+++ /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