From 38050005b068d6dd5d7766d0fe16d763f1744d8b Mon Sep 17 00:00:00 2001
From: Hector Plahar <HAPlahar@lbl.gov>
Date: Wed, 16 Sep 2015 09:32:19 -0700
Subject: [PATCH 1/2] updating pigeoncad url and removing labels

---
 .../entry/sequence/composers/pigeon/PigeonSBOLv.java | 12 +++++++-----
 .../webapp/scripts/entry/general-information.html    |  3 +--
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/src/main/java/org/jbei/ice/lib/entry/sequence/composers/pigeon/PigeonSBOLv.java b/src/main/java/org/jbei/ice/lib/entry/sequence/composers/pigeon/PigeonSBOLv.java
index 528ffb5c5..854c35eb4 100644
--- a/src/main/java/org/jbei/ice/lib/entry/sequence/composers/pigeon/PigeonSBOLv.java
+++ b/src/main/java/org/jbei/ice/lib/entry/sequence/composers/pigeon/PigeonSBOLv.java
@@ -25,7 +25,7 @@
 public class PigeonSBOLv {
 
     private static final String NEWLINE = System.getProperty("line.separator");
-    private static final String PIGEON_URL = "http://cidar1.bu.edu:5801/dev/perch2.php";
+    private static final String PIGEON_URL = "http://128.197.173.22:5801/dev/perch2.php";
     private static final HashMap<String, String> map = new HashMap<>();
 
     static {
@@ -110,7 +110,7 @@ public static URI generatePigeonVisual(Sequence sequence) {
 
         StringBuilder sb = new StringBuilder();
         if (visitor.getDnaComponent() != null) {
-            sb.append(toPigeon(visitor.getDnaComponent(), null));
+            sb.append(toPigeon(visitor.getDnaComponent(), null, false));
         }
 
         sb.append("# Arcs").append(NEWLINE);
@@ -126,14 +126,14 @@ public static String generatePigeonScript(Sequence sequence) {
 
         StringBuilder sb = new StringBuilder();
         if (visitor.getDnaComponent() != null) {
-            sb.append(toPigeon(visitor.getDnaComponent(), null));
+            sb.append(toPigeon(visitor.getDnaComponent(), null, false));
         }
 
         sb.append("# Arcs").append(NEWLINE);
         return sb.toString();
     }
 
-    private static String toPigeon(DnaComponent component, StrandType strandType) {
+    private static String toPigeon(DnaComponent component, StrandType strandType, boolean addLabel) {
         if (component == null)
             return "";
 
@@ -158,11 +158,13 @@ private static String toPigeon(DnaComponent component, StrandType strandType) {
                 if (replacedSpaces.trim().isEmpty())
                     replacedSpaces = "unnamed";
                 sb.append(pigeonType).append(" ").append(replacedSpaces).append(" ").append(split[1]);
+                if (!addLabel)
+                    sb.append(" nl");
                 sb.append(NEWLINE);
             }
         } else {
             for (SequenceAnnotation sa : component.getAnnotations()) {
-                sb.append(toPigeon(sa.getSubComponent(), sa.getStrand()));
+                sb.append(toPigeon(sa.getSubComponent(), sa.getStrand(), false));
             }
         }
 
diff --git a/src/main/webapp/scripts/entry/general-information.html b/src/main/webapp/scripts/entry/general-information.html
index 53b1c63a3..7435f32b0 100644
--- a/src/main/webapp/scripts/entry/general-information.html
+++ b/src/main/webapp/scripts/entry/general-information.html
@@ -444,8 +444,7 @@
             <div style="width: 100%; overflow: auto; position: relative; zoom: 1;"
                  ng-if='entry.hasSequence && showSBOL'>
                 <div style="width: 0;">
-                    <img height="130px"
-                         ng-src="download?sid={{sessionId}}&amp;rid={{entry.recordId}}">
+                    <img height="100px" ng-src="download?sid={{sessionId}}&amp;rid={{entry.recordId}}">
                 </div>
             </div>
 

From ccabb5cfa0da8556d30600f142196c1fcd79c62a Mon Sep 17 00:00:00 2001
From: Hector Plahar <HAPlahar@lbl.gov>
Date: Wed, 16 Sep 2015 09:33:13 -0700
Subject: [PATCH 2/2] bump version #

---
 pom.xml                   | 2 +-
 src/main/webapp/index.jsp | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pom.xml b/pom.xml
index a37da7a0c..0ecc0da73 100755
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
     <groupId>org.jbei</groupId>
     <artifactId>ice</artifactId>
     <packaging>war</packaging>
-    <version>4.4.1</version>
+    <version>4.4.2</version>
     <name>ice</name>
     <description>Inventory of Composable Elements (ICE) for Synthetic Biology</description>
     <repositories>
diff --git a/src/main/webapp/index.jsp b/src/main/webapp/index.jsp
index b5d85654b..144aa9b55 100644
--- a/src/main/webapp/index.jsp
+++ b/src/main/webapp/index.jsp
@@ -90,7 +90,7 @@
             </div>
             <div class="text-right">
                 &copy;&nbsp;<a href="https://github.com/JBEI/ice">JBEI ICE Registry</a> <span
-                    class="label label-primary">v4.4.1</span><br>
+                    class="label label-primary">v4.4.2</span><br>
                 All rights reserved. <br>
                 <a href="https://github.com/JBEI/ice/issues/new">Submit an Issue</a>&nbsp; <span class="text-muted">|</span> &nbsp;<a
                     href="http://public-registry.jbei.org/manual">Help</a>