X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=ba72831c4f402de84217a42bdad948a8cfd59c5d;hb=fd86db8856109e69c21a5f4102bc8dd94664ae1f;hp=2d57bc4ce916f7a90b696d6069e23003d88f417a;hpb=173c541c3bdef7cee4f72a76cc8e23e8902a8614;p=jalview.git

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 2d57bc4..ba72831 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -6,7 +6,6 @@ import java.net.URISyntaxException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
-import java.util.EnumSet;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
@@ -15,11 +14,11 @@ import java.util.Map;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Jalview.ExitCode;
 import jalview.bin.argparser.Arg;
 import jalview.bin.argparser.ArgParser;
 import jalview.bin.argparser.ArgParser.Position;
 import jalview.bin.argparser.ArgValue;
-import jalview.bin.argparser.ArgValues;
 import jalview.bin.argparser.ArgValuesMap;
 import jalview.bin.argparser.SubVals;
 import jalview.datamodel.AlignmentI;
@@ -45,6 +44,9 @@ import jalview.io.FileLoader;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
+import jalview.io.exceptions.ImageOutputException;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
 import jalview.structure.StructureImportSettings.TFType;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.FileUtils;
@@ -65,10 +67,14 @@ public class Commands
 
   private Map<String, AlignFrame> afMap;
 
+  private Map<String, List<StructureViewer>> svMap;
+
   private boolean commandArgsProvided = false;
 
   private boolean argsWereParsed = false;
 
+  private List<String> errors = new ArrayList<>();
+
   public Commands(ArgParser argparser, boolean headless)
   {
     this(Desktop.instance, argparser, headless);
@@ -80,16 +86,15 @@ 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)
@@ -98,17 +103,35 @@ 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);
+        while (af != null && af.getViewport().isCalcInProgress())
+        {
+          try
+          {
+            Thread.sleep(25);
+          } catch (Exception q)
+          {
+          }
+          ;
+        }
+
         theseArgsWereParsed &= processImages(id);
+
         if (processLinkedOkay)
+        {
           theseArgsWereParsed &= processOutput(id);
+        }
 
         // close ap
         if (avm.getBoolean(Arg.CLOSE))
         {
-          AlignFrame af = afMap.get(id);
+          af = afMap.get(id);
           if (af != null)
           {
             af.closeMenuItem_actionPerformed(true);
@@ -118,9 +141,18 @@ public class Commands
       }
 
     }
+
+    // report errors
+    Console.warn(
+            "The following errors and warnings occurred whilst processing files:\n"
+                    + errorsToString());
+    // gui errors reported in Jalview
+
     if (argParser.getBoolean(Arg.QUIT))
     {
-      Jalview.getInstance().quit();
+      Jalview.getInstance().exit(
+              "Exiting due to " + Arg.QUIT.argString() + " argument.",
+              ExitCode.OK);
       return true;
     }
     // carry on with jalview.bin.Jalview
@@ -138,25 +170,20 @@ public class Commands
     return argsWereParsed;
   }
 
-  protected boolean processUnlinked(String id)
-  {
-    return processLinked(id);
-  }
-
   protected boolean processLinked(String id)
   {
     boolean theseArgsWereParsed = false;
     ArgValuesMap avm = argParser.getLinkedArgs(id);
     if (avm == null)
+    {
       return true;
+    }
+
+    Boolean isError = Boolean.valueOf(false);
+
+    // set wrap scope here so it can be applied after structures are opened
+    boolean wrap = false;
 
-    /*
-     * // script to execute after all loading is completed one way or another String
-     * groovyscript = m.get(Arg.GROOVY) == null ? null :
-     * m.get(Arg.GROOVY).getValue(); String file = m.get(Arg.OPEN) == null ? null :
-     * m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null;
-     * DataSourceType protocol = null;
-     */
     if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
     {
       commandArgsProvided = true;
@@ -205,7 +232,9 @@ public class Commands
           {
             if (!(new File(openFile)).exists())
             {
-              Console.warn("Can't find file '" + openFile + "'");
+              addError("Can't find file '" + openFile + "'");
+              isError = true;
+              continue;
             }
           }
         }
@@ -219,7 +248,9 @@ public class Commands
           format = new IdentifyFile().identify(openFile, protocol);
         } catch (FileFormatException e1)
         {
-          Console.error("Unknown file format for '" + openFile + "'");
+          addError("Unknown file format for '" + openFile + "'");
+          isError = true;
+          continue;
         }
 
         af = afMap.get(id);
@@ -236,21 +267,46 @@ public class Commands
           Console.debug(
                   "Opening '" + openFile + "' in new alignment frame");
           FileLoader fileLoader = new FileLoader(!headless);
-
-          af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
-                  format);
-
-          // wrap alignment?
-          boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
-                  null, "WRAP_ALIGNMENT", false);
-          af.getCurrentView().setWrapAlignment(wrap);
+          boolean xception = false;
+          try
+          {
+            af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
+                    format);
+          } catch (Throwable thr)
+          {
+            xception = true;
+            addError("Couldn't open '" + openFile + "' as " + format + " "
+                    + thr.getLocalizedMessage()
+                    + " (Enable debug for full stack trace)");
+            isError = true;
+            Console.debug("Exception when opening '" + openFile + "'", thr);
+          } finally
+          {
+            if (af == null && !xception)
+            {
+              addInfo("Ignoring '" + openFile
+                      + "' - no alignment data found.");
+              continue;
+            }
+          }
 
           // colour alignment?
           String colour = ArgParser.getFromSubValArgOrPref(avm, av,
                   Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
           if ("" != colour)
           {
-            af.changeColour_actionPerformed(colour);
+            ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+                    af.getViewport(), af.getViewport().getAlignment(),
+                    colour);
+
+            if (cs == null && !"None".equals(colour))
+            {
+              addWarn("Couldn't parse '" + colour + "' as a colourscheme.");
+            }
+            else
+            {
+              af.changeColour(cs);
+            }
             Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
           }
 
@@ -309,7 +365,8 @@ public class Commands
                       "examples/testdata/uniref50_test_tree", treefile);
             } catch (IOException e)
             {
-              Console.warn("Couldn't add tree " + treefile, e);
+              addError("Couldn't add tree " + treefile, e);
+              isError = true;
             }
           }
 
@@ -337,6 +394,12 @@ public class Commands
                     false, false);
           }
 
+          // wrap alignment? do this last for formatting reasons
+          wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv, null,
+                  "WRAP_ALIGNMENT", false);
+          // af.setWrapFormat(wrap) is applied after structures are opened for
+          // annotation reasons
+
           // store the AlignFrame for this id
           afMap.put(id, af);
 
@@ -369,11 +432,12 @@ public class Commands
       {
         if (headless)
         {
-          Jalview.exit("Could not open any files in headless mode", 1);
+          Jalview.exit("Could not open any files in headless mode",
+                  ExitCode.NO_FILES);
         }
         else
         {
-          Console.warn("No more files to open");
+          Console.info("No more files to open");
         }
       }
       if (progressBarSet && desktop != null)
@@ -403,10 +467,8 @@ public class Commands
 
           if (seq == null)
           {
-            Console.warn("Could not find sequence for argument "
+            addWarn("Could not find sequence for argument "
                     + Arg.STRUCTURE.argString() + "=" + val);
-            // you probably want to continue here, not break
-            // break;
             continue;
           }
           File structureFile = null;
@@ -439,28 +501,20 @@ public class Commands
 
           if (structureFile == null)
           {
-            Console.warn("Not provided structure file with '" + val + "'");
+            addWarn("Not provided structure file with '" + val + "'");
             continue;
           }
 
           if (!structureFile.exists())
           {
-            Console.warn("Structure file '"
-                    + structureFile.getAbsoluteFile() + "' not found.");
+            addWarn("Structure file '" + structureFile.getAbsoluteFile()
+                    + "' not found.");
             continue;
           }
 
           Console.debug("Using structure file "
                   + structureFile.getAbsolutePath());
 
-          // ##### Does this need to happen? Follow
-          // openStructureFileForSequence() below
-          /*
-          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-                  .associatePdbWithSeq(structureFile.getAbsolutePath(),
-                          DataSourceType.FILE, seq, true, Desktop.instance);
-                          */
-
           // open structure view
           AlignmentPanel ap = af.alignPanel;
           if (headless)
@@ -486,7 +540,7 @@ public class Commands
             } catch (IOException e)
             {
               paeFilepath = paeFile.getAbsolutePath();
-              Console.warn("Problem with the PAE file path: '"
+              addWarn("Problem with the PAE file path: '"
                       + paeFile.getPath() + "'");
             }
           }
@@ -502,18 +556,10 @@ public class Commands
                   .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
                           Arg.TEMPFAC, Position.AFTER, av, subVals, null,
                           null, null);
-          boolean notempfac = ArgParser.getBoolFromSubValOrArg(avm,
-                  Arg.NOTEMPFAC, subVals);
+          boolean notempfac = ArgParser.getFromSubValArgOrPref(avm,
+                  Arg.NOTEMPFAC, subVals, null, "ADD_TEMPFACT_ANN", false,
+                  true);
           TFType tft = notempfac ? null : TFType.DEFAULT;
-          /*
-          String tftString = subVals.get("tempfac");
-          ArgValue tftAv = getArgAssociatedWithStructure(Arg.TEMPFAC, avm,
-                  af, structureFilepath);
-          if (tftString == null && tftAv != null)
-          {
-            tftString = tftAv.getSubVals().getContent();
-          }
-          */
           if (tftString != null && !notempfac)
           {
             // get kind of temperature factor annotation
@@ -537,31 +583,14 @@ public class Commands
                 if (it.hasNext())
                   sb.append(", ");
               }
-              Console.warn(sb.toString());
+              addWarn(sb.toString());
             }
           }
 
           String sViewer = ArgParser.getFromSubValArgOrPref(avm,
                   Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null,
                   null, "jmol");
-          ViewerType viewerType = null;
-          if (!"none".equals(sViewer))
-          {
-            for (ViewerType v : EnumSet.allOf(ViewerType.class))
-            {
-              String name = v.name().toLowerCase(Locale.ROOT)
-                      .replaceAll(" ", "");
-              if (sViewer.equals(name))
-              {
-                viewerType = v;
-                break;
-              }
-            }
-          }
-
-          boolean addTempFac = notempfac ? false
-                  : ((tft != null)
-                          || Cache.getDefault("ADD_TEMPFACT_ANN", false));
+          ViewerType viewerType = ViewerType.getFromString(sViewer);
 
           // TODO use ssFromStructure
           StructureViewer sv = StructureChooser
@@ -569,26 +598,73 @@ public class Commands
                           structureFilepath, tft, paeFilepath, false,
                           ssFromStructure, false, viewerType);
 
-          if (headless)
+          if (sv == null)
+          {
+            addError("Failed to import and open structure view for file '"
+                    + structureFile + "'.");
+            continue;
+          }
+          try
+          {
+            long tries = 1000;
+            while (sv.isBusy() && tries > 0)
+            {
+              Thread.sleep(25);
+              if (sv.isBusy())
+              {
+                tries--;
+                Console.debug(
+                        "Waiting for viewer for " + structureFilepath);
+              }
+            }
+            if (tries == 0 && sv.isBusy())
+            {
+              addWarn("Gave up waiting for structure viewer to load file '"
+                      + structureFile
+                      + "'. Something may have gone wrong.");
+            }
+          } catch (Exception x)
+          {
+            addError("Exception whilst waiting for structure viewer "
+                    + structureFilepath, x);
+            isError = true;
+          }
+
+          // add StructureViewer to svMap list
+          if (svMap == null)
+          {
+            svMap = new HashMap<>();
+          }
+          if (svMap.get(id) == null)
           {
-            sv.setAsync(false);
+            svMap.put(id, new ArrayList<>());
           }
+          svMap.get(id).add(sv);
 
+          Console.debug(
+                  "Successfully opened viewer for " + structureFilepath);
           String structureImageFilename = ArgParser.getValueFromSubValOrArg(
                   avm, av, Arg.STRUCTUREIMAGE, subVals);
           if (sv != null && structureImageFilename != null)
           {
+            ArgValue siAv = avm.getClosestNextArgValueOfArg(av,
+                    Arg.STRUCTUREIMAGE);
+            SubVals sisv = null;
+            if (structureImageFilename.equals(siAv.getValue()))
+            {
+              sisv = siAv.getSubVals();
+            }
             File structureImageFile = new File(structureImageFilename);
             String width = ArgParser.getValueFromSubValOrArg(avm, av,
-                    Arg.STRUCTUREIMAGEWIDTH, subVals);
+                    Arg.STRUCTUREIMAGEWIDTH, sisv);
             String height = ArgParser.getValueFromSubValOrArg(avm, av,
-                    Arg.STRUCTUREIMAGEHEIGHT, subVals);
+                    Arg.STRUCTUREIMAGEHEIGHT, sisv);
             String scale = ArgParser.getValueFromSubValOrArg(avm, av,
-                    Arg.STRUCTUREIMAGESCALE, subVals);
+                    Arg.STRUCTUREIMAGESCALE, sisv);
             String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
-                    Arg.STRUCTUREIMAGETEXTRENDERER, subVals);
+                    Arg.STRUCTUREIMAGETEXTRENDERER, sisv);
             String typeS = ArgParser.getValueFromSubValOrArg(avm, av,
-                    Arg.STRUCTUREIMAGETYPE, subVals);
+                    Arg.STRUCTUREIMAGETYPE, sisv);
             if (typeS == null || typeS.length() == 0)
             {
               typeS = FileUtils.getExtension(structureImageFile);
@@ -600,42 +676,66 @@ public class Commands
                       typeS.toUpperCase(Locale.ROOT));
             } catch (IllegalArgumentException e)
             {
-              Console.warn("Do not know image format '" + typeS
+              addWarn("Do not know image format '" + typeS
                       + "', using PNG");
               imageType = TYPE.PNG;
             }
             BitmapImageSizing userBis = ImageMaker
                     .parseScaleWidthHeightStrings(scale, width, height);
-            switch (sv.getViewerType())
+            // TODO MAKE THIS VIEWER INDEPENDENT!!
+            switch (StructureViewer.getViewerType())
             {
             case JMOL:
-              try
-              {
-                Thread.sleep(1000);
-              } catch (InterruptedException e)
-              {
-                // TODO Auto-generated catch block
-                e.printStackTrace();
-              }
               JalviewStructureDisplayI sview = sv
                       .getJalviewStructureDisplay();
               if (sview instanceof AppJmol)
               {
                 AppJmol jmol = (AppJmol) sview;
-                jmol.makePDBImage(structureImageFile, imageType, renderer,
-                        userBis);
+                try
+                {
+                  boolean success = this.checksBeforeWritingToFile(avm,
+                          subVals, false, structureImageFilename,
+                          "structure image", isError);
+                  if (!success)
+                  {
+                    continue;
+                  }
+
+                  Console.debug("Rendering image to " + structureImageFile);
+                  jmol.makePDBImage(structureImageFile, imageType, renderer,
+                          userBis);
+                  Console.debug("Finished Rendering image to "
+                          + structureImageFile);
+
+                } catch (ImageOutputException ioexc)
+                {
+                  addError("Unexpected error whilst exporting image to "
+                          + structureImageFile, ioexc);
+                  isError = true;
+                  continue;
+                }
+
               }
               break;
             default:
-              Console.warn("Cannot export image for structure viewer "
+              addWarn("Cannot export image for structure viewer "
                       + sv.getViewerType() + " yet");
-              break;
+              continue;
             }
           }
         }
       }
     }
 
+    if (wrap)
+    {
+      AlignFrame af = afMap.get(id);
+      if (af != null)
+      {
+        af.setWrapFormat(wrap, true);
+      }
+    }
+
     /*
     boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
     if (doShading)
@@ -653,7 +753,7 @@ public class Commands
     }
     */
 
-    return theseArgsWereParsed;
+    return theseArgsWereParsed && !isError;
   }
 
   protected void processGroovyScript(String id)
@@ -663,7 +763,7 @@ public class Commands
 
     if (af == null)
     {
-      Console.warn("Did not have an alignment window for id=" + id);
+      addWarn("Did not have an alignment window for id=" + id);
       return;
     }
 
@@ -687,10 +787,11 @@ public class Commands
 
     if (af == null)
     {
-      Console.warn("Did not have an alignment window for id=" + id);
+      addWarn("Did not have an alignment window for id=" + id);
       return false;
     }
 
+    Boolean isError = Boolean.valueOf(false);
     if (avm.containsArg(Arg.IMAGE))
     {
       for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
@@ -732,57 +833,73 @@ public class Commands
 
         Console.info("Writing " + file);
 
-        switch (type)
+        boolean success = checksBeforeWritingToFile(avm, subVal, false,
+                fileName, "image", isError);
+        if (!success)
         {
+          continue;
+        }
 
-        case "svg":
-          Console.debug("Outputting type '" + type + "' to " + fileName);
-          af.createSVG(file, renderer);
-          break;
-
-        case "png":
-          Console.debug("Outputting type '" + type + "' to " + fileName);
-          af.createPNG(file, null, userBis);
-          break;
-
-        case "html":
-          Console.debug("Outputting type '" + type + "' to " + fileName);
-          HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
-          htmlSVG.exportHTML(fileName, renderer);
-          break;
-
-        case "biojs":
-          try
-          {
-            BioJsHTMLOutput.refreshVersionInfo(
-                    BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
-          } catch (URISyntaxException e)
+        try
+        {
+          switch (type)
           {
-            e.printStackTrace();
-          }
-          BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
-          bjs.exportHTML(fileName);
-          Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName);
-          break;
-
-        case "eps":
-          af.createEPS(file, name);
-          Console.debug("Creating EPS file: " + fileName);
-          break;
 
-        case "imagemap":
-          af.createImageMap(file, name);
-          Console.debug("Creating ImageMap file: " + fileName);
-          break;
-
-        default:
-          Console.warn(Arg.IMAGE.argString() + " type '" + type
-                  + "' not known. Ignoring");
-          break;
+          case "svg":
+            Console.debug("Outputting type '" + type + "' to " + fileName);
+            af.createSVG(file, renderer);
+            break;
+
+          case "png":
+            Console.debug("Outputting type '" + type + "' to " + fileName);
+            af.createPNG(file, null, userBis);
+            break;
+
+          case "html":
+            Console.debug("Outputting type '" + type + "' to " + fileName);
+            HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+            htmlSVG.exportHTML(fileName, renderer);
+            break;
+
+          case "biojs":
+            Console.debug(
+                    "Outputting BioJS MSA Viwer HTML file: " + fileName);
+            try
+            {
+              BioJsHTMLOutput.refreshVersionInfo(
+                      BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+            } catch (URISyntaxException e)
+            {
+              e.printStackTrace();
+            }
+            BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+            bjs.exportHTML(fileName);
+            break;
+
+          case "eps":
+            Console.debug("Outputting EPS file: " + fileName);
+            af.createEPS(file, renderer);
+            break;
+
+          case "imagemap":
+            Console.debug("Outputting ImageMap file: " + fileName);
+            af.createImageMap(file, name);
+            break;
+
+          default:
+            addWarn(Arg.IMAGE.argString() + " type '" + type
+                    + "' not known. Ignoring");
+            break;
+          }
+        } catch (Exception ioex)
+        {
+          addError("Unexpected error during export to '" + fileName + "'",
+                  ioex);
+          isError = true;
         }
       }
     }
-    return true;
+    return !isError;
   }
 
   protected boolean processOutput(String id)
@@ -792,10 +909,12 @@ public class Commands
 
     if (af == null)
     {
-      Console.warn("Did not have an alignment window for id=" + id);
+      addWarn("Did not have an alignment window for id=" + id);
       return false;
     }
 
+    Boolean isError = Boolean.valueOf(false);
+
     if (avm.containsArg(Arg.OUTPUT))
     {
       for (ArgValue av : avm.getArgValueList(Arg.OUTPUT))
@@ -803,25 +922,8 @@ public class Commands
         String val = av.getValue();
         SubVals subVals = av.getSubVals();
         String fileName = subVals.getContent();
+        boolean stdout = ArgParser.STDOUTFILENAME.equals(fileName);
         File file = new File(fileName);
-        boolean overwrite = ArgParser.getFromSubValArgOrPref(avm,
-                Arg.OVERWRITE, subVals, null, "OVERWRITE_OUTPUT", false);
-        // backups. Use the Arg.BACKUPS or subval "backups" setting first,
-        // otherwise if headless assume false, if not headless use the user
-        // preference with default true.
-        boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS,
-                subVals, null,
-                Platform.isHeadless() ? null : BackupFiles.ENABLED,
-                !Platform.isHeadless());
-
-        // if backups is not true then --overwrite must be specified
-        if (file.exists() && !(overwrite || backups))
-        {
-          Console.error("Won't overwrite file '" + fileName + "' without "
-                  + Arg.OVERWRITE.argString() + " or "
-                  + Arg.BACKUPS.argString() + " set");
-          return false;
-        }
 
         String name = af.getName();
         String format = ArgParser.getValueFromSubValOrArg(avm, av,
@@ -853,52 +955,62 @@ public class Commands
         }
         if (ff == null)
         {
-          StringBuilder validSB = new StringBuilder();
-          for (String f : validFormats)
-          {
-            if (validSB.length() > 0)
-              validSB.append(", ");
-            validSB.append(f);
-            FileFormatI tff = ffs.forName(f);
-            validSB.append(" (");
-            validSB.append(tff.getExtensions());
-            validSB.append(")");
-          }
-
-          Jalview.exit("No valid format specified for "
-                  + Arg.OUTPUT.argString() + ". Valid formats are "
-                  + validSB.toString() + ".", 1);
-          // this return really shouldn't happen
-          return false;
+          if (stdout)
+          {
+            ff = FileFormat.Fasta;
+          }
+          else
+          {
+            StringBuilder validSB = new StringBuilder();
+            for (String f : validFormats)
+            {
+              if (validSB.length() > 0)
+                validSB.append(", ");
+              validSB.append(f);
+              FileFormatI tff = ffs.forName(f);
+              validSB.append(" (");
+              validSB.append(tff.getExtensions());
+              validSB.append(")");
+            }
+
+            addError("No valid format specified for "
+                    + Arg.OUTPUT.argString() + ". Valid formats are "
+                    + validSB.toString() + ".");
+            continue;
+          }
+        }
+
+        boolean success = checksBeforeWritingToFile(avm, subVals, true,
+                fileName, ff.getName(), isError);
+        if (!success)
+        {
+          continue;
         }
 
-        String savedBackupsPreference = Cache
-                .getDefault(BackupFiles.ENABLED, null);
-        Console.debug("Setting backups to " + backups);
-        Cache.applicationProperties.put(BackupFiles.ENABLED,
-                Boolean.toString(backups));
+        boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS,
+                subVals, null,
+                Platform.isHeadless() ? null : BackupFiles.ENABLED,
+                !Platform.isHeadless());
 
         Console.info("Writing " + fileName);
 
-        af.saveAlignment(fileName, ff);
-        Console.debug("Returning backups to " + savedBackupsPreference);
-        if (savedBackupsPreference != null)
-          Cache.applicationProperties.put(BackupFiles.ENABLED,
-                  savedBackupsPreference);
+        af.saveAlignment(fileName, ff, stdout, backups);
         if (af.isSaveAlignmentSuccessful())
         {
           Console.debug("Written alignment '" + name + "' in "
-                  + ff.getName() + " format to " + file);
+                  + ff.getName() + " format to '" + file + "'");
         }
         else
         {
-          Console.warn("Error writing file " + file + " in " + ff.getName()
+          addError("Error writing file '" + file + "' in " + ff.getName()
                   + " format!");
+          isError = true;
+          continue;
         }
 
       }
     }
-    return true;
+    return !isError;
   }
 
   private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm,
@@ -909,9 +1021,15 @@ public class Commands
     SequenceI seq = null;
     if (subVals == null && idAv == null)
       return null;
+    if (af == null || af.getCurrentView() == null)
+    {
+      return null;
+    }
     AlignmentI al = af.getCurrentView().getAlignment();
     if (al == null)
+    {
       return null;
+    }
     if (subVals != null)
     {
       if (subVals.has(Arg.SEQID.getName()))
@@ -924,60 +1042,125 @@ public class Commands
         seq = al.getSequenceAt(subVals.getIndex());
       }
     }
-    else if (idAv != null)
+    if (seq == null && idAv != null)
     {
       seq = al.findName(idAv.getValue());
     }
     return seq;
   }
 
-  // returns the first Arg value intended for the structure structFilename
-  // (in the given AlignFrame from the ArgValuesMap)
-  private ArgValue getArgAssociatedWithStructure(Arg arg, ArgValuesMap avm,
-          AlignFrame af, String structFilename)
+  public AlignFrame[] getAlignFrames()
   {
-    if (af != null)
+    AlignFrame[] afs = null;
+    if (afMap != null)
     {
-      for (ArgValue av : avm.getArgValueList(arg))
-      {
-        SubVals subVals = av.getSubVals();
-        String structid = subVals.get("structid");
-        String structfile = subVals.get("structfile");
+      afs = (AlignFrame[]) afMap.values().toArray();
+    }
 
-        // let's find a structure
-        if (structfile == null && structid == null)
-        {
-          ArgValue likelyStructure = avm.getClosestPreviousArgValueOfArg(av,
-                  Arg.STRUCTURE);
-          if (likelyStructure != null)
-          {
-            SubVals sv = likelyStructure.getSubVals();
-            if (sv != null && sv.has(ArgValues.ID))
-            {
-              structid = sv.get(ArgValues.ID);
-            }
-            else
-            {
-              structfile = likelyStructure.getValue();
-            }
-          }
-        }
+    return afs;
+  }
 
-        if (structfile == null && structid != null)
-        {
-          StructureSelectionManager ssm = StructureSelectionManager
-                  .getStructureSelectionManager(Desktop.instance);
-          if (ssm != null)
-          {
-            structfile = ssm.findFileForPDBId(structid);
-          }
-        }
-        if (structfile != null && structfile.equals(structFilename))
+  public List<StructureViewer> getStructureViewers()
+  {
+    List<StructureViewer> svs = null;
+    if (svMap != null)
+    {
+      for (List<StructureViewer> svList : svMap.values())
+      {
+        if (svs == null)
         {
-          return av;
+          svs = new ArrayList<>();
         }
+        svs.addAll(svList);
       }
     }
-    return null;
+    return svs;
+  }
+
+  private void addInfo(String errorMessage)
+  {
+    Console.info(errorMessage);
+    errors.add(errorMessage);
+  }
+
+  private void addWarn(String errorMessage)
+  {
+    Console.warn(errorMessage);
+    errors.add(errorMessage);
+  }
+
+  private void addError(String errorMessage)
+  {
+    addError(errorMessage, null);
+  }
+
+  private void addError(String errorMessage, Exception e)
+  {
+    Console.error(errorMessage, e);
+    errors.add(errorMessage);
+  }
+
+  private boolean checksBeforeWritingToFile(ArgValuesMap avm,
+          SubVals subVal, boolean includeBackups, String filename,
+          String adjective, Boolean isError)
+  {
+    File file = new File(filename);
+
+    boolean overwrite = ArgParser.getFromSubValArgOrPref(avm, Arg.OVERWRITE,
+            subVal, null, "OVERWRITE_OUTPUT", false);
+    boolean stdout = false;
+    boolean backups = false;
+    if (includeBackups)
+    {
+      stdout = ArgParser.STDOUTFILENAME.equals(filename);
+      // backups. Use the Arg.BACKUPS or subval "backups" setting first,
+      // otherwise if headless assume false, if not headless use the user
+      // preference with default true.
+      backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS, subVal,
+              null, Platform.isHeadless() ? null : BackupFiles.ENABLED,
+              !Platform.isHeadless());
+    }
+
+    if (file.exists() && !(overwrite || backups || stdout))
+    {
+      addWarn("Won't overwrite file '" + filename + "' without "
+              + Arg.OVERWRITE.argString()
+              + (includeBackups ? " or " + Arg.BACKUPS.argString() : "")
+              + " set");
+      return false;
+    }
+
+    boolean mkdirs = ArgParser.getFromSubValArgOrPref(avm, Arg.MKDIRS,
+            subVal, null, "MKDIRS_OUTPUT", false);
+
+    if (!FileUtils.checkParentDir(file, mkdirs))
+    {
+      addError("Directory '"
+              + FileUtils.getParentDir(file).getAbsolutePath()
+              + "' does not exist for " + adjective + " file '" + filename
+              + "'."
+              + (mkdirs ? "" : "  Try using " + Arg.MKDIRS.argString()));
+      isError = true;
+      return false;
+    }
+
+    return true;
+  }
+
+  public List<String> getErrors()
+  {
+    return errors;
+  }
+
+  public String errorsToString()
+  {
+    StringBuilder sb = new StringBuilder();
+    for (String error : errors)
+    {
+      if (sb.length() > 0)
+        sb.append("\n");
+      sb.append("- " + error);
+    }
+    return sb.toString();
   }
 }