From: Jim Procter 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;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 *