X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;fp=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=dabec6d6e8eb5a8c51c2565a6496b6e6cf3a7442;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=6003416ea2f11e477b51b2c53921173b6c2af55f;hpb=914a9aaf5a2eeb3cdedf136c2e6b4b6e4b5d6174;p=jalview.git diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java index 6003416..dabec6d 100644 --- a/src/jalview/gui/VamsasApplication.java +++ b/src/jalview/gui/VamsasApplication.java @@ -21,6 +21,7 @@ package jalview.gui; import jalview.bin.Cache; +import jalview.bin.Console; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; @@ -201,8 +202,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource } catch (Exception e) { - jalview.bin.Cache.log.error("Couldn't instantiate vamsas client !", - e); + Console.error("Couldn't instantiate vamsas client !", e); return false; } return true; @@ -225,12 +225,12 @@ public class VamsasApplication implements SelectionSource, VamsasSource } } catch (Error e) { - Cache.log.warn( + Console.warn( "Probable SERIOUS VAMSAS client incompatibility - carrying on regardless", e); } catch (Exception e) { - Cache.log.warn( + Console.warn( "Probable VAMSAS client incompatibility - carrying on regardless", e); } @@ -244,7 +244,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource private ClientHandle getJalviewHandle() { return new ClientHandle("jalview.bin.Jalview", - jalview.bin.Cache.getProperty("VERSION")); + Cache.getProperty("VERSION")); } /** @@ -264,19 +264,18 @@ public class VamsasApplication implements SelectionSource, VamsasSource { if (!inSession()) { - throw new Error(MessageManager.getString( - "error.implementation_error_vamsas_operation_not_init")); + throw new Error( + "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."); + Console.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."); + Console.debug("... finished update for the first time."); } /** @@ -306,7 +305,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource } } catch (Exception e) { - Cache.log.warn( + Console.warn( "Exception whilst refreshing jalview windows after a vamsas document update.", e); } @@ -320,10 +319,10 @@ public class VamsasApplication implements SelectionSource, VamsasSource @Override public void run() { - Cache.log.info("Jalview updating to the Vamsas Session."); + Console.info("Jalview updating to the Vamsas Session."); dealWithDocumentUpdate(true); - Cache.log.info("Jalview finished updating to the Vamsas Session."); + Console.info("Jalview finished updating to the Vamsas Session."); } }, "UpdateVamsas"); @@ -351,10 +350,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource { if (!inSession()) { - throw new Error(MessageManager - .getString("error.jalview_no_connected_vamsas_session")); + throw new Error("Jalview not connected to Vamsas session"); } - Cache.log.info("Jalview disconnecting from the Vamsas Session."); + Console.info("Jalview disconnecting from the Vamsas Session."); try { if (joinedSession) @@ -362,12 +360,12 @@ public class VamsasApplication implements SelectionSource, VamsasSource boolean ourprompt = this.promptUser; this.promptUser = promptUser; vclient.finalizeClient(); - Cache.log.info("Jalview has left the session."); + Console.info("Jalview has left the session."); this.promptUser = ourprompt; // restore default value } else { - Cache.log.warn( + Console.warn( "JV Client leaving a session that's its not joined yet."); } joinedSession = false; @@ -378,13 +376,13 @@ public class VamsasApplication implements SelectionSource, VamsasSource vobj2jv = null; } catch (Exception e) { - Cache.log.error("Vamsas Session finalization threw exceptions!", e); + Console.error("Vamsas Session finalization threw exceptions!", e); } } public void updateJalview(IClientDocument cdoc) { - Cache.log.debug("Jalview updating from sesion document .."); + Console.debug("Jalview updating from sesion document .."); ensureJvVamsas(); VamsasAppDatastore vds = new VamsasAppDatastore(cdoc, vobj2jv, jv2vobj, baseProvEntry(), alRedoState); @@ -393,7 +391,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource vds.updateToJalview(); } catch (Exception e) { - Cache.log.error("Failed to update Jalview from vamsas document.", e); + Console.error("Failed to update Jalview from vamsas document.", e); } try { @@ -405,10 +403,10 @@ public class VamsasApplication implements SelectionSource, VamsasSource } } catch (Exception e) { - Cache.log.error( + Console.error( "Exception when updating Jalview settings from Appdata.", e); } - Cache.log.debug(".. finished updating from sesion document."); + Console.debug(".. finished updating from sesion document."); } @@ -482,10 +480,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource } catch (Exception e) { errorsDuringUpdate = true; - Cache.log.error("Exception synchronizing " + af.getTitle() - + " " - + (af.getViewport().viewName == null ? "" - : " view " + af.getViewport().viewName) + Console.error("Exception synchronizing " + af.getTitle() + " " + + (af.getViewport().getViewName() == null ? "" + : " view " + af.getViewport().getViewName()) + " to document.", e); stored = false; } @@ -520,7 +517,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource } } catch (Exception e) { - Cache.log.error("Exception synchronizing Views to Document :", e); + Console.error("Exception synchronizing Views to Document :", e); errorsDuringUpdate = true; } @@ -537,7 +534,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource } } catch (Exception e) { - Cache.log.error("Client Appdata Write exception", e); + Console.error("Client Appdata Write exception", e); errorsDuringAppUpdate = true; } vds.clearSkipList(); @@ -565,32 +562,32 @@ public class VamsasApplication implements SelectionSource, VamsasSource { int storedviews = 0; // called by update handler for document update. - Cache.log.debug("Updating jalview from changed vamsas document."); + Console.debug("Updating jalview from changed vamsas document."); disableGui(true); try { long time = System.currentTimeMillis(); IClientDocument cdoc = vclient.getClientDocument(); - if (Cache.log.isDebugEnabled()) + if (Console.isDebugEnabled()) { - Cache.log.debug("Time taken to get ClientDocument = " + Console.debug("Time taken to get ClientDocument = " + (System.currentTimeMillis() - time)); time = System.currentTimeMillis(); } if (fromJalview) { storedviews += updateVamsasDocument(cdoc); - if (Cache.log.isDebugEnabled()) + if (Console.isDebugEnabled()) { - Cache.log.debug( + Console.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 (Console.isDebugEnabled()) { - Cache.log.debug("Time taken to set Document Roots\t\t= " + Console.debug("Time taken to set Document Roots\t\t= " + (System.currentTimeMillis() - time)); time = System.currentTimeMillis(); } @@ -598,9 +595,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource else { updateJalview(cdoc); - if (Cache.log.isDebugEnabled()) + if (Console.isDebugEnabled()) { - Cache.log.debug( + Console.debug( "Time taken to update Jalview from vamsas document Roots\t= " + (System.currentTimeMillis() - time)); time = System.currentTimeMillis(); @@ -608,9 +605,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource } vclient.updateDocument(cdoc); - if (Cache.log.isDebugEnabled()) + if (Console.isDebugEnabled()) { - Cache.log.debug("Time taken to update Session Document\t= " + Console.debug("Time taken to update Session Document\t= " + (System.currentTimeMillis() - time)); time = System.currentTimeMillis(); } @@ -624,7 +621,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource recover_objectMappingBackup(); storedviews = 0; } - Cache.log.debug("Finished updating from document change."); + Console.debug("Finished updating from document change."); disableGui(false); return storedviews; } @@ -637,12 +634,12 @@ public class VamsasApplication implements SelectionSource, VamsasSource @Override public void propertyChange(PropertyChangeEvent evt) { - Cache.log.debug("Dealing with document update event."); + Console.debug("Dealing with document update event."); client.dealWithDocumentUpdate(false); - Cache.log.debug("finished dealing with event."); + Console.debug("finished dealing with event."); } }); - Cache.log.debug("Added Jalview handler for vamsas document updates."); + Console.debug("Added Jalview handler for vamsas document updates."); } private void addStoreDocumentHandler() @@ -657,7 +654,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource { if (client.promptUser) { - Cache.log.debug( + Console.debug( "Asking user if the vamsas session should be stored."); int reply = JvOptionPane.showInternalConfirmDialog( Desktop.desktop, @@ -668,27 +665,27 @@ public class VamsasApplication implements SelectionSource, VamsasSource if (reply == JvOptionPane.YES_OPTION) { - Cache.log.debug("Prompting for vamsas store filename."); + Console.debug("Prompting for vamsas store filename."); Desktop.instance.vamsasSave_actionPerformed(null); - Cache.log - .debug("Finished attempt at storing document."); + Console.debug("Finished attempt at storing document."); } - Cache.log.debug( + Console.debug( "finished dealing with REQUESTTOCLOSE event."); } else { - Cache.log.debug( + Console.debug( "Ignoring store document request (promptUser==false)"); } } }); - Cache.log.debug("Added Jalview handler for vamsas document updates."); + Console.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; @@ -721,8 +718,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource return; } - throw new Error(MessageManager.getString( - "error.implementation_error_cannot_recover_vamsas_object_mappings")); + throw new Error( + "IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made"); } jv2vobj.clear(); Iterator el = _backup_jv2vobj.entrySet().iterator(); @@ -756,7 +753,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource } catch (Exception e) { // Complain to GUI - Cache.log.error("Failed to join vamsas session.", e); + Console.error("Failed to join vamsas session.", e); vclient = null; } try @@ -785,16 +782,16 @@ public class VamsasApplication implements SelectionSource, VamsasSource { 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, @@ -980,7 +977,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource 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; @@ -1001,7 +998,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource { if (vobj2jv == null) { - Cache.log.warn( + Console.warn( "Selection listener still active for dead session."); // not in a session. return; @@ -1074,16 +1071,16 @@ public class VamsasApplication implements SelectionSource, VamsasSource } else { - // int[] intervals = colsel.getVisibleContigs( - // seqsel.getStartRes(), seqsel.getEndRes() + 1); - int[] intervals = hidden.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); } @@ -1101,7 +1098,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource if (sm != null) { sm.validate(); // debug - Cache.log.debug("Selection Message\n" + sm.getRawMessage()); + Console.debug("Selection Message\n" + sm.getRawMessage()); pm.sendMessage(sm); } } @@ -1112,7 +1109,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource ssm.addSelectionListener(selecter); } catch (Exception e) { - Cache.log.error("Failed to init Vamsas Picking", e); + Console.error("Failed to init Vamsas Picking", e); } } }