From 3f578998521236c208e9d3c7790d4d5ac4da0a50 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 16 Mar 2005 14:53:03 +0000
Subject: [PATCH] uses jalviewfilechooser

---
 src/jalview/gui/AlignFrame.java         |    4 ++--
 src/jalview/gui/AlignmentPanel.java     |    6 +++---
 src/jalview/gui/Desktop.java            |    8 ++++----
 src/jalview/gui/TreePanel.java          |    4 ++--
 src/jalview/gui/UserDefinedColours.java |    9 +++++----
 src/jalview/io/HTMLOutput.java          |    4 ++--
 6 files changed, 18 insertions(+), 17 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index c679559..9d7e2b7 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -63,12 +63,12 @@ public class AlignFrame extends GAlignFrame
 
   protected void saveAs_actionPerformed(ActionEvent e)
   {
-    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
     chooser.setToolTipText("Save");
     int value = chooser.showSaveDialog(this);
-    if(value == JFileChooser.APPROVE_OPTION)
+    if(value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice =  chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 296bb80..da68ab9 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -383,7 +383,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     Color currentTextColor=null;
     for(int i=startSeq; i<endSeq; i++)
     {
-      if (av.alignment.findGroup(av.getAlignment().getSequenceAt(i))==null)
+      if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
       {
         currentColor = Color.gray;
         currentTextColor = Color.black;
@@ -488,14 +488,14 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       catch (Exception ex)
       {}
 
-      javax.swing.JFileChooser chooser = new javax.swing.JFileChooser(jalview.bin.Cache.getProperty(
+      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
           "LAST_DIRECTORY"));
       chooser.setFileView(new jalview.io.JalviewFileView());
       chooser.setDialogTitle("Create JPG image from alignment");
       chooser.setToolTipText("Save");
 
       int value = chooser.showSaveDialog(this);
-      if (value == javax.swing.JFileChooser.APPROVE_OPTION)
+      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
       {
 
         FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index bfbdc1d..eaa2c5e 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -96,8 +96,8 @@ public void windowClosing(WindowEvent evt)
     catch (java.beans.PropertyVetoException e)
     {}
     frame.setResizable(true);
-    frame.setSize(845, 200);
-    frame.setLocation( (int)((getWidth()-845) /2), (int)((getHeight()-240) /2));
+    frame.setSize(750, 160);
+    frame.setLocation( (int)((getWidth()-750) /2), (int)((getHeight()-160) /2));
     frame.setClosable(false);
     frame.setIconifiable(false);
     frame.setMaximizable(false);
@@ -146,12 +146,12 @@ public void windowClosing(WindowEvent evt)
 
  public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
  {
-   JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+   JalviewFileChooser chooser = new JalviewFileChooser();
    chooser.setFileView(new JalviewFileView());
    chooser.setDialogTitle("Open local file");
    chooser.setToolTipText("Open");
    int value = chooser.showOpenDialog(this);
-   if(value == JFileChooser.APPROVE_OPTION)
+   if(value == JalviewFileChooser.APPROVE_OPTION)
    {
      String choice =  chooser.getSelectedFile().getPath();
      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index f723fdc..58c668f 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -234,11 +234,11 @@ public void propertiesInit() {
   {
 
     try{
-      JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
       chooser.setDialogTitle("Save Tree as postscript file");
       chooser.setToolTipText("Save");
       int value = chooser.showSaveDialog(this);
-      if (value == JFileChooser.APPROVE_OPTION)
+      if (value == JalviewFileChooser.APPROVE_OPTION)
       {
         String choice = chooser.getSelectedFile().getPath();
         jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index a96cf52..6fed854 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -2,6 +2,7 @@ package jalview.gui;
 
 import jalview.jbgui.GUserDefinedColours;
 import jalview.datamodel.*;
+import jalview.io.*;
 import javax.swing.*;
 import java.awt.*;
 import java.awt.event.*;
@@ -123,12 +124,12 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
 
   protected void loadbutton_actionPerformed(ActionEvent e)
   {
-    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle("Load colour scheme");
     chooser.setToolTipText("Load");
     int value = chooser.showOpenDialog(this);
-    if (value == JFileChooser.APPROVE_OPTION)
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY",  choice);
@@ -156,12 +157,12 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
 
   protected void savebutton_actionPerformed(ActionEvent e)
   {
-    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle("Save colour scheme");
     chooser.setToolTipText("Save");
     int value = chooser.showSaveDialog(this);
-    if (value == JFileChooser.APPROVE_OPTION)
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", choice);
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 82b75a1..af894e0 100755
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -19,12 +19,12 @@ public class HTMLOutput
   {
     this.av = av;
     sr = new SequenceRenderer(av);
-    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save as HTML");
     chooser.setToolTipText("Save");
     int value = chooser.showSaveDialog(null);
-    if(value == JFileChooser.APPROVE_OPTION)
+    if(value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice =  chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY",  choice);
-- 
1.7.10.2