X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=d2086e0788a736b71acc3cfd51dbb4b463756ca7;hb=53b99b41ed7f26f2724f3ed87d524eb83c5208f4;hp=5ee7e36821a730cb8f29b3bbd6a3d61655a9d1bf;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 5ee7e36..d2086e0 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * 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.
*
* 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.
+ * 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 Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
@@ -21,6 +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;
@@ -29,18 +32,18 @@ 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;
@@ -153,8 +156,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource
{
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
{
@@ -170,13 +173,13 @@ public class VamsasApplication implements SelectionSource, VamsasSource
}
} 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);
}
}
@@ -198,8 +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;
@@ -222,14 +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);
}
}
@@ -261,15 +264,15 @@ public class VamsasApplication implements SelectionSource, VamsasSource
{
if (!inSession())
{
- throw new Error(
- "Impementation error! Vamsas Operations when client not initialised and connected.");
+ 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.
@@ -303,9 +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);
}
}
@@ -314,6 +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.");
@@ -346,7 +350,10 @@ public class VamsasApplication implements SelectionSource, VamsasSource
public void end_session(boolean promptUser)
{
if (!inSession())
- throw new Error("Jalview not connected to Vamsas session.");
+ {
+ throw new Error(MessageManager
+ .getString("error.jalview_no_connected_vamsas_session"));
+ }
Cache.log.info("Jalview disconnecting from the Vamsas Session.");
try
{
@@ -360,8 +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;
@@ -475,11 +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().viewName == null ? ""
+ : " view " + af.getViewport().viewName)
+ " to document.", e);
stored = false;
}
@@ -576,8 +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();
}
@@ -594,8 +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();
}
@@ -628,6 +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.");
@@ -645,34 +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)");
}
}
});
@@ -714,8 +721,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource
return;
}
- throw new Error(
- "IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made.");
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_cannot_recover_vamsas_object_mappings"));
}
jv2vobj.clear();
Iterator el = _backup_jv2vobj.entrySet().iterator();
@@ -762,6 +769,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
{
String last = null;
+ @Override
public void handleMessage(Message message)
{
if (vobj2jv == null)
@@ -805,7 +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;
@@ -921,8 +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);
}
@@ -939,7 +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++)
@@ -958,11 +966,14 @@ 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);
@@ -983,13 +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;
}
@@ -998,19 +1011,21 @@ 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)
- && (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
{
@@ -1050,18 +1065,18 @@ 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)
{