JAL-629 Fix --structureimage and options

[jalview.git] / src / jalview / bin / Commands.java

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 17a1af2..e409c77 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -67,6 +67,8 @@ public class Commands
 
   private Map<String, AlignFrame> afMap;
 
+  private Map<String, List<StructureViewer>> svMap;
+
   private boolean commandArgsProvided = false;
 
   private boolean argsWereParsed = false;
@@ -82,16 +84,15 @@ public class Commands
     headless = h;
     desktop = d;
     afMap = new HashMap<>();
-    if (argparser != null)
-    {
-      processArgs(argparser, headless);
-    }
   }
 
-  private boolean processArgs(ArgParser argparser, boolean h)
+  protected boolean processArgs()
   {
-    argParser = argparser;
-    headless = h;
+    if (argParser == null)
+    {
+      return true;
+    }
+
     boolean theseArgsWereParsed = false;
 
     if (argParser != null && argParser.getLinkedIds() != null)
@@ -100,9 +101,10 @@ public class Commands
       {
         ArgValuesMap avm = argParser.getLinkedArgs(id);
         theseArgsWereParsed = true;
-        theseArgsWereParsed &= processLinked(id);
+        boolean processLinkedOkay = processLinked(id);
+        theseArgsWereParsed &= processLinkedOkay;
+
         processGroovyScript(id);
-        boolean processLinkedOkay = theseArgsWereParsed;
 
         // wait around until alignFrame isn't busy
         AlignFrame af = afMap.get(id);
@@ -118,8 +120,11 @@ public class Commands
         }
 
         theseArgsWereParsed &= processImages(id);
+
         if (processLinkedOkay)
+        {
           theseArgsWereParsed &= processOutput(id);
+        }
 
         // close ap
         if (avm.getBoolean(Arg.CLOSE))
@@ -154,11 +159,6 @@ public class Commands
     return argsWereParsed;
   }
 
-  protected boolean processUnlinked(String id)
-  {
-    return processLinked(id);
-  }
-
   protected boolean processLinked(String id)
   {
     boolean theseArgsWereParsed = false;
@@ -605,6 +605,18 @@ public class Commands
             Console.warn("Exception whilst waiting for structure viewer "
                     + structureFilepath, x);
           }
+
+          // add StructureViewer to svMap list
+          if (svMap == null)
+          {
+            svMap = new HashMap<>();
+          }
+          if (svMap.get(id) == null)
+          {
+            svMap.put(id, new ArrayList<>());
+          }
+          svMap.get(id).add(sv);
+
           Console.debug(
                   "Successfully opened viewer for " + structureFilepath);
           String structureImageFilename = ArgParser.getValueFromSubValOrArg(
@@ -650,14 +662,6 @@ public class Commands
             switch (StructureViewer.getViewerType())
             {
             case JMOL:
-              try
-              {
-                Thread.sleep(1000); // WHY ???
-              } catch (InterruptedException e)
-              {
-                // TODO Auto-generated catch block
-                e.printStackTrace();
-              }
               JalviewStructureDisplayI sview = sv
                       .getJalviewStructureDisplay();
               if (sview instanceof AppJmol)
@@ -1003,4 +1007,32 @@ public class Commands
     }
     return seq;
   }
+
+  public AlignFrame[] getAlignFrames()
+  {
+    AlignFrame[] afs = null;
+    if (afMap != null)
+    {
+      afs = (AlignFrame[]) afMap.values().toArray();
+    }
+
+    return afs;
+  }
+
+  public List<StructureViewer> getStructureViewers()
+  {
+    List<StructureViewer> svs = null;
+    if (svMap != null)
+    {
+      for (List<StructureViewer> svList : svMap.values())
+      {
+        if (svs == null)
+        {
+          svs = new ArrayList<>();
+        }
+        svs.addAll(svList);
+      }
+    }
+    return svs;
+  }
 }