X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=17a1af23857becde1dd2db1095896f1b3e58ae6b;hb=91bb9b5c473c14f3381fbea3570b4dc1875b68f2;hp=a0209fd531d6d48581999e0e7c11074b28f4db25;hpb=9b365118ea304f5843ddcf6c8be8478a9d387330;p=jalview.git

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index a0209fd..17a1af2 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -14,11 +14,11 @@ import java.util.Locale;
 import java.util.Map;
 
 import jalview.analysis.AlignmentUtils;
+import jalview.api.structures.JalviewStructureDisplayI;
 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;
@@ -26,6 +26,7 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignmentPanel;
+import jalview.gui.AppJmol;
 import jalview.gui.Desktop;
 import jalview.gui.Preferences;
 import jalview.gui.StructureChooser;
@@ -43,11 +44,18 @@ 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;
 import jalview.util.HttpUtils;
+import jalview.util.ImageMaker;
+import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.util.imagemaker.BitmapImageSizing;
 
 public class Commands
 {
@@ -73,7 +81,7 @@ public class Commands
     argParser = argparser;
     headless = h;
     desktop = d;
-    afMap = new HashMap<String, AlignFrame>();
+    afMap = new HashMap<>();
     if (argparser != null)
     {
       processArgs(argparser, headless);
@@ -95,6 +103,20 @@ public class Commands
         theseArgsWereParsed &= processLinked(id);
         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);
@@ -102,7 +124,7 @@ public class Commands
         // close ap
         if (avm.getBoolean(Arg.CLOSE))
         {
-          AlignFrame af = afMap.get(id);
+          af = afMap.get(id);
           if (af != null)
           {
             af.closeMenuItem_actionPerformed(true);
@@ -244,7 +266,19 @@ public class Commands
                   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))
+            {
+              Console.warn(
+                      "Couldn't parse '" + colour + "' as a colourscheme.");
+            }
+            else
+            {
+              af.changeColour(cs);
+            }
             Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
           }
 
@@ -309,7 +343,7 @@ public class Commands
 
           // Show secondary structure annotations?
           boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
-                  Arg.SSANNOTATIONS, av.getSubVals(), null,
+                  Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
                   "STRUCT_FROM_PDB", true);
           af.setAnnotationsVisibility(showSSAnnotations, true, false);
 
@@ -330,33 +364,6 @@ public class Commands
                     af.getCurrentView().getAlignment(), hideThese, null,
                     false, false);
           }
-          else
-          /*
-           * comment out hacky approach up to here and add this line: if
-           * (showTemperatureFactor)
-           */
-          {
-            /*
-            if (avm.containsArg(Arg.TEMPFAC_LABEL))
-            {
-              AlignmentAnnotation aa = AlignmentUtils
-                      .getFirstSequenceAnnotationOfType(
-                              af.getCurrentView().getAlignment(),
-                              AlignmentAnnotation.LINE_GRAPH);
-              String label = avm.getValue(Arg.TEMPFAC_LABEL);
-              if (aa != null)
-              {
-                aa.label = label;
-              }
-              else
-              {
-                Console.info(
-                        "Could not find annotation to apply tempfac_label '"
-                                + label);
-              }
-            }
-            */
-          }
 
           // store the AlignFrame for this id
           afMap.put(id, af);
@@ -413,7 +420,7 @@ public class Commands
         {
           String val = av.getValue();
           SubVals subVals = av.getSubVals();
-          SequenceI seq = getSpecifiedSequence(af, subVals);
+          SequenceI seq = getSpecifiedSequence(af, avm, av);
           if (seq == null)
           {
             // Could not find sequence from subId, let's assume the first
@@ -474,14 +481,6 @@ public class Commands
           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)
@@ -493,14 +492,13 @@ public class Commands
           String structureFilepath = structureFile.getAbsolutePath();
 
           // get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
-          String paeFilepath = subVals.getWithSubstitutions(argParser, id,
-                  "paematrix");
-          ArgValue paeAv = getArgAssociatedWithStructure(Arg.PAEMATRIX, avm,
-                  af, structureFilepath);
-          if (paeFilepath == null && paeAv != null)
+          String paeFilepath = ArgParser
+                  .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
+                          Arg.PAEMATRIX, Position.AFTER, av, subVals, null,
+                          null, null);
+          if (paeFilepath != null)
           {
-            SubVals sv = paeAv.getSubVals();
-            File paeFile = new File(sv.getContent());
+            File paeFile = new File(paeFilepath);
 
             try
             {
@@ -515,21 +513,20 @@ public class Commands
 
           // showing annotations from structure file or not
           boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm,
-                  Arg.SSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
+                  Arg.SHOWSSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
                   true);
 
           // get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
           // reference annotations
-          String tftString = subVals.get("tempfac");
-          TFType tft = avm.getBoolean(Arg.NOTEMPFAC) ? null
-                  : TFType.DEFAULT;
-          ArgValue tftAv = getArgAssociatedWithStructure(Arg.TEMPFAC, avm,
-                  af, structureFilepath);
-          if (tftString == null && tftAv != null)
-          {
-            tftString = tftAv.getSubVals().getContent();
-          }
-          if (tftString != null)
+          String tftString = ArgParser
+                  .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
+                          Arg.TEMPFAC, Position.AFTER, av, subVals, null,
+                          null, null);
+          boolean notempfac = ArgParser.getFromSubValArgOrPref(avm,
+                  Arg.NOTEMPFAC, subVals, null, "ADD_TEMPFACT_ANN", false,
+                  true);
+          TFType tft = notempfac ? null : TFType.DEFAULT;
+          if (tftString != null && !notempfac)
           {
             // get kind of temperature factor annotation
             try
@@ -574,13 +571,120 @@ public class Commands
             }
           }
 
-          boolean addTempFac = tft != null
-                  || Cache.getDefault("ADD_TEMPFACT_ANN", false);
-
           // TODO use ssFromStructure
-          StructureChooser.openStructureFileForSequence(null, null, ap, seq,
-                  false, structureFilepath, tft, paeFilepath, false,
-                  ssFromStructure, false, viewerType);
+          StructureViewer sv = StructureChooser
+                  .openStructureFileForSequence(null, null, ap, seq, false,
+                          structureFilepath, tft, paeFilepath, false,
+                          ssFromStructure, false, viewerType);
+
+          if (sv == null)
+          {
+            Console.error("Failed to import and open structure view.");
+            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())
+            {
+              Console.warn(
+                      "Gave up waiting for structure viewer to load. Something may have gone wrong.");
+            }
+          } catch (Exception x)
+          {
+            Console.warn("Exception whilst waiting for structure viewer "
+                    + structureFilepath, x);
+          }
+          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, sisv);
+            String height = ArgParser.getValueFromSubValOrArg(avm, av,
+                    Arg.STRUCTUREIMAGEHEIGHT, sisv);
+            String scale = ArgParser.getValueFromSubValOrArg(avm, av,
+                    Arg.STRUCTUREIMAGESCALE, sisv);
+            String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
+                    Arg.STRUCTUREIMAGETEXTRENDERER, sisv);
+            String typeS = ArgParser.getValueFromSubValOrArg(avm, av,
+                    Arg.STRUCTUREIMAGETYPE, sisv);
+            if (typeS == null || typeS.length() == 0)
+            {
+              typeS = FileUtils.getExtension(structureImageFile);
+            }
+            TYPE imageType;
+            try
+            {
+              imageType = Enum.valueOf(TYPE.class,
+                      typeS.toUpperCase(Locale.ROOT));
+            } catch (IllegalArgumentException e)
+            {
+              Console.warn("Do not know image format '" + typeS
+                      + "', using PNG");
+              imageType = TYPE.PNG;
+            }
+            BitmapImageSizing userBis = ImageMaker
+                    .parseScaleWidthHeightStrings(scale, width, height);
+            // TODO MAKE THIS VIEWER INDEPENDENT!!
+            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)
+              {
+                AppJmol jmol = (AppJmol) sview;
+                try
+                {
+                  Console.debug("Rendering image to " + structureImageFile);
+                  jmol.makePDBImage(structureImageFile, imageType, renderer,
+                          userBis);
+                  Console.debug("Finished Rendering image to "
+                          + structureImageFile);
+
+                } catch (ImageOutputException ioexc)
+                {
+                  Console.warn("Unexpected error whilst exporting image to "
+                          + structureImageFile, ioexc);
+                }
+
+              }
+              break;
+            default:
+              Console.warn("Cannot export image for structure viewer "
+                      + sv.getViewerType() + " yet");
+              break;
+            }
+          }
         }
       }
     }
@@ -654,6 +758,16 @@ public class Commands
         if (renderer == null)
           renderer = "text";
         String type = "png"; // default
+
+        String scale = ArgParser.getValueFromSubValOrArg(avm, av, Arg.SCALE,
+                subVal);
+        String width = ArgParser.getValueFromSubValOrArg(avm, av, Arg.WIDTH,
+                subVal);
+        String height = ArgParser.getValueFromSubValOrArg(avm, av,
+                Arg.HEIGHT, subVal);
+        BitmapImageSizing userBis = ImageMaker
+                .parseScaleWidthHeightStrings(scale, width, height);
+
         type = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TYPE, subVal);
         if (type == null && fileName != null)
         {
@@ -669,53 +783,61 @@ public class Commands
         Cache.setPropsAreReadOnly(true);
         Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
 
-        switch (type)
+        Console.info("Writing " + file);
+        try
         {
-
-        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);
-          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)
+          switch (type)
           {
-            e.printStackTrace();
+
+          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(
+                    "Creating 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("Creating EPS file: " + fileName);
+            af.createEPS(file, name);
+            break;
+
+          case "imagemap":
+            Console.debug("Creating ImageMap file: " + fileName);
+            af.createImageMap(file, name);
+            break;
+
+          default:
+            Console.warn(Arg.IMAGE.argString() + " type '" + type
+                    + "' not known. Ignoring");
+            break;
           }
-          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;
+        } catch (Exception ioex)
+        {
+          Console.warn("Unexpected error during export", ioex);
         }
       }
     }
@@ -740,6 +862,7 @@ 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);
@@ -752,7 +875,7 @@ public class Commands
                 !Platform.isHeadless());
 
         // if backups is not true then --overwrite must be specified
-        if (file.exists() && !(overwrite || backups))
+        if (file.exists() && !(overwrite || backups || stdout))
         {
           Console.error("Won't overwrite file '" + fileName + "' without "
                   + Arg.OVERWRITE.argString() + " or "
@@ -790,23 +913,30 @@ 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(")");
+          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(")");
+            }
 
-          Jalview.exit("No valid format specified for "
-                  + Arg.OUTPUT.argString() + ". Valid formats are "
-                  + validSB.toString() + ".", 1);
-          // this return really shouldn't happen
-          return false;
+            Jalview.exit("No valid format specified for "
+                    + Arg.OUTPUT.argString() + ". Valid formats are "
+                    + validSB.toString() + ".", 1);
+            // this return really shouldn't happen
+            return false;
+          }
         }
 
         String savedBackupsPreference = Cache
@@ -814,7 +944,10 @@ public class Commands
         Console.debug("Setting backups to " + backups);
         Cache.applicationProperties.put(BackupFiles.ENABLED,
                 Boolean.toString(backups));
-        af.saveAlignment(fileName, ff);
+
+        Console.info("Writing " + fileName);
+
+        af.saveAlignment(fileName, ff, stdout);
         Console.debug("Returning backups to " + savedBackupsPreference);
         if (savedBackupsPreference != null)
           Cache.applicationProperties.put(BackupFiles.ENABLED,
@@ -835,70 +968,39 @@ public class Commands
     return true;
   }
 
-  private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
+  private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm,
+          ArgValue av)
   {
-    if (subId == null)
+    SubVals subVals = av.getSubVals();
+    ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID);
+    SequenceI seq = null;
+    if (subVals == null && idAv == null)
       return null;
-    AlignmentI al = af.getCurrentView().getAlignment();
-    if (subId.has("seqid"))
+    if (af == null || af.getCurrentView() == null)
     {
-      return al.findName(subId.get("seqid"));
+      return null;
     }
-    else if (-1 < subId.getIndex()
-            && subId.getIndex() < al.getSequences().size())
+    AlignmentI al = af.getCurrentView().getAlignment();
+    if (al == null)
     {
-      return al.getSequenceAt(subId.getIndex());
+      return null;
     }
-    return null;
-  }
-
-  // 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)
-  {
-    if (af != null)
+    if (subVals != null)
     {
-      for (ArgValue av : avm.getArgValueList(arg))
+      if (subVals.has(Arg.SEQID.getName()))
       {
-        SubVals subVals = av.getSubVals();
-        String structid = subVals.get("structid");
-        String structfile = subVals.get("structfile");
-
-        // 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();
-            }
-          }
-        }
-
-        if (structfile == null && structid != null)
-        {
-          StructureSelectionManager ssm = StructureSelectionManager
-                  .getStructureSelectionManager(Desktop.instance);
-          if (ssm != null)
-          {
-            structfile = ssm.findFileForPDBId(structid);
-          }
-        }
-        if (structfile != null && structfile.equals(structFilename))
-        {
-          return av;
-        }
+        seq = al.findName(subVals.get(Arg.SEQID.getName()));
       }
+      else if (-1 < subVals.getIndex()
+              && subVals.getIndex() < al.getSequences().size())
+      {
+        seq = al.getSequenceAt(subVals.getIndex());
+      }
+    }
+    else if (idAv != null)
+    {
+      seq = al.findName(idAv.getValue());
     }
-    return null;
+    return seq;
   }
 }