X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=c094b1c362ffce4ffbe320cf23b771e5ee2bb7d1;hb=7e82e1fed011077e5cd4cc40ac8ad3519d7c47a8;hp=4630fd1e9db67edfb3dc685ebb56cb73ac74f749;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java index 4630fd1..c094b1c 100644 --- a/src/jalview/gui/VamsasApplication.java +++ b/src/jalview/gui/VamsasApplication.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -23,6 +23,7 @@ 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; @@ -43,7 +44,6 @@ 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; @@ -156,9 +156,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource { if (sess != null) { - throw new Error( - MessageManager - .getString("error.implementation_error_cannot_import_vamsas_doc")); + throw new Error(MessageManager.getString( + "error.implementation_error_cannot_import_vamsas_doc")); } try { @@ -174,15 +173,13 @@ public class VamsasApplication implements SelectionSource, VamsasSource } } catch (InvalidSessionDocumentException e) { - JOptionPane - .showInternalMessageDialog( - Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager - .getString("label.vamsas_doc_couldnt_be_opened_as_new_session"), - MessageManager - .getString("label.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); } } @@ -204,8 +201,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource } catch (Exception e) { - jalview.bin.Cache.log - .error("Couldn't instantiate vamsas client !", e); + jalview.bin.Cache.log.error("Couldn't instantiate vamsas client !", + e); return false; } return true; @@ -228,14 +225,14 @@ public class VamsasApplication implements SelectionSource, VamsasSource } } catch (Error e) { - Cache.log - .warn("Probable SERIOUS VAMSAS client incompatibility - carrying on regardless", - e); + Cache.log.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.log.warn( + "Probable VAMSAS client incompatibility - carrying on regardless", + e); } } @@ -267,16 +264,15 @@ public class VamsasApplication implements SelectionSource, VamsasSource { if (!inSession()) { - throw new Error( - MessageManager - .getString("error.implementation_error_vamsas_operation_not_init")); + throw new Error(MessageManager.getString( + "error.implementation_error_vamsas_operation_not_init")); } addDocumentUpdateHandler(); addStoreDocumentHandler(); startSession(); inInitialUpdate = true; - Cache.log - .debug("Jalview loading the Vamsas Session for the first time."); + Cache.log.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. @@ -310,9 +306,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource } } catch (Exception e) { - Cache.log - .warn("Exception whilst refreshing jalview windows after a vamsas document update.", - e); + Cache.log.warn( + "Exception whilst refreshing jalview windows after a vamsas document update.", + e); } } @@ -321,6 +317,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource Thread udthread = new Thread(new Runnable() { + @Override public void run() { Cache.log.info("Jalview updating to the Vamsas Session."); @@ -354,9 +351,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource { if (!inSession()) { - throw new Error( - MessageManager - .getString("error.jalview_no_connected_vamsas_session")); + throw new Error(MessageManager + .getString("error.jalview_no_connected_vamsas_session")); } Cache.log.info("Jalview disconnecting from the Vamsas Session."); try @@ -371,8 +367,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource } else { - Cache.log - .warn("JV Client leaving a session that's its not joined yet."); + Cache.log.warn( + "JV Client leaving a session that's its not joined yet."); } joinedSession = false; vclient = null; @@ -486,11 +482,10 @@ public class VamsasApplication implements SelectionSource, VamsasSource } catch (Exception e) { errorsDuringUpdate = true; - Cache.log.error("Exception synchronizing " - + af.getTitle() + Cache.log.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; } @@ -587,8 +582,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource storedviews += updateVamsasDocument(cdoc); if (Cache.log.isDebugEnabled()) { - Cache.log - .debug("Time taken to update Vamsas Document from jalview\t= " + Cache.log.debug( + "Time taken to update Vamsas Document from jalview\t= " + (System.currentTimeMillis() - time)); time = System.currentTimeMillis(); } @@ -605,8 +600,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource updateJalview(cdoc); if (Cache.log.isDebugEnabled()) { - Cache.log - .debug("Time taken to update Jalview from vamsas document Roots\t= " + Cache.log.debug( + "Time taken to update Jalview from vamsas document Roots\t= " + (System.currentTimeMillis() - time)); time = System.currentTimeMillis(); } @@ -639,6 +634,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource final VamsasApplication client = this; vclient.addDocumentUpdateHandler(new PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { Cache.log.debug("Dealing with document update event."); @@ -656,34 +652,34 @@ public class VamsasApplication implements SelectionSource, VamsasSource 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.log.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."); Desktop.instance.vamsasSave_actionPerformed(null); Cache.log .debug("Finished attempt at storing document."); } - Cache.log - .debug("finished dealing with REQUESTTOCLOSE event."); + Cache.log.debug( + "finished dealing with REQUESTTOCLOSE event."); } else { - Cache.log - .debug("Ignoring store document request (promptUser==false)"); + Cache.log.debug( + "Ignoring store document request (promptUser==false)"); } } }); @@ -725,9 +721,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource return; } - throw new Error( - MessageManager - .getString("error.implementation_error_cannot_recover_vamsas_object_mappings")); + throw new Error(MessageManager.getString( + "error.implementation_error_cannot_recover_vamsas_object_mappings")); } jv2vobj.clear(); Iterator el = _backup_jv2vobj.entrySet().iterator(); @@ -774,6 +769,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource { String last = null; + @Override public void handleMessage(Message message) { if (vobj2jv == null) @@ -817,7 +813,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource { // 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; @@ -933,8 +929,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource { jselection.setStartRes(prange[p + l] - 1); } - if (jselection.getEndRes() <= maxWidth - && prange[p + u] == (jselection.getEndRes() + 2)) + if (jselection.getEndRes() <= maxWidth && prange[p + + u] == (jselection.getEndRes() + 2)) { jselection.setEndRes(prange[p + u] - 1); } @@ -951,7 +947,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource } if (send) { - ssm.sendSelection(jselection, colsel, me); + ssm.sendSelection(jselection, colsel, null, me); } // discard message. for (int c = 0; c < jvobjs.length; c++) @@ -998,13 +994,15 @@ public class VamsasApplication implements SelectionSource, VamsasSource 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.log.warn( + "Selection listener still active for dead session."); // not in a session. return; } @@ -1017,15 +1015,17 @@ public class VamsasApplication implements SelectionSource, VamsasSource } 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[] { ((AlignmentViewport) source) - .getSequenceSetId() }, null, true); + new String[] + { ((AlignmentViewport) source) + .getSequenceSetId() }, + null, true); } else { @@ -1065,24 +1065,25 @@ public class VamsasApplication implements SelectionSource, VamsasSource { // gather selected columns outwith the sequence positions // too - for (Object obj : colsel.getSelected()) + for (Integer ival : colsel.getSelected()) { - int ival = ((Integer) obj).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); }