+ + "' deparsed as [" + from + "," + to + "]");
+ }
+ }
+ else
+ {
+ int r = -1;
+ try
+ {
+ r = new Integer(cl).intValue();
+ r--;
+ } catch (NumberFormatException ex)
+ {
+ if (cl.toLowerCase().equals("sequence"))
+ {
+ // we are in the dataset sequence's coordinate frame.
+ inseqpos = true;
+ }
+ else
+ {
+ System.err.println(
+ "ERROR: Couldn't parse integer from point selection element of column selection string '"
+ + cl + "'");
+ return;
+ }
+ }
+ if (r >= 0 && r <= alw)
+ {
+ if (!seset)
+ {
+ start = r;
+ end = r;
+ seset = true;
+ }
+ else
+ {
+ // comment to prevent range extension
+ if (start > r)
+ {
+ start = r;
+ }
+ if (end < r)
+ {
+ end = r;
+ }
+ }
+ csel.addElement(r);
+ if (debug)
+ {
+ System.err.println("Point selection '" + cl
+ + "' deparsed as [" + r + "]");
+ }
+ }
+ else
+ {
+ System.err.println("ERROR: Invalid Point selection '" + cl
+ + "' deparsed as [" + r + "]");
+ }
+ }
+ }
+ }
+ if (seqsfound)
+ {
+ // we only propagate the selection when it was the null selection, or the
+ // given sequences were found in the alignment.
+ if (inseqpos && sel.getSize() > 0)
+ {
+ // assume first sequence provides reference frame ?
+ SequenceI rs = sel.getSequenceAt(0);
+ start = rs.findIndex(start);
+ end = rs.findIndex(end);
+ List<Integer> cs = new ArrayList<>(csel.getSelected());
+ csel.clear();
+ for (Integer selectedCol : cs)
+ {
+ csel.addElement(rs.findIndex(selectedCol));
+ }
+ }
+ sel.setStartRes(start);
+ sel.setEndRes(end);
+ EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ ((AlignFrame) alf).select(sel, csel, ((AlignFrame) alf)
+ .getCurrentView().getAlignment().getHiddenColumns());
+ }
+ });
+ }
+ }
+
+ public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
+ {
+ AlignmentI alorder = ((AlignFrame) alf).getViewport().getAlignment();
+ String[] order = new String[alorder.getHeight()];
+ for (int i = 0; i < order.length; i++)
+ {
+ order[i] = alorder.getSequenceAt(i).getName();
+ }
+ return arrayToSeparatorList(order, sep);
+ }
+
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ String format, String suffix)
+ {
+ try
+ {
+ AlignViewport vp = ((AlignFrame) alf).getViewport();
+ FileFormatI theFormat = FileFormats.getInstance().forName(format);
+ boolean seqlimits = (suffix == null
+ || suffix.equalsIgnoreCase("true"));
+ if (vp.getSelectionGroup() != null)
+ {
+ // JBPNote: getSelectionAsNewSequence behaviour has changed - this
+ // method now returns a full copy of sequence data
+ // TODO consider using getSequenceSelection instead here
+ String reply = new AppletFormatAdapter().formatSequences(theFormat,
+ new Alignment(vp.getSelectionAsNewSequence()),
+ seqlimits);
+ return reply;
+ }
+ } catch (IllegalArgumentException ex)
+ {
+ ex.printStackTrace();
+ return "Error retrieving alignment, possibly invalid format specifier: "
+ + format;
+ }
+ return "";
+ }
+
+ public String orderAlignmentBy(AlignFrameI alf, String order,
+ String undoName, String sep)
+ {
+ if (sep == null || sep.length() == 0)
+ {
+ sep = separator;
+ }
+ String[] ids = JalviewAppLoader.separatorListToArray(order, sep);
+ SequenceI[] sqs = null;
+ if (ids != null && ids.length > 0)
+ {
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ ((AlignFrame) alf).getViewport().getAlignment()
+ .getSequencesArray());
+ int s = 0;
+ sqs = new SequenceI[ids.length];
+ for (int i = 0; i < ids.length; i++)
+ {
+ if (ids[i].trim().length() == 0)
+ {
+ continue;
+ }
+ SequenceI sq = matcher.findIdMatch(ids[i]);
+ if (sq != null)
+ {
+ sqs[s++] = sq;
+ }
+ }
+ if (s > 0)
+ {
+ SequenceI[] sqq = new SequenceI[s];
+ System.arraycopy(sqs, 0, sqq, 0, s);
+ sqs = sqq;
+ }
+ else
+ {
+ sqs = null;
+ }
+ }
+ if (sqs == null)
+ {
+ return "";
+ }
+ ;
+ final AlignmentOrder aorder = new AlignmentOrder(sqs);
+
+ if (undoName != null && undoName.trim().length() == 0)
+ {
+ undoName = null;
+ }
+ final String _undoName = undoName;
+ // TODO: deal with synchronization here: cannot raise any events until after
+ // this has returned.
+ return ((AlignFrame) alf).sortBy(aorder, _undoName) ? "true" : "";
+ }
+
+ public String getAlignmentFrom(AlignFrameI alf, String format,
+ String suffix)
+ {
+ try
+ {
+ boolean seqlimits = (suffix == null
+ || suffix.equalsIgnoreCase("true"));
+
+ FileFormatI theFormat = FileFormats.getInstance().forName(format);
+ String reply = new AppletFormatAdapter().formatSequences(theFormat,
+ ((AlignFrame) alf).getViewport().getAlignment(), seqlimits);
+ return reply;
+ } catch (IllegalArgumentException ex)
+ {
+ ex.printStackTrace();
+ return "Error retrieving alignment, possibly invalid format specifier: "
+ + format;
+ }
+ }
+
+ public void loadAnnotationFrom(AlignFrameI alf, String annotation)
+ {
+ if (new AnnotationFile().annotateAlignmentView(
+ ((AlignFrame) alf).getViewport(), annotation,
+ DataSourceType.PASTE))
+ {
+ ((AlignFrame) alf).alignPanel.fontChanged();
+ ((AlignFrame) alf).alignPanel.setScrollValues(0, 0);
+ }
+ else
+ {
+ ((AlignFrame) alf).parseFeaturesFile(annotation,
+ DataSourceType.PASTE);
+ }
+ }
+
+ public boolean loadFeaturesFrom(AlignFrameI alf, String features,
+ boolean autoenabledisplay)
+ {
+ boolean ret = ((AlignFrame) alf).parseFeaturesFile(features,
+ DataSourceType.PASTE);
+ if (!ret)
+ {
+ return false;
+ }
+ if (autoenabledisplay)
+ {
+ ((AlignFrame) alf).getViewport().setShowSequenceFeatures(true);
+ // this next was for a checkbox in JalviewLite
+ // ((AlignFrame) alf).getViewport().sequenceFeatures.setState(true);
+ }
+ return true;
+ }
+
+ public String getFeaturesFrom(AlignFrameI alf, String format)
+ {
+ AlignFrame f = ((AlignFrame) alf);
+
+ String features;
+ FeaturesFile formatter = new FeaturesFile();
+ if (format.equalsIgnoreCase("Jalview"))
+ {
+ features = formatter.printJalviewFormat(
+ f.getViewport().getAlignment().getSequencesArray(),
+ f.alignPanel.getFeatureRenderer(), true);
+ }
+ else
+ {
+ features = formatter.printGffFormat(
+ f.getViewport().getAlignment().getSequencesArray(),
+ f.alignPanel.getFeatureRenderer(), true);
+ }
+
+ if (features == null)
+ {
+ features = "";
+ }
+ return features;
+
+ }
+
+ public String getAnnotationFrom(AlignFrameI alf)
+ {
+ AlignFrame f = (AlignFrame) alf;
+ String annotation = new AnnotationFile()
+ .printAnnotationsForView(f.getViewport());
+ return annotation;
+ }
+
+ public AlignFrameI newViewFrom(AlignFrameI alf, String name)
+ {
+ return (AlignFrameI) ((AlignFrame) alf).newView(name, true);
+ }
+
+ public String[] separatorListToArray(String list)
+ {
+ return separatorListToArray(list, separator);
+ }
+
+ public Object[] getSelectionForListener(AlignFrameI currentFrame,
+ SequenceGroup seqsel, ColumnSelection colsel,
+ HiddenColumns hidden, SelectionSource source, Object alignFrame)
+ {
+ // System.err.println("Testing selection event relay to
+ // jsfunction:"+_listener);
+ String setid = "";
+ AlignFrame src = (AlignFrame) alignFrame;
+ if (source != null)
+ {
+ if (source instanceof AlignViewport
+ && ((AlignFrame) currentFrame).getViewport() == source)
+ {
+ // should be valid if it just generated an event!
+ src = (AlignFrame) currentFrame;
+
+ }
+ }
+ String[] seqs = new String[] {};
+ String[] cols = new String[] {};
+ int strt = 0, end = (src == null) ? -1
+ : src.alignPanel.av.getAlignment().getWidth();
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ seqs = new String[seqsel.getSize()];
+ for (int i = 0; i < seqs.length; i++)
+ {
+ seqs[i] = seqsel.getSequenceAt(i).getName();
+ }
+ if (strt < seqsel.getStartRes())
+ {
+ strt = seqsel.getStartRes();
+ }
+ if (end == -1 || end > seqsel.getEndRes())
+ {
+ end = seqsel.getEndRes();
+ }
+ }
+ if (colsel != null && !colsel.isEmpty())
+ {
+ if (end == -1)
+ {
+ end = colsel.getMax() + 1;
+ }
+ cols = new String[colsel.getSelected().size()];
+ for (int i = 0; i < cols.length; i++)
+ {
+ cols[i] = "" + (1 + colsel.getSelected().get(i).intValue());
+ }
+ }
+ else
+ {
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ // send a valid range, otherwise we send the empty selection
+ cols = new String[2];
+ cols[0] = "" + (1 + strt) + "-" + (1 + end);
+ }
+ }
+ return new Object[] { src, setid, arrayToSeparatorList(seqs),
+ arrayToSeparatorList(cols) };
+ }
+
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff