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Merge branch 'bug/JAL-2634' into develop
[jalview.git]
/
src
/
jalview
/
ws
/
rest
/
RestClient.java
diff --git
a/src/jalview/ws/rest/RestClient.java
b/src/jalview/ws/rest/RestClient.java
index
03918a8
..
27f5271
100644
(file)
--- a/
src/jalview/ws/rest/RestClient.java
+++ b/
src/jalview/ws/rest/RestClient.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * 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.
*
*
* This file is part of Jalview.
*
@@
-26,6
+26,7
@@
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.gui.WebserviceInfo;
import jalview.io.packed.DataProvider.JvDataType;
import jalview.util.MessageManager;
import jalview.gui.WebserviceInfo;
import jalview.io.packed.DataProvider.JvDataType;
import jalview.util.MessageManager;
@@
-40,7
+41,6
@@
import java.util.Vector;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
@@
-259,7
+259,8
@@
public class RestClient extends WSClient implements WSClientI,
{
// intersect groups with selected region
_input = new AlignmentView(av.getAlignment(),
{
// intersect groups with selected region
_input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(), av.getSelectionGroup(),
+ av.getAlignment()
+ .getHiddenColumns(), av.getSelectionGroup(),
av.hasHiddenColumns(), true, true);
viewTitle = MessageManager.formatMessage(
"label.select_visible_region_of",
av.hasHiddenColumns(), true, true);
viewTitle = MessageManager.formatMessage(
"label.select_visible_region_of",
@@
-272,7
+273,8
@@
public class RestClient extends WSClient implements WSClientI,
{
// use selected region to partition alignment
_input = new AlignmentView(av.getAlignment(),
{
// use selected region to partition alignment
_input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(), av.getSelectionGroup(),
+ av.getAlignment()
+ .getHiddenColumns(), av.getSelectionGroup(),
av.hasHiddenColumns(), false, true);
}
viewTitle = MessageManager.formatMessage(
av.hasHiddenColumns(), false, true);
}
viewTitle = MessageManager.formatMessage(
@@
-286,7
+288,8
@@
public class RestClient extends WSClient implements WSClientI,
{
// just take selected region intersection
_input = new AlignmentView(av.getAlignment(),
{
// just take selected region intersection
_input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(), av.getSelectionGroup(),
+ av.getAlignment()
+ .getHiddenColumns(), av.getSelectionGroup(),
av.hasHiddenColumns(), true, true);
viewTitle = MessageManager.formatMessage(
"label.select_visible_region_of",
av.hasHiddenColumns(), true, true);
viewTitle = MessageManager.formatMessage(
"label.select_visible_region_of",
@@
-300,7
+303,8
@@
public class RestClient extends WSClient implements WSClientI,
{
// standard alignment view without selection present
_input = new AlignmentView(av.getAlignment(),
{
// standard alignment view without selection present
_input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(), null, av.hasHiddenColumns(), false,
+ av.getAlignment()
+ .getHiddenColumns(), null, av.hasHiddenColumns(), false,
true);
viewTitle = ""
+ (av.hasHiddenColumns() ? (new StringBuffer(" ")
true);
viewTitle = ""
+ (av.hasHiddenColumns() ? (new StringBuffer(" ")
@@
-324,7
+328,7
@@
public class RestClient extends WSClient implements WSClientI,
else
{
// TODO: try to tell the user why the job couldn't be started.
else
{
// TODO: try to tell the user why the job couldn't be started.
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
(jobsthread.hasWarnings() ? jobsthread.getWarnings()
.showMessageDialog(
Desktop.desktop,
(jobsthread.hasWarnings() ? jobsthread.getWarnings()
@@
-332,7
+336,7
@@
public class RestClient extends WSClient implements WSClientI,
.getString("label.job_couldnt_be_started_check_input")),
MessageManager
.getString("label.unable_start_web_service_analysis"),
.getString("label.job_couldnt_be_started_check_input")),
MessageManager
.getString("label.unable_start_web_service_analysis"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
}
}
}