From fc10d42ea93d8c41a0a3a668074b1303d051f744 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Mon, 27 Nov 2023 19:53:58 +0000
Subject: [PATCH] JAL-4238 minor errors fixed for JalviewJS structure
 colouring

---
 src/jalview/structure/StructureCommandsBase.java           |    6 ++++--
 src/jalview/structures/models/AAStructureBindingModel.java |   12 ++++++++++++
 2 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/src/jalview/structure/StructureCommandsBase.java b/src/jalview/structure/StructureCommandsBase.java
index ec6032d..02efe70 100644
--- a/src/jalview/structure/StructureCommandsBase.java
+++ b/src/jalview/structure/StructureCommandsBase.java
@@ -26,8 +26,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 
-import jalview.bin.Console;
-
 /**
  * A base class holding methods useful to all classes that implement commands
  * for structure viewers
@@ -133,6 +131,10 @@ public abstract class StructureCommandsBase implements StructureCommandsI
   public List<StructureCommandI> colourBySequence(
           Map<Object, AtomSpecModel> colourMap)
   {
+    if (colourMap == null)
+    {
+      return null;
+    }
     List<StructureCommandI> commands = new ArrayList<>();
     StringBuilder sb = new StringBuilder(colourMap.size() * 20);
     boolean first = true;
diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index dc3cc1e..b984725 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -750,6 +750,10 @@ public abstract class AAStructureBindingModel
     /*
      * give up after 10 secs plus 1 sec per file
      */
+    if (files == null)
+    {
+      return true;
+    }
     long starttime = System.currentTimeMillis();
     long endTime = 10000 + 1000 * files.length + starttime;
     String notLoaded = null;
@@ -1095,6 +1099,10 @@ public abstract class AAStructureBindingModel
   public List<String> executeCommands(List<StructureCommandI> commands,
           boolean getReply, String msg)
   {
+    if (commands == null)
+    {
+      return null;
+    }
     return executeCommand(getReply, msg,
             commands.toArray(new StructureCommandI[commands.size()]));
   }
@@ -1350,6 +1358,10 @@ public abstract class AAStructureBindingModel
           AlignmentViewPanel viewPanel)
   {
     String[] files = getStructureFiles();
+    if (files == null)
+    {
+      return null;
+    }
     SequenceRenderer sr = getSequenceRenderer(viewPanel);
     FeatureRenderer fr = viewPanel.getFeatureRenderer();
     FeatureColourFinder finder = new FeatureColourFinder(fr);
-- 
1.7.10.2