From 3e313eab680734bb0bd49d3366c5ae6ad8330ef4 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 1 Dec 2004 16:57:15 +0000
Subject: [PATCH] New classes

---
 src/jalview/gui/Finder.java       |  129 +++++++++++++++++++++++++++++++++++++
 src/jalview/gui/SplashScreen.java |   81 +++++++++++++++++++++++
 2 files changed, 210 insertions(+)
 create mode 100755 src/jalview/gui/Finder.java
 create mode 100755 src/jalview/gui/SplashScreen.java

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
new file mode 100755
index 0000000..c5a2cf4
--- /dev/null
+++ b/src/jalview/gui/Finder.java
@@ -0,0 +1,129 @@
+package jalview.gui;
+
+import jalview.jbgui.GFinder;
+import jalview.datamodel.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+import java.util.*;
+
+
+public class Finder extends GFinder
+{
+  AlignViewport av;
+  AlignmentPanel ap;
+  JInternalFrame frame;
+  String searchString;
+
+  int seqIndex = 0;
+  int resIndex = 0;
+  public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
+  {
+    this.av = av;
+    this.ap = ap;
+    frame = f;
+
+    // all a big pain, but we need to wait until the frame is visible before the textfield can
+    // obtain the focus/////////////////////////
+    frame.addInternalFrameListener(new InternalFrameAdapter()
+    {
+      public void internalFrameOpened(InternalFrameEvent evt)
+      {
+        SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            textfield.requestFocus();
+          }
+       });
+   }
+});
+
+  }
+
+  public void textfield_actionPerformed(ActionEvent e)
+  {
+    doSearch(false);
+  }
+
+  public void findNext_actionPerformed(ActionEvent e)
+  {
+    doSearch(false);
+  }
+
+  public void findAll_actionPerformed(ActionEvent e)
+  {
+    resIndex=0;
+    seqIndex=0;
+    doSearch(true);
+  }
+
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    try{
+      frame.setClosed(true);
+    }catch(Exception ex){}
+
+  }
+
+  void doSearch(boolean findAll)
+  {
+    searchString = textfield.getText().toUpperCase();
+
+    ArrayList searchResults = new ArrayList();
+    int [] allResults = null;
+
+    Sequence seq;
+    String item;
+    boolean found = false;
+    while( !found && seqIndex<av.getAlignment().getHeight())
+    {
+      seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);
+      item = seq.getSequence();
+
+      for(int r = resIndex; r<item.length(); r++)
+      {
+       if(item.indexOf(searchString,r)>-1)
+       {
+         resIndex = item.indexOf(searchString,r);
+         searchResults.add( Integer.toString(seqIndex) );
+         searchResults.add( Integer.toString( resIndex) );
+         searchResults.add( Integer.toString( (resIndex+searchString.length()-1) ) );
+         if(!findAll)
+         {
+           // thats enough, break and display the result
+           found = true;
+           resIndex++;
+           break;
+         }
+       }
+      }
+      if(!found)
+      {
+        seqIndex++;
+        resIndex = 0;
+      }
+    }
+
+    if(searchResults.size()>0)
+    {
+
+      allResults = new int[searchResults.size()];
+      for(int i=0; i<searchResults.size(); i++)
+        allResults[i] = Integer.parseInt(searchResults.get(i).toString());
+
+
+      ap.highlightSearchResults( allResults );
+    }
+    else
+    {
+      JOptionPane.showInternalMessageDialog(this, "Finished searching", null,
+                                            JOptionPane.INFORMATION_MESSAGE);
+      resIndex=0;
+      seqIndex=0;
+    }
+
+
+  }
+
+}
diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java
new file mode 100755
index 0000000..522215d
--- /dev/null
+++ b/src/jalview/gui/SplashScreen.java
@@ -0,0 +1,81 @@
+package jalview.gui;
+
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.*;
+
+public class SplashScreen extends JPanel implements Runnable
+{
+  boolean visible = true;
+  JInternalFrame iframe;
+  Image image;
+
+  public SplashScreen(JInternalFrame iframe, Image i)
+  {
+    this.iframe = iframe;
+    image = i;
+    Thread t = new Thread(this);
+    t.start();
+    addMouseListener(new MouseAdapter()
+    { public void mousePressed(MouseEvent evt)
+      {
+        try
+        {   closeSplash();  }
+        catch (Exception ex)
+        {}
+      }
+      });
+  }
+
+
+  public void run()
+  {
+    long startTime =  System.currentTimeMillis()/1000;
+
+    while( visible )
+    {
+      if( System.currentTimeMillis()/1000 - startTime > 8)
+        visible = false;
+
+      try{
+        Thread.sleep(400);
+        iframe.setSelected(true);
+      }
+      catch(Exception ex){}
+    }
+
+    closeSplash();
+
+  }
+
+  public void closeSplash()
+  {
+    try
+    {
+      iframe.setClosed(true);
+      Desktop.splashScreenClosing();
+    }
+    catch (Exception ex)
+    {}
+
+  }
+
+
+  public void paintComponent(Graphics g)
+  {
+    g.setColor(Color.white);
+    g.fillRect(0,0,getWidth(),getHeight());
+    g.setColor(Color.black);
+    g.setFont( new Font("Verdana", Font.BOLD, 18));
+    if(image!=null)
+    g.drawImage(image, 5,60,this);
+    g.drawString("JalView 2005", 50,50);
+    g.setFont( new Font("Verdana", Font.BOLD, 14));
+    g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse and Geoff Barton.",50,70);
+    g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",50,90);
+    g.drawString("If  you use JalView, please cite:",50,110);
+    g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",50,130);
+
+  }
+
+}
-- 
1.7.10.2