X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=d58cb5ad784492b37a9173899e6eadaa373b9290;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=6daaf6888d02b7c71a718761d77685cfa67c9be0;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java index 6daaf68..d58cb5a 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 2.8.2b1) - * Copyright (C) 2014 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; @@ -32,18 +33,17 @@ 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; @@ -156,7 +156,9 @@ 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 { @@ -172,13 +174,15 @@ public class VamsasApplication implements SelectionSource, VamsasSource } } catch (InvalidSessionDocumentException e) { - JOptionPane + 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); } } @@ -263,7 +267,9 @@ 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(); @@ -315,6 +321,7 @@ 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."); @@ -347,7 +354,11 @@ public class VamsasApplication implements SelectionSource, VamsasSource public void end_session(boolean promptUser) { 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 { @@ -629,6 +640,7 @@ 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."); @@ -646,21 +658,22 @@ 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 + int reply = JvOptionPane .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); + JvOptionPane.YES_NO_OPTION, + JvOptionPane.QUESTION_MESSAGE); - if (reply == JOptionPane.YES_OPTION) + if (reply == JvOptionPane.YES_OPTION) { Cache.log.debug("Prompting for vamsas store filename."); Desktop.instance.vamsasSave_actionPerformed(null); @@ -715,7 +728,9 @@ 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(); @@ -762,6 +777,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource { String last = null; + @Override public void handleMessage(Message message) { if (vobj2jv == null) @@ -805,7 +821,7 @@ 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; @@ -939,7 +955,7 @@ 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++) @@ -958,11 +974,14 @@ public class VamsasApplication implements SelectionSource, VamsasSource 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); @@ -983,8 +1002,10 @@ 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) { @@ -998,7 +1019,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource AlignmentI visal = null; if (source instanceof AlignViewport) { - visal = ((AlignViewport) source).getAlignment(); + visal = ((AlignmentViewport) source).getAlignment(); } SelectionMessage sm = null; if ((seqsel == null || seqsel.getSize() == 0) @@ -1008,9 +1029,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource 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 { @@ -1050,18 +1071,18 @@ public class VamsasApplication implements SelectionSource, VamsasSource { // 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( + // 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) {