From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 28 Nov 2014 13:55:05 +0000 (+0000)
Subject: JAL-1517 formatting/tidy
X-Git-Tag: Jalview_2_9~136^2~13
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6940b5ac884139626e962201ae00c56c66d18039;hp=319e6804f17a0a18821f9ea8e67719d125641a59;p=jalview.git

JAL-1517 formatting/tidy
---

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 007fefd..fea381d 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1064,7 +1064,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(viewport);
-    Desktop.addInternalFrame(cap, MessageManager.getString("label.cut_paste_alignmen_file"), 600, 500);
+    Desktop.addInternalFrame(cap,
+            MessageManager.getString("label.cut_paste_alignmen_file"),
+            true, 600, 500);
   }
 
   /*
diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java
index 8dcf72a..8c06771 100644
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.java
@@ -20,21 +20,40 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.jbgui.GWebserviceInfo;
+import jalview.util.MessageManager;
+import jalview.ws.WSClientI;
 
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.GridLayout;
+import java.awt.Image;
+import java.awt.MediaTracker;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.image.BufferedImage;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+import javax.swing.JTextArea;
 import javax.swing.event.HyperlinkEvent;
 import javax.swing.event.HyperlinkListener;
 import javax.swing.text.html.HTMLEditorKit;
 import javax.swing.text.html.StyleSheet;
 
-import jalview.jbgui.*;
-import jalview.util.MessageManager;
-import jalview.ws.WSClientI;
-
 /**
  * Base class for web service client thread and gui TODO: create StAX parser to
  * extract html body content reliably when preparing html formatted job statuses
diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java
index 1a96464..1c506b8 100644
--- a/src/jalview/ws/jws1/JPredClient.java
+++ b/src/jalview/ws/jws1/JPredClient.java
@@ -20,18 +20,28 @@
  */
 package jalview.ws.jws1;
 
+import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
+
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.util.*;
+import java.util.Hashtable;
 
-import javax.swing.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
 
-import ext.vamsas.*;
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.util.MessageManager;
+import ext.vamsas.Jpred;
+import ext.vamsas.JpredServiceLocator;
+import ext.vamsas.JpredSoapBindingStub;
+import ext.vamsas.ServiceHandle;
 
 public class JPredClient extends WS1Client
 {
diff --git a/src/jalview/ws/jws2/Jws2Client.java b/src/jalview/ws/jws2/Jws2Client.java
index afefe65..751d330 100644
--- a/src/jalview/ws/jws2/Jws2Client.java
+++ b/src/jalview/ws/jws2/Jws2Client.java
@@ -20,17 +20,6 @@
  */
 package jalview.ws.jws2;
 
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.List;
-
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
-
-import compbio.metadata.Argument;
 import jalview.api.AlignCalcWorkerI;
 import jalview.bin.Cache;
 import jalview.gui.AlignFrame;
@@ -45,6 +34,18 @@ import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws.uimodel.AlignAnalysisUIText;
 
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.List;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+import compbio.metadata.Argument;
+
 /**
  * provides metadata for a jabaws2 service instance - resolves names, etc.
  * 
@@ -148,7 +149,7 @@ public abstract class Jws2Client extends jalview.ws.WSClient
     {
       return new WebserviceInfo(WebServiceJobTitle, WebServiceJobTitle
               + " using service hosted at " + serv.hosturl + "\n"
-              + (serv.description != null ? serv.description : ""));
+              + (serv.description != null ? serv.description : ""), false);
     }
     return null;
   }
diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 5e8cb98..635f92b 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -20,7 +20,29 @@
  */
 package jalview.ws.jws2;
 
-import java.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
+import jalview.ws.AWsJob;
+import jalview.ws.JobStateSummary;
+import jalview.ws.WSClientI;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.params.WsParamSetI;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
 
 import compbio.data.msa.MsaWS;
 import compbio.metadata.Argument;
@@ -28,17 +50,6 @@ import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;
 import compbio.metadata.Preset;
 
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.util.MessageManager;
-import jalview.ws.AWsJob;
-import jalview.ws.WSClientI;
-import jalview.ws.JobStateSummary;
-import jalview.ws.jws2.dm.JabaWsParamSet;
-import jalview.ws.params.WsParamSetI;
-
 class MsaWSThread extends AWS2Thread implements WSClientI
 {
   boolean submitGaps = false; // pass sequences including gaps to alignment
diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java
index cd4bb23..1acecb4 100644
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -20,17 +20,6 @@
  */
 package jalview.ws.rest;
 
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
-
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
@@ -44,6 +33,17 @@ import jalview.ws.WSClient;
 import jalview.ws.WSClientI;
 import jalview.ws.WSMenuEntryProviderI;
 
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
 /**
  * @author JimP
  *