X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=7881ec9d1af7aca6dd9172bf01d7da1b241b341a;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=777d71bbeef0d60da9df32b6a636b08530bdaed2;hpb=3642de417a2240bef7edc3810a0d0cbe24b03da3;p=jalview.git diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java index 777d71b..7881ec9 100644 --- a/src/jalview/gui/VamsasApplication.java +++ b/src/jalview/gui/VamsasApplication.java @@ -1,26 +1,29 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.VamsasAppDatastore; @@ -28,24 +31,24 @@ import jalview.structure.SelectionListener; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasListener; +import jalview.structure.VamsasSource; +import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.io.File; import java.io.IOException; -import java.util.Enumeration; import java.util.Hashtable; import java.util.IdentityHashMap; import java.util.Iterator; import javax.swing.JInternalFrame; -import javax.swing.JOptionPane; import uk.ac.vamsas.client.ClientHandle; import uk.ac.vamsas.client.IClient; import uk.ac.vamsas.client.IClientDocument; import uk.ac.vamsas.client.InvalidSessionDocumentException; -import uk.ac.vamsas.client.NoDefaultSessionException; import uk.ac.vamsas.client.UserHandle; import uk.ac.vamsas.client.VorbaId; import uk.ac.vamsas.client.picking.IMessageHandler; @@ -62,7 +65,7 @@ import uk.ac.vamsas.objects.core.Seg; * @author jimp * */ -public class VamsasApplication implements SelectionSource +public class VamsasApplication implements SelectionSource, VamsasSource { IClient vclient = null; @@ -72,12 +75,13 @@ public class VamsasApplication implements SelectionSource Desktop jdesktop = null; // our jalview desktop reference - private boolean inInitialUpdate=true; + private boolean inInitialUpdate = true; // Cache.preferences for vamsas client session arena // preferences for check for default session at startup. // user and organisation stuff. - public VamsasApplication(Desktop jdesktop, File sessionPath, String sessionName) + public VamsasApplication(Desktop jdesktop, File sessionPath, + String sessionName) { // JBPNote: // we should create a session URI from the sessionPath and pass it to @@ -86,7 +90,6 @@ public class VamsasApplication implements SelectionSource initClientSession(null, sessionPath, sessionName); } - private static uk.ac.vamsas.client.IClientFactory getClientFactory() throws IOException { @@ -138,10 +141,11 @@ public class VamsasApplication implements SelectionSource */ private void initClientSession(String sess, File vamsasDocument) { - initClientSession(sess,vamsasDocument,null); + initClientSession(sess, vamsasDocument, null); } - private boolean initClientSession(String sess, File vamsasDocument, String newDocSessionName) + private boolean initClientSession(String sess, File vamsasDocument, + String newDocSessionName) { try { @@ -152,28 +156,30 @@ public class VamsasApplication implements SelectionSource { if (sess != null) { - throw new Error( - "Implementation Error - cannot import existing vamsas document into an existing session, Yet!"); + throw new Error(MessageManager.getString( + "error.implementation_error_cannot_import_vamsas_doc")); } try { - if (newDocSessionName!=null) + if (newDocSessionName != null) { vclient = clientfactory.openAsNewSessionIClient(app, - vamsasDocument,newDocSessionName); - } else { + vamsasDocument, newDocSessionName); + } + else + { vclient = clientfactory.openAsNewSessionIClient(app, - vamsasDocument); + vamsasDocument); } } catch (InvalidSessionDocumentException e) { - JOptionPane - .showInternalMessageDialog( - Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, - "VAMSAS Document could not be opened as a new session - please choose another", - "VAMSAS Document Import Failed", - JOptionPane.ERROR_MESSAGE); + MessageManager.getString( + "label.vamsas_doc_couldnt_be_opened_as_new_session"), + MessageManager + .getString("label.vamsas_document_import_failed"), + JvOptionPane.ERROR_MESSAGE); } } @@ -195,8 +201,8 @@ public class VamsasApplication implements SelectionSource } catch (Exception e) { - jalview.bin.Cache.log - .error("Couldn't instantiate vamsas client !", e); + Cache.error("Couldn't instantiate vamsas client !", + e); return false; } return true; @@ -219,16 +225,14 @@ public class VamsasApplication implements SelectionSource } } catch (Error e) { - Cache.log - .warn( - "Probable SERIOUS VAMSAS client incompatibility - carrying on regardless", - e); + Cache.warn( + "Probable SERIOUS VAMSAS client incompatibility - carrying on regardless", + e); } catch (Exception e) { - Cache.log - .warn( - "Probable VAMSAS client incompatibility - carrying on regardless", - e); + Cache.warn( + "Probable VAMSAS client incompatibility - carrying on regardless", + e); } } @@ -239,8 +243,8 @@ public class VamsasApplication implements SelectionSource */ private ClientHandle getJalviewHandle() { - return new ClientHandle("jalview.bin.Jalview", jalview.bin.Cache - .getProperty("VERSION")); + return new ClientHandle("jalview.bin.Jalview", + Cache.getProperty("VERSION")); } /** @@ -261,18 +265,18 @@ public class VamsasApplication implements SelectionSource if (!inSession()) { throw new Error( - "Impementation error! Vamsas Operations when client not initialised and connected."); + "Implementation error! Vamsas Operations when client not initialised and connected"); } addDocumentUpdateHandler(); addStoreDocumentHandler(); startSession(); inInitialUpdate = true; - Cache.log - .debug("Jalview loading the Vamsas Session for the first time."); + Cache.debug( + "Jalview loading the Vamsas Session for the first time."); dealWithDocumentUpdate(false); // we don't push an update out to the inInitialUpdate = false; // document yet. - Cache.log.debug("... finished update for the first time."); + Cache.debug("... finished update for the first time."); } /** @@ -302,10 +306,9 @@ public class VamsasApplication implements SelectionSource } } catch (Exception e) { - Cache.log - .warn( - "Exception whilst refreshing jalview windows after a vamsas document update.", - e); + Cache.warn( + "Exception whilst refreshing jalview windows after a vamsas document update.", + e); } } @@ -314,13 +317,13 @@ public class VamsasApplication implements SelectionSource Thread udthread = new Thread(new Runnable() { + @Override public void run() { - Cache.log.info("Jalview updating to the Vamsas Session."); + Cache.info("Jalview updating to the Vamsas Session."); - dealWithDocumentUpdate(true); - Cache.log.info("Jalview finished updating to the Vamsas Session."); + Cache.info("Jalview finished updating to the Vamsas Session."); } }); @@ -347,8 +350,10 @@ public class VamsasApplication implements SelectionSource public void end_session(boolean promptUser) { if (!inSession()) - throw new Error("Jalview not connected to Vamsas session."); - Cache.log.info("Jalview disconnecting from the Vamsas Session."); + { + throw new Error("Jalview not connected to Vamsas session"); + } + Cache.info("Jalview disconnecting from the Vamsas Session."); try { if (joinedSession) @@ -356,13 +361,13 @@ public class VamsasApplication implements SelectionSource boolean ourprompt = this.promptUser; this.promptUser = promptUser; vclient.finalizeClient(); - Cache.log.info("Jalview has left the session."); + Cache.info("Jalview has left the session."); this.promptUser = ourprompt; // restore default value } else { - Cache.log - .warn("JV Client leaving a session that's its not joined yet."); + Cache.warn( + "JV Client leaving a session that's its not joined yet."); } joinedSession = false; vclient = null; @@ -372,13 +377,13 @@ public class VamsasApplication implements SelectionSource vobj2jv = null; } catch (Exception e) { - Cache.log.error("Vamsas Session finalization threw exceptions!", e); + Cache.error("Vamsas Session finalization threw exceptions!", e); } } public void updateJalview(IClientDocument cdoc) { - Cache.log.debug("Jalview updating from sesion document .."); + Cache.debug("Jalview updating from sesion document .."); ensureJvVamsas(); VamsasAppDatastore vds = new VamsasAppDatastore(cdoc, vobj2jv, jv2vobj, baseProvEntry(), alRedoState); @@ -387,7 +392,7 @@ public class VamsasApplication implements SelectionSource vds.updateToJalview(); } catch (Exception e) { - Cache.log.error("Failed to update Jalview from vamsas document.", e); + Cache.error("Failed to update Jalview from vamsas document.", e); } try { @@ -399,10 +404,10 @@ public class VamsasApplication implements SelectionSource } } catch (Exception e) { - Cache.log.error( + Cache.error( "Exception when updating Jalview settings from Appdata.", e); } - Cache.log.debug(".. finished updating from sesion document."); + Cache.debug(".. finished updating from sesion document."); } @@ -441,7 +446,7 @@ public class VamsasApplication implements SelectionSource */ public int updateVamsasDocument(IClientDocument doc) { - int storedviews=0; + int storedviews = 0; ensureJvVamsas(); errorsDuringUpdate = false; errorsDuringAppUpdate = false; @@ -476,11 +481,10 @@ public class VamsasApplication implements SelectionSource } catch (Exception e) { errorsDuringUpdate = true; - Cache.log.error("Exception synchronizing " - + af.getTitle() + Cache.error("Exception synchronizing " + af.getTitle() + " " - + (af.getViewport().viewName == null ? "" : " view " - + af.getViewport().viewName) + + (af.getViewport().getViewName() == null ? "" + : " view " + af.getViewport().getViewName()) + " to document.", e); stored = false; } @@ -515,7 +519,7 @@ public class VamsasApplication implements SelectionSource } } catch (Exception e) { - Cache.log.error("Exception synchronizing Views to Document :", e); + Cache.error("Exception synchronizing Views to Document :", e); errorsDuringUpdate = true; } @@ -532,7 +536,7 @@ public class VamsasApplication implements SelectionSource } } catch (Exception e) { - Cache.log.error("Client Appdata Write exception", e); + Cache.error("Client Appdata Write exception", e); errorsDuringAppUpdate = true; } vds.clearSkipList(); @@ -554,38 +558,38 @@ public class VamsasApplication implements SelectionSource * * @param fromJalview * true to update from jalview to the vamsas document - * @return total number of stored alignments in the document after the update + * @return total number of stored alignments in the document after the update */ protected int dealWithDocumentUpdate(boolean fromJalview) { int storedviews = 0; // called by update handler for document update. - Cache.log.debug("Updating jalview from changed vamsas document."); + Cache.debug("Updating jalview from changed vamsas document."); disableGui(true); try { long time = System.currentTimeMillis(); IClientDocument cdoc = vclient.getClientDocument(); - if (Cache.log.isDebugEnabled()) + if (Cache.isDebugEnabled()) { - Cache.log.debug("Time taken to get ClientDocument = " + Cache.debug("Time taken to get ClientDocument = " + (System.currentTimeMillis() - time)); time = System.currentTimeMillis(); } if (fromJalview) { - storedviews+=updateVamsasDocument(cdoc); - if (Cache.log.isDebugEnabled()) + storedviews += updateVamsasDocument(cdoc); + if (Cache.isDebugEnabled()) { - Cache.log - .debug("Time taken to update Vamsas Document from jalview\t= " + Cache.debug( + "Time taken to update Vamsas Document from jalview\t= " + (System.currentTimeMillis() - time)); time = System.currentTimeMillis(); } cdoc.setVamsasRoots(cdoc.getVamsasRoots()); - if (Cache.log.isDebugEnabled()) + if (Cache.isDebugEnabled()) { - Cache.log.debug("Time taken to set Document Roots\t\t= " + Cache.debug("Time taken to set Document Roots\t\t= " + (System.currentTimeMillis() - time)); time = System.currentTimeMillis(); } @@ -593,19 +597,19 @@ public class VamsasApplication implements SelectionSource else { updateJalview(cdoc); - if (Cache.log.isDebugEnabled()) + if (Cache.isDebugEnabled()) { - Cache.log - .debug("Time taken to update Jalview from vamsas document Roots\t= " + Cache.debug( + "Time taken to update Jalview from vamsas document Roots\t= " + (System.currentTimeMillis() - time)); time = System.currentTimeMillis(); } } vclient.updateDocument(cdoc); - if (Cache.log.isDebugEnabled()) + if (Cache.isDebugEnabled()) { - Cache.log.debug("Time taken to update Session Document\t= " + Cache.debug("Time taken to update Session Document\t= " + (System.currentTimeMillis() - time)); time = System.currentTimeMillis(); } @@ -617,9 +621,9 @@ public class VamsasApplication implements SelectionSource // recover object map backup, since its probably corrupted with references // to Vobjects that don't exist anymore. recover_objectMappingBackup(); - storedviews=0; + storedviews = 0; } - Cache.log.debug("Finished updating from document change."); + Cache.debug("Finished updating from document change."); disableGui(false); return storedviews; } @@ -629,14 +633,15 @@ public class VamsasApplication implements SelectionSource final VamsasApplication client = this; vclient.addDocumentUpdateHandler(new PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { - Cache.log.debug("Dealing with document update event."); + Cache.debug("Dealing with document update event."); client.dealWithDocumentUpdate(false); - Cache.log.debug("finished dealing with event."); + Cache.debug("finished dealing with event."); } }); - Cache.log.debug("Added Jalview handler for vamsas document updates."); + Cache.debug("Added Jalview handler for vamsas document updates."); } private void addStoreDocumentHandler() @@ -646,43 +651,43 @@ public class VamsasApplication implements SelectionSource uk.ac.vamsas.client.Events.DOCUMENT_REQUESTTOCLOSE, new PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (client.promptUser) { - Cache.log - .debug("Asking user if the vamsas session should be stored."); - int reply = JOptionPane - .showInternalConfirmDialog( - Desktop.desktop, - "The current VAMSAS session has unsaved data - do you want to save it ?", - "VAMSAS Session Shutdown", - JOptionPane.YES_NO_OPTION, - JOptionPane.QUESTION_MESSAGE); - - if (reply == JOptionPane.YES_OPTION) + Cache.debug( + "Asking user if the vamsas session should be stored."); + int reply = JvOptionPane.showInternalConfirmDialog( + Desktop.desktop, + "The current VAMSAS session has unsaved data - do you want to save it ?", + "VAMSAS Session Shutdown", + JvOptionPane.YES_NO_OPTION, + JvOptionPane.QUESTION_MESSAGE); + + if (reply == JvOptionPane.YES_OPTION) { - Cache.log.debug("Prompting for vamsas store filename."); + Cache.debug("Prompting for vamsas store filename."); Desktop.instance.vamsasSave_actionPerformed(null); - Cache.log - .debug("Finished attempt at storing document."); + Cache.debug("Finished attempt at storing document."); } - Cache.log - .debug("finished dealing with REQUESTTOCLOSE event."); + Cache.debug( + "finished dealing with REQUESTTOCLOSE event."); } else { - Cache.log - .debug("Ignoring store document request (promptUser==false)"); + Cache.debug( + "Ignoring store document request (promptUser==false)"); } } }); - Cache.log.debug("Added Jalview handler for vamsas document updates."); + Cache.debug("Added Jalview handler for vamsas document updates."); } public void disableGui(boolean b) { - Desktop.instance.setVamsasUpdate(b); + // JAL-3311 TODO: remove this class! + // Desktop.instance.setVamsasUpdate(b); } Hashtable _backup_vobj2jv; @@ -709,13 +714,14 @@ public class VamsasApplication implements SelectionSource { if (_backup_vobj2jv == null) { - if (inInitialUpdate) { + if (inInitialUpdate) + { // nothing to recover so just return; } - + throw new Error( - "IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made."); + "IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made"); } jv2vobj.clear(); Iterator el = _backup_jv2vobj.entrySet().iterator(); @@ -749,19 +755,20 @@ public class VamsasApplication implements SelectionSource } catch (Exception e) { // Complain to GUI - Cache.log.error("Failed to join vamsas session.", e); + Cache.error("Failed to join vamsas session.", e); vclient = null; } try { final IPickManager pm = vclient.getPickManager(); final StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(); - final SelectionSource me = this; + .getStructureSelectionManager(Desktop.instance); + final VamsasApplication me = this; pm.registerMessageHandler(new IMessageHandler() { String last = null; + @Override public void handleMessage(Message message) { if (vobj2jv == null) @@ -777,20 +784,20 @@ public class VamsasApplication implements SelectionSource { return; } - // if (Cache.log.isDebugEnabled()) + // if (Cache.isDebugEnabled()) // { - // Cache.log.debug("Received MouseOverMessage "+mm.getVorbaID()+" + // Cache.debug("Received MouseOverMessage "+mm.getVorbaID()+" // "+mm.getPosition()); // } Object jvobj = vobj2jv.get(mm.getVorbaID()); if (jvobj != null && jvobj instanceof SequenceI) { last = mstring; - // Cache.log.debug("Handling Mouse over "+mm.getVorbaID()+" + // Cache.debug("Handling Mouse over "+mm.getVorbaID()+" // bound to "+jvobj+" at "+mm.getPosition()); // position is character position in aligned sequence - ssm.mouseOverVamsasSequence((SequenceI) jvobj, mm - .getPosition()); + ssm.mouseOverVamsasSequence((SequenceI) jvobj, + mm.getPosition(), me); } } if (message instanceof uk.ac.vamsas.client.picking.SelectionMessage) @@ -805,7 +812,7 @@ public class VamsasApplication implements SelectionSource { // TODO: rationalise : can only clear a selection over a // referred to object - ssm.sendSelection(null, null, me); + ssm.sendSelection(null, null, null, me); return; } Class type = null; @@ -910,23 +917,22 @@ public class VamsasApplication implements SelectionSource for (int p = 0; p < prange.length; p += 2) { int d = (prange[p] <= prange[p + 1]) ? 1 : -1; - // try to join up adjacent columns to make a larger - // selection - // lower and upper bounds - int l = (d < 0) ? 1 : 0; - int u = (d > 0) ? 1 : 0; - - if (jselection.getStartRes() > 0 - && prange[p + l] == jselection - .getStartRes()) - { - jselection.setStartRes(prange[p + l] - 1); - } - if (jselection.getEndRes() <= maxWidth - && prange[p + u] == (jselection.getEndRes() + 2)) - { - jselection.setEndRes(prange[p + u] - 1); - } + // try to join up adjacent columns to make a larger + // selection + // lower and upper bounds + int l = (d < 0) ? 1 : 0; + int u = (d > 0) ? 1 : 0; + + if (jselection.getStartRes() > 0 + && prange[p + l] == jselection.getStartRes()) + { + jselection.setStartRes(prange[p + l] - 1); + } + if (jselection.getEndRes() <= maxWidth && prange[p + + u] == (jselection.getEndRes() + 2)) + { + jselection.setEndRes(prange[p + u] - 1); + } // mark all the columns in the range. for (int sr = prange[p], er = prange[p + 1], de = er + d; sr != de; sr += d) @@ -940,7 +946,7 @@ public class VamsasApplication implements SelectionSource } if (send) { - ssm.sendSelection(jselection, colsel, me); + ssm.sendSelection(jselection, colsel, null, me); } // discard message. for (int c = 0; c < jvobjs.length; c++) @@ -959,17 +965,21 @@ public class VamsasApplication implements SelectionSource int i = -1; - public void mouseOver(SequenceI seq, int index) + @Override + public void mouseOverSequence(SequenceI seq, int index, + VamsasSource source) { if (jv2vobj == null) + { return; + } if (seq != last || i != index) { VorbaId v = (VorbaId) jv2vobj.get(seq); if (v != null) { // this should really be a trace message. - // Cache.log.debug("Mouse over " + v.getId() + " bound to " + // Cache.debug("Mouse over " + v.getId() + " bound to " // + seq + " at " + index); last = seq; i = index; @@ -983,13 +993,15 @@ public class VamsasApplication implements SelectionSource selecter = new SelectionListener() { + @Override public void selection(SequenceGroup seqsel, - ColumnSelection colsel, SelectionSource source) + ColumnSelection colsel, HiddenColumns hidden, + SelectionSource source) { if (vobj2jv == null) { - Cache.log - .warn("Selection listener still active for dead session."); + Cache.warn( + "Selection listener still active for dead session."); // not in a session. return; } @@ -998,19 +1010,21 @@ public class VamsasApplication implements SelectionSource AlignmentI visal = null; if (source instanceof AlignViewport) { - visal = ((AlignViewport) source).getAlignment(); + visal = ((AlignmentViewport) source).getAlignment(); } SelectionMessage sm = null; if ((seqsel == null || seqsel.getSize() == 0) - && (colsel == null || colsel.getSelected() == null || colsel - .getSelected().size() == 0)) + && (colsel == null || colsel.getSelected() == null + || colsel.getSelected().size() == 0)) { if (source instanceof AlignViewport) { // the empty selection. - sm = new SelectionMessage("jalview", new String[] - { ((AlignViewport) source).getSequenceSetId() }, null, - true); + sm = new SelectionMessage("jalview", + new String[] + { ((AlignmentViewport) source) + .getSequenceSetId() }, + null, true); } else { @@ -1022,10 +1036,8 @@ public class VamsasApplication implements SelectionSource { String[] vobj = new String[seqsel.getSize()]; int o = 0; - Enumeration sels = seqsel.getSequences(null).elements(); - while (sels.hasMoreElements()) + for (SequenceI sel : seqsel.getSequences(null)) { - SequenceI sel = (SequenceI) sels.nextElement(); VorbaId v = (VorbaId) jv2vobj.get(sel); if (v != null) { @@ -1052,25 +1064,25 @@ public class VamsasApplication implements SelectionSource { // gather selected columns outwith the sequence positions // too - Enumeration cols = colsel.getSelected().elements(); - while (cols.hasMoreElements()) + for (Integer ival : colsel.getSelected()) { - int ival = ((Integer) cols.nextElement()).intValue(); Pos p = new Pos(); - p.setI(ival + 1); + p.setI(ival.intValue() + 1); range.addPos(p); } } else { - int[] intervals = colsel.getVisibleContigs(seqsel - .getStartRes(), seqsel.getEndRes() + 1); - for (int iv = 0; iv < intervals.length; iv += 2) + Iterator intervals = hidden + .getVisContigsIterator(seqsel.getStartRes(), + seqsel.getEndRes() + 1, false); + while (intervals.hasNext()) { + int[] region = intervals.next(); Seg s = new Seg(); - s.setStart(intervals[iv] + 1); // vamsas indices begin at - // 1, not zero. - s.setEnd(intervals[iv + 1] + 1); + s.setStart(region[0] + 1); // vamsas indices begin at 1, + // not zero. + s.setEnd(region[1] + 1); s.setInclusive(true); range.addSeg(s); } @@ -1088,7 +1100,7 @@ public class VamsasApplication implements SelectionSource if (sm != null) { sm.validate(); // debug - Cache.log.debug("Selection Message\n" + sm.getRawMessage()); + Cache.debug("Selection Message\n" + sm.getRawMessage()); pm.sendMessage(sm); } } @@ -1099,7 +1111,7 @@ public class VamsasApplication implements SelectionSource ssm.addSelectionListener(selecter); } catch (Exception e) { - Cache.log.error("Failed to init Vamsas Picking", e); + Cache.error("Failed to init Vamsas Picking", e); } } }