From 00b0456440bdc984b117a815e0c5265bdfe60419 Mon Sep 17 00:00:00 2001
From: "U-MATIS\\sigmar" <sigmar@srv-starlimsdat.matis.local>
Date: Fri, 14 Oct 2011 11:59:24 +0000
Subject: [PATCH] ok

---
 Taxonomy/src/org/simmi/client/Taxonomy.java       | 12 +++++++++---
 .../src/org/simmi/server/GreetingServiceImpl.java |  1 +
 distann/src/org/simmi/GeneSet.java                | 15 +++++++++++----
 3 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/Taxonomy/src/org/simmi/client/Taxonomy.java b/Taxonomy/src/org/simmi/client/Taxonomy.java
index f901af8fa..ebd3a8256 100644
--- a/Taxonomy/src/org/simmi/client/Taxonomy.java
+++ b/Taxonomy/src/org/simmi/client/Taxonomy.java
@@ -198,7 +198,7 @@ public void onSuccess(String result) {
 							db.setAutoHideEnabled( true );
 							cap.setText("Fasta");
 							TextArea ta = new TextArea();
-							ta.setSize("400px", "300px");
+							ta.setSize("512px", "384px");
 							db.add( ta );
 							
 							ta.setText( result );
@@ -294,7 +294,8 @@ public void stuff( String str, TreeItem rootitem ) {
 		for( String s : split ) {
 			boolean gogg = s.startsWith(">");
 			boolean svig = s.startsWith("(");
-			if( s.length() > 0 && !svig && !gogg && !first ) {
+			boolean nohi = s.startsWith("*");
+			if( s.length() > 0 && !svig && !gogg && !nohi && !first ) {
 				String[] subs = s.split("\\:");
 				if( subs.length > 1 ) {
 					current = rootitem;
@@ -331,13 +332,15 @@ public void stuff( String str, TreeItem rootitem ) {
 				for( String splstr : spl ) {
 					current.addItem( splstr );
 				}
+			} else if( nohi ) {
+				current = current.addItem("*** No hits ***");
 			} else {
 				current = rootitem;
 			}
 			first = false;
 		}
 		
-		recursiveCount( rootitem );
+		//recursiveCount( rootitem );
 	}
 	
 	public int recursiveCount( TreeItem item ) {
@@ -346,6 +349,9 @@ public int recursiveCount( TreeItem item ) {
 		if( item.getText().startsWith(">") ) {
 			String[] ss = item.getText().split("[\t ]+");
 			total = Integer.parseInt( ss[ss.length-1] );
+		} else if( item.getText().startsWith("*") ) {
+			total = item.getChildCount();
+			item.setText( item.getText()+" ("+total+")" );
 		} else {
 			for( int i = 0; i < item.getChildCount(); i++ ) {
 				TreeItem ti = item.getChild(i);
diff --git a/Taxonomy/src/org/simmi/server/GreetingServiceImpl.java b/Taxonomy/src/org/simmi/server/GreetingServiceImpl.java
index 831475d0f..fb676b5c8 100644
--- a/Taxonomy/src/org/simmi/server/GreetingServiceImpl.java
+++ b/Taxonomy/src/org/simmi/server/GreetingServiceImpl.java
@@ -17,6 +17,7 @@
 @SuppressWarnings("serial")
 public class GreetingServiceImpl extends RemoteServiceServlet implements GreetingService {
 
+	
 	public String greetServer(String input, String searchnum) throws IllegalArgumentException {		
 		StringBuilder ret = new StringBuilder();
 		
diff --git a/distann/src/org/simmi/GeneSet.java b/distann/src/org/simmi/GeneSet.java
index 6c0f1aa0a..f2944b351 100644
--- a/distann/src/org/simmi/GeneSet.java
+++ b/distann/src/org/simmi/GeneSet.java
@@ -2440,9 +2440,16 @@ private static void loci2gene( Reader rd, String outfile, String filtercont, Map
 						boolean first = true;
 						List<String>	res = maplist.get(nid);
 						for( String rstr : res ) {
-							if( rstr != null ) {  
+							if( rstr != null ) {
 								String[] rspl = rstr.split("\t");
-								if( rspl.length == 4 ) {
+								if( rspl.length == 1 ) {
+									if( first ) {
+										first = false;
+										fw.write( rspl[0] );
+									} else {
+										fw.write( "," + rspl[0] );
+									}
+								} else if( rspl.length == 4 ) {
 									if( first ) {
 										first = false;
 										fw.write( rspl[0] + " " + rspl[2] );
@@ -4460,8 +4467,8 @@ public static void main(String[] args) {
 			}*/
 			loci2gene( new FileReader("c:/viggo/6.blastout"), "c:/viggo/6v3.txt", null, freqmap );
 			
-			//Map<String,Integer>	freqmap = loadFrequency( new FileReader("/home/sigmar/arciformis_repeat.blastout") );
-			//loci2gene( new FileReader("/home/sigmar/arciformis_repeat.blastout"), "/home/sigmar/arciformis_v1.txt", null, freqmap );			
+			//Map<String,Integer>	freqmap = loadFrequency( new FileReader("c:/viggo//arciformis_repeat.blastout") );
+			//loci2gene( new FileReader("c:/viggo/arciformis_repeat.blastout"), "c:/viggo/arciformis_v1.txt", null, freqmap );			
 			
 			/*loci2gene( new FileReader("/home/horfrae/viggo/1.blastout"), "/home/horfrae/viggo/1v.txt", null );
 			loci2gene( new FileReader("/home/horfrae/viggo/2.blastout"), "/home/horfrae/viggo/2v.txt", null );