JAL-629 Fix --headless for new args. Fix progressbar for non-headless commands. Add...
[jalview.git] / src / jalview / bin / Commands.java
index 2a71e74..b42f08e 100644 (file)
@@ -1,6 +1,7 @@
 package jalview.bin;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -13,14 +14,21 @@ import java.util.Map;
 import jalview.analysis.AlignmentUtils;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.ArgParser.Arg;
-import jalview.bin.ArgParser.ArgValues;
-import jalview.bin.ArgParser.SubVal;
+import jalview.bin.ArgParser.ArgValue;
+import jalview.bin.ArgParser.ArgValuesMap;
+import jalview.bin.ArgParser.SubVals;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignmentPanel;
+import jalview.gui.AssociatePdbFileWithSeq;
 import jalview.gui.Desktop;
+import jalview.gui.Preferences;
 import jalview.gui.StructureChooser;
+import jalview.gui.StructureViewer;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
@@ -28,10 +36,15 @@ import jalview.io.FileFormatI;
 import jalview.io.FileLoader;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.TFType;
+import jalview.structure.StructureSelectionManager;
 import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.dbsources.EBIAlfaFold;
+import mc_view.PDBChain;
 
 public class Commands
 {
@@ -43,10 +56,23 @@ public class Commands
 
   private Map<String, AlignFrame> afMap;
 
-  public static void processArgs(ArgParser ap, boolean h)
+  private static boolean commandArgsProvided = false;
+
+  public static boolean commandArgsProvided()
+  {
+    return commandArgsProvided;
+  }
+
+  public static boolean processArgs(ArgParser ap, boolean h)
   {
     argParser = ap;
     headless = h;
+    boolean argsWereParsed = true;
+    if (headless)
+    {
+      System.setProperty("java.awt.headless", "true");
+    }
+
     if (argParser != null && argParser.linkedIds() != null)
     {
       for (String id : argParser.linkedIds())
@@ -55,19 +81,32 @@ public class Commands
         if (id == null)
         {
           cmds.processUnlinked(id);
+          argsWereParsed &= cmds.wereParsed();
         }
         else
         {
           cmds.processLinked(id);
+          argsWereParsed &= cmds.wereParsed();
         }
         cmds.processImages(id);
+        argsWereParsed &= cmds.wereParsed();
       }
 
-      if (argParser.getBool(Arg.QUIT))
-      {
-        Jalview.getInstance().quit();
-      }
     }
+    if (argParser.getBool(Arg.QUIT))
+    {
+      Jalview.getInstance().quit();
+      return true;
+    }
+    // carry on with jalview.bin.Jalview
+    return argsWereParsed;
+  }
+
+  boolean argsWereParsed = true; // set false as soon as an arg is found
+
+  private boolean wereParsed()
+  {
+    return argsWereParsed;
   }
 
   public Commands()
@@ -88,7 +127,11 @@ public class Commands
 
   protected void processLinked(String id)
   {
-    Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+    ArgValuesMap avm = argParser.linkedArgs(id);
+    if (avm == null)
+      return;
+    else
+      argsWereParsed = false;
 
     /*
     // script to execute after all loading is completed one way or another
@@ -100,27 +143,31 @@ public class Commands
     FileFormatI format = null;
     DataSourceType protocol = null;
     */
-
-    if (ArgParser.getArgValues(m, Arg.OPEN) != null)
+    if (avm.containsArg(Arg.OPEN))
     {
+      commandArgsProvided = true;
       long progress = -1;
 
       boolean first = true;
+      boolean progressBarSet = false;
       AlignFrame af;
-      OPEN: for (String openFile : ArgParser.getValues(m, Arg.OPEN))
+      for (ArgValue av : avm.getArgValueList(Arg.OPEN))
       {
+        String openFile = av.getValue();
         if (openFile == null)
-          continue OPEN;
+          continue;
 
+        argsWereParsed = true;
         if (first)
         {
           first = false;
-          if (!headless)
+          if (!headless && desktop != null)
           {
             desktop.setProgressBar(
                     MessageManager.getString(
                             "status.processing_commandline_args"),
                     progress = System.currentTimeMillis());
+            progressBarSet = true;
           }
         }
 
@@ -136,7 +183,6 @@ public class Commands
             if (!(new File(openFile)).exists())
             {
               Console.warn("Can't find file '" + openFile + "'");
-              continue OPEN;
             }
           }
         }
@@ -187,14 +233,15 @@ public class Commands
            */
 
           // get kind of temperature factor annotation
-          AlignmentAnnotation.TFType tempfacType = null;
-          if ((!ArgParser.getBoolean(m, Arg.NOTEMPFAC))
-                  && ArgParser.getArgValues(m, Arg.TEMPFAC) != null)
+          StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
+          if ((!avm.getBoolean(Arg.NOTEMPFAC))
+                  && avm.containsArg(Arg.TEMPFAC))
           {
             try
             {
-              tempfacType = AlignmentAnnotation.TFType.valueOf(ArgParser
-                      .getValue(m, Arg.TEMPFAC).toUpperCase(Locale.ROOT));
+              tempfacType = StructureImportSettings.TFType
+                      .valueOf(avm.getArgValue(Arg.TEMPFAC).getValue()
+                              .toUpperCase(Locale.ROOT));
               Console.debug("Obtained Temperature Factor type of '"
                       + tempfacType + "'");
             } catch (IllegalArgumentException e)
@@ -204,8 +251,8 @@ public class Commands
                       .append(Arg.TEMPFAC.getName()).append(" to '")
                       .append(tempfacType)
                       .append("', ignoring.  Valid values are: ");
-              Iterator<AlignmentAnnotation.TFType> it = Arrays
-                      .stream(AlignmentAnnotation.TFType.values())
+              Iterator<StructureImportSettings.TFType> it = Arrays
+                      .stream(StructureImportSettings.TFType.values())
                       .iterator();
               while (it.hasNext())
               {
@@ -220,22 +267,31 @@ public class Commands
           Console.debug(
                   "Opening '" + openFile + "' in new alignment frame");
           FileLoader fileLoader = new FileLoader(!headless);
-          af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, format,
-                  tempfacType);
+
+          StructureImportSettings.setTemperatureFactorType(tempfacType);
+
+          af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
+                  format);
 
           // wrap alignment?
-          if (ArgParser.getBoolean(m, Arg.WRAP))
+          if (avm.getBoolean(Arg.WRAP))
           {
             af.getCurrentView().setWrapAlignment(true);
           }
 
+          // colour aligment?
+          if (avm.containsArg(Arg.COLOUR))
+          {
+            af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
+          }
+
           // change alignment frame title
-          if (ArgParser.getValue(m, Arg.TITLE) != null)
-            af.setTitle(ArgParser.getValue(m, Arg.TITLE));
+          if (avm.containsArg(Arg.TITLE))
+            af.setTitle(avm.getValue(Arg.TITLE));
 
           /* hacky approach to hiding the annotations */
           // show secondary structure annotations?
-          if (ArgParser.getBoolean(m, Arg.SSANNOTATION))
+          if (avm.getBoolean(Arg.SSANNOTATION))
           {
             // do this better (annotation types?)
             AlignmentUtils.showOrHideSequenceAnnotations(
@@ -245,13 +301,12 @@ public class Commands
           }
 
           // show temperature factor annotations?
-          if (ArgParser.getBoolean(m, Arg.NOTEMPFAC))
+          if (avm.getBoolean(Arg.NOTEMPFAC))
           {
             // do this better (annotation types?)
             List<String> hideThese = new ArrayList<>();
             hideThese.add("Temperature Factor");
-            hideThese.add(MessageManager
-                    .getString("label.alphafold_reliability"));
+            hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
             AlignmentUtils.showOrHideSequenceAnnotations(
                     af.getCurrentView().getAlignment(), hideThese, null,
                     false, false);
@@ -261,13 +316,13 @@ public class Commands
            if (showTemperatureFactor)
              */
           {
-            if (ArgParser.getValue(m, Arg.TEMPFAC_LABEL) != null)
+            if (avm.containsArg(Arg.TEMPFAC_LABEL))
             {
               AlignmentAnnotation aa = AlignmentUtils
                       .getFirstSequenceAnnotationOfType(
                               af.getCurrentView().getAlignment(),
                               AlignmentAnnotation.LINE_GRAPH);
-              String label = ArgParser.getValue(m, Arg.TEMPFAC_LABEL);
+              String label = avm.getValue(Arg.TEMPFAC_LABEL);
               if (aa != null)
               {
                 aa.label = label;
@@ -283,6 +338,16 @@ public class Commands
 
           // store the AlignFrame for this id
           afMap.put(id, af);
+
+          // is it its own structure file?
+          if (format.isStructureFile())
+          {
+            StructureSelectionManager ssm = StructureSelectionManager
+                    .getStructureSelectionManager(Desktop.instance);
+            SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
+            ssm.computeMapping(false, new SequenceI[] { seq }, null,
+                    openFile, DataSourceType.FILE, null, null, null);
+          }
         }
         else
         {
@@ -291,8 +356,7 @@ public class Commands
           af.getCurrentView().addFile(new File(openFile), format);
         }
 
-        System.out
-                .println("Command " + Arg.OPEN + " executed successfully!");
+        Console.debug("Command " + Arg.OPEN + " executed successfully!");
 
       }
       if (first) // first=true means nothing opened
@@ -302,62 +366,58 @@ public class Commands
           Console.error("Could not open any files in headless mode");
           System.exit(1);
         }
-      }
-      else
-      {
-        Console.warn("No more files to open");
-        if (desktop != null)
-          desktop.setProgressBar(null, progress);
-      }
-
-    }
-
-    // load a pAE file if given
-    if (ArgParser.getValues(m, Arg.PAEMATRIX) != null)
-    {
-      AlignFrame af = afMap.get(id);
-      if (af != null)
-      {
-        for (String val : ArgParser.getValues(m, Arg.PAEMATRIX))
+        else
         {
-          SubVal subVal = ArgParser.getSubVal(val);
-          File paeFile = new File(subVal.content);
-          EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
-                  paeFile, subVal.index,
-                  "id".equals(subVal.keyName) ? subVal.keyValue : null);
-          // required to readjust the height and position of the pAE
-          // annotation
-          for (AlignmentViewPanel ap : af.getAlignPanels())
-          {
-            ap.adjustAnnotationHeight();
-          }
+          Console.warn("No more files to open");
         }
       }
+      if (progressBarSet && desktop != null)
+        desktop.setProgressBar(null, progress);
+
     }
 
     // open the structure (from same PDB file or given PDBfile)
-    if (!ArgParser.getBoolean(m, Arg.NOSTRUCTURE))
+    if (!avm.getBoolean(Arg.NOSTRUCTURE))
     {
       AlignFrame af = afMap.get(id);
-      if (ArgParser.getArgValues(m, Arg.STRUCTURE) != null)
+      if (avm.containsArg(Arg.STRUCTURE))
       {
-        STRUCTURE: for (String val : ArgParser.getValues(m, Arg.STRUCTURE))
+        commandArgsProvided = true;
+        for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
         {
-          SubVal subId = new SubVal(val);
+          String val = av.getValue();
+          SubVals subId = new SubVals(val);
           SequenceI seq = getSpecifiedSequence(af, subId);
           if (seq == null)
           {
             Console.warn("Could not find sequence for argument --"
                     + Arg.STRUCTURE + "=" + val);
-            break STRUCTURE;
+            // you probably want to continue here, not break
+            // break;
+            continue;
           }
           File structureFile = null;
-          if (subId.content != null && subId.content.length() != 0)
+          if (subId.getContent() != null
+                  && subId.getContent().length() != 0)
           {
-            structureFile = new File(subId.content);
+            structureFile = new File(subId.getContent());
             Console.debug("Using structure file (from argument) '"
                     + structureFile.getAbsolutePath() + "'");
           }
+
+          // TRY THIS
+          /*
+           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+                  .associatePdbWithSeq(selectedPdbFileName,
+                          DataSourceType.FILE, selectedSequence, true,
+                          Desktop.instance);
+                          
+           sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
+                  ap, new SequenceI[]
+                  { selectedSequence });
+          
+           */
+
           /* THIS DOESN'T WORK */
           else if (seq.getAllPDBEntries() != null
                   && seq.getAllPDBEntries().size() > 0)
@@ -371,31 +431,121 @@ public class Commands
           if (structureFile == null)
           {
             Console.warn("Not provided structure file with '" + val + "'");
-            continue STRUCTURE;
+            continue;
           }
 
           if (!structureFile.exists())
           {
             Console.warn("Structure file '"
                     + structureFile.getAbsoluteFile() + "' not found.");
-            continue STRUCTURE;
+            continue;
           }
 
           Console.debug("Using structure file "
                   + structureFile.getAbsolutePath());
 
+          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+                  .associatePdbWithSeq(structureFile.getAbsolutePath(),
+                          DataSourceType.FILE, seq, true, Desktop.instance);
+
           // open structure view
           AlignmentPanel ap = af.alignPanel;
-          StructureChooser.openStructureFileForSequence(ap, seq,
-                  structureFile);
+          if (headless)
+          {
+            Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
+                    StructureViewer.ViewerType.JMOL.toString());
+          }
+
+          // get tft, paeFilename, label?
+          /*
+          ArgValue tftAv = avm.getArgValuesReferringTo("structid", structId,
+                  Arg.TEMPFAC);
+           */
+          StructureChooser.openStructureFileForSequence(null, null, ap, seq,
+                  false, structureFile.getAbsolutePath(), null, null); // tft,
+                                                                       // paeFilename);
         }
       }
     }
+
+    // load a pAE file if given
+    if (avm.containsArg(Arg.PAEMATRIX))
+    {
+      AlignFrame af = afMap.get(id);
+      if (af != null)
+      {
+        for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
+        {
+          String val = av.getValue();
+          SubVals subVals = ArgParser.getSubVals(val);
+          File paeFile = new File(subVals.getContent());
+          String paePath = null;
+          try
+          {
+            paePath = paeFile.getCanonicalPath();
+          } catch (IOException e)
+          {
+            paePath = paeFile.getAbsolutePath();
+            Console.warn(
+                    "Problem with the PAE file path: '" + paePath + "'");
+          }
+          String structId = subVals.get("structid");
+          if (subVals.notSet())
+          {
+            // take structid from pdbfilename
+          }
+          if (subVals.has("structfile"))
+          {
+            Console.info("***** Attaching paeFile '" + paePath + "' to "
+                    + "structfile=" + subVals.get("structfile"));
+            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+                    paeFile, subVals.getIndex(), subVals.get("structfile"),
+                    true, false);
+          }
+          else if (subVals.has("structid"))
+          {
+            Console.info("***** Attaching paeFile '" + paePath + "' to "
+                    + "structid=" + subVals.get("structid"));
+            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+                    paeFile, subVals.getIndex(), subVals.get("structid"),
+                    true, true);
+          }
+          else
+          {
+            Console.debug("***** Attaching paeFile '" + paePath
+                    + "' to sequence index " + subVals.getIndex());
+            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+                    paeFile, subVals.getIndex(), null, false, false);
+            // required to readjust the height and position of the pAE
+            // annotation
+          }
+          for (AlignmentViewPanel ap : af.getAlignPanels())
+          {
+            ap.adjustAnnotationHeight();
+          }
+        }
+      }
+    }
+
+    boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
+    if (doShading)
+    {
+      AlignFrame af = afMap.get(id);
+      for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
+              .findAnnotation(PDBChain.class.getName().toString()))
+      {
+        AnnotationColourGradient acg = new AnnotationColourGradient(aa,
+                af.alignPanel.av.getGlobalColourScheme(), 0);
+        acg.setSeqAssociated(true);
+        af.changeColour(acg);
+        Console.info("Changed colour " + acg.toString());
+      }
+    }
   }
 
   protected void processImages(String id)
   {
-    Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+    ArgValuesMap avm = argParser.linkedArgs(id);
     AlignFrame af = afMap.get(id);
 
     if (af == null)
@@ -404,17 +554,18 @@ public class Commands
       return;
     }
 
-    if (ArgParser.getValues(m, Arg.IMAGE) != null)
+    if (avm.containsArg(Arg.IMAGE))
     {
-      for (String val : ArgParser.getValues(m, Arg.IMAGE))
+      for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
       {
-        SubVal subVal = new SubVal(val);
+        String val = av.getValue();
+        SubVals subVal = new SubVals(val);
         String type = "png"; // default
-        String fileName = subVal.content;
+        String fileName = subVal.getContent();
         File file = new File(fileName);
-        if ("type".equals(subVal.keyName))
+        if (subVal.has("type"))
         {
-          type = subVal.keyValue;
+          type = subVal.get("type");
         }
         else if (fileName != null)
         {
@@ -426,43 +577,45 @@ public class Commands
             }
           }
         }
+        // for moment we disable JSON export
+        Cache.setPropsAreReadOnly(true);
+        Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
+
         switch (type)
         {
         case "svg":
+          Console.debug("Outputting type '" + type + "' to " + fileName);
           af.createSVG(file);
           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);
           break;
+        default:
+          Console.warn("--image type '" + type + "' not known. Ignoring");
+          break;
         }
       }
     }
   }
 
-  private SequenceI getSpecifiedSequence(AlignFrame af, SubVal subId)
+  private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
   {
-    SequenceI seq = null;
-    SequenceI[] sequences = af.getCurrentView().getAlignment()
-            .getSequencesArray();
-    if (-1 < subId.index && subId.index < sequences.length)
+    AlignmentI al = af.getCurrentView().getAlignment();
+    if (-1 < subId.getIndex()
+            && subId.getIndex() < al.getSequences().size())
     {
-      seq = sequences[subId.index];
+      return al.getSequenceAt(subId.getIndex());
     }
-    else if ("id".equals(subId.keyName))
+    else if (subId.has("seqid"))
     {
-      for (SequenceI s : sequences)
-      {
-        if (s.getDisplayId(false).equals(subId.keyValue))
-        {
-          seq = s;
-          break;
-        }
-      }
+      return al.findName(subId.get("seqid"));
     }
-    return seq;
+    return null;
   }
 }