From 01218585457b22243771439d85aa43b6ccb2b62a Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 2 Jun 2005 11:06:21 +0000
Subject: [PATCH] Reverse order for windows, readin from url

---
 src/jalview/gui/Jalview2XML.java |   74 +++++++++++++++++++++++++-------------
 1 file changed, 49 insertions(+), 25 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 3eebf5c..fa8e50b 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -7,6 +7,7 @@ import java.util.jar.*;
 import jalview.binding.*;
 import jalview.schemes.*;
 import javax.swing.JInternalFrame;
+import java.net.URL;
 
 
 public class Jalview2XML
@@ -17,6 +18,9 @@ public class Jalview2XML
   {
       long creation = System.currentTimeMillis();
       JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+      if(frames==null)
+        return;
+
       try{
         FileOutputStream fos = new FileOutputStream(statefile);
         JarOutputStream jout = new JarOutputStream(fos);
@@ -25,7 +29,8 @@ public class Jalview2XML
         PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));
 
         Vector shortNames = new Vector();
-        for (int i = 0; i < frames.length; i++)
+        //REVERSE ORDER
+        for (int i = frames.length-1; i > -1; i--)
         {
           if (frames[i] instanceof AlignFrame)
           {
@@ -33,8 +38,9 @@ public class Jalview2XML
 
             String shortName = af.getTitle();
 
-            shortName = shortName.replace('/', '_');
-            shortName = shortName.replace('\\', '_');
+            if(shortName.indexOf(File.separatorChar)>-1)
+              shortName = shortName.substring(
+                    shortName.lastIndexOf(File.separatorChar)+1);
 
             int count=1;
             while( shortNames.contains(shortName) )
@@ -331,11 +337,20 @@ public class Jalview2XML
     JalviewModel object = new JalviewModel();
     try{
       //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
-      JarInputStream jin = new JarInputStream(new FileInputStream(file));
+
+      URL url = null;
+      if( file.startsWith("http://"))
+       url = new URL(file);
+
+      JarInputStream jin = null;
       JarEntry jarentry=null;
       int entryCount = 1;
       do{
-        jin = new JarInputStream(new FileInputStream(file));
+        if (url != null)
+          jin = new JarInputStream(url.openStream());
+        else
+          jin = new JarInputStream(new FileInputStream(file));
+
         for(int i=0; i<entryCount; i++)
           jarentry = jin.getNextJarEntry();
 
@@ -431,15 +446,18 @@ public class Jalview2XML
       for (int i = 0; i < groups.length; i++)
       {
        ColourSchemeI cs=null;
-       if(groups[i].getColour().startsWith("ucs"))
-         cs = GetUserColourScheme(jms,groups[i].getColour());
-       else
-         cs = ColourSchemeProperty.getColour(al, groups[i].getColour() );
-
-       if (cs instanceof ResidueColourScheme)
-         ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());
-       else if (cs instanceof ScoreColourScheme)
-      ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());
+       if(groups[i].getColour()!=null)
+       {
+         if (groups[i].getColour().startsWith("ucs"))
+           cs = GetUserColourScheme(jms, groups[i].getColour());
+         else
+           cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
+
+         if (cs instanceof ResidueColourScheme)
+           ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());
+         else if (cs instanceof ScoreColourScheme)
+           ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());
+       }
 
         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup
                 (groups[i].getName(),
@@ -504,19 +522,25 @@ public class Jalview2XML
     af.viewport.setShowText( view.getShowText() );
 
     ColourSchemeI cs=null;
-    if (view.getBgColour().startsWith("ucs"))
-      cs = GetUserColourScheme(jms, view.getBgColour());
-    else
-      cs = ColourSchemeProperty.getColour(al, view.getBgColour());
-    af.viewport.setGlobalColourScheme( cs );
+    if(view.getBgColour()!=null)
+    {
+
+      if (view.getBgColour().startsWith("ucs"))
+        cs = GetUserColourScheme(jms, view.getBgColour());
+      else
+        cs = ColourSchemeProperty.getColour(al, view.getBgColour());
 
-    if(cs instanceof ConservationColourScheme)
-      ( (ConservationColourScheme) cs).inc = view.getConsThreshold();
+      if (cs instanceof ConservationColourScheme)
+        ( (ConservationColourScheme) cs).inc = view.getConsThreshold();
+
+      if (cs instanceof ResidueColourScheme)
+        ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());
+      else if (cs instanceof ScoreColourScheme)
+        ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());
+
+    }
+    af.viewport.setGlobalColourScheme( cs );
 
-    if (cs instanceof ResidueColourScheme)
-      ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());
-    else if (cs instanceof ScoreColourScheme)
-      ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());
 
     af.viewport.setColourAppliesToAllGroups(false);
     af.changeColour(af.viewport.getGlobalColourScheme());
-- 
1.7.10.2