JAL-629 More consistent printing of --arguments. Example nf-core argfile

diff --git a/examples/test_fab41.result/argfile.txt b/examples/test_fab41.result/argfile.txt
new file mode 100644 (file)
index 0000000..ed450dd
--- /dev/null
+++ b/examples/test_fab41.result/argfile.txt
@@ -0,0 +1,14 @@
+--substitutions
+--open={argfiledirname}/sample.a2m
+--colour=gecos:flower
+--structure={argfiledirname}/test_fab41_unrelaxed_rank_1_model_3.pdb
+--paematrix=[label=pAE R1-M3]{argfiledirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json
+--structure={argfiledirname}/test_fab41_unrelaxed_rank_2_model_4.pdb
+--paematrix=[label=pAE R2-M4]{argfiledirname}/test_fab41_unrelaxed_rank_2_model_4_scores.json
+--structure={argfiledirname}/test_fab41_unrelaxed_rank_3_model_2.pdb
+--paematrix=[label=pAE R3-M2]{argfiledirname}/test_fab41_unrelaxed_rank_3_model_2_scores.json
+--structure={argfiledirname}/test_fab41_unrelaxed_rank_4_model_5.pdb
+--paematrix=[label=pAE R4-M5]{argfiledirname}/test_fab41_unrelaxed_rank_4_model_5_scores.json
+--structure={argfiledirname}/test_fab41_unrelaxed_rank_5_model_1.pdb
+--paematrix=[label=pAE R5-M1]{argfiledirname}/test_fab41_unrelaxed_rank_5_model_1_scores.json
+--image={dirname}/{basename}.html

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index e92ee61..e4be614 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -150,15 +150,12 @@ public class Commands
       return true;
 
     /*
-    // 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;
-    */
+     * // 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.OPEN) || avm.containsArg(Arg.OPENNEW))
     {
       commandArgsProvided = true;
@@ -233,33 +230,19 @@ public class Commands
                 || a == Arg.OPENNEW || format == FileFormat.Jalview)
         {
           /*
-           * this approach isn't working yet
-          // get default annotations before opening AlignFrame
-          if (m.get(Arg.SSANNOTATION) != null)
-          {
-            Console.debug("***** SSANNOTATION="
-                    + m.get(Arg.SSANNOTATION).getBoolean());
-          }
-          if (m.get(Arg.NOTEMPFAC) != null)
-          {
-            Console.debug(
-                    "***** NOTEMPFAC=" + m.get(Arg.NOTEMPFAC).getBoolean());
-          }
-          boolean showSecondaryStructure = (m.get(Arg.SSANNOTATION) != null)
-                  ? m.get(Arg.SSANNOTATION).getBoolean()
-                  : false;
-          boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null)
-                  ? !m.get(Arg.NOTEMPFAC).getBoolean()
-                  : false;
-          Console.debug("***** tempfac=" + showTemperatureFactor
-                  + ", showSS=" + showSecondaryStructure);
-          StructureSelectionManager ssm = StructureSelectionManager
-                  .getStructureSelectionManager(Desktop.instance);
-          if (ssm != null)
-          {
-            ssm.setAddTempFacAnnot(showTemperatureFactor);
-            ssm.setProcessSecondaryStructure(showSecondaryStructure);
-          }
+           * this approach isn't working yet // get default annotations before opening
+           * AlignFrame if (m.get(Arg.SSANNOTATION) != null) {
+           * Console.debug("##### SSANNOTATION=" + m.get(Arg.SSANNOTATION).getBoolean());
+           * } if (m.get(Arg.NOTEMPFAC) != null) { Console.debug( "##### NOTEMPFAC=" +
+           * m.get(Arg.NOTEMPFAC).getBoolean()); } boolean showSecondaryStructure =
+           * (m.get(Arg.SSANNOTATION) != null) ? m.get(Arg.SSANNOTATION).getBoolean() :
+           * false; boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null) ?
+           * !m.get(Arg.NOTEMPFAC).getBoolean() : false; Console.debug("##### tempfac=" +
+           * showTemperatureFactor + ", showSS=" + showSecondaryStructure);
+           * StructureSelectionManager ssm = StructureSelectionManager
+           * .getStructureSelectionManager(Desktop.instance); if (ssm != null) {
+           * ssm.setAddTempFacAnnot(showTemperatureFactor);
+           * ssm.setProcessSecondaryStructure(showSecondaryStructure); }
            */
 
           // get kind of temperature factor annotation
@@ -277,8 +260,8 @@ public class Commands
             } catch (IllegalArgumentException e)
             {
               // Just an error message!
-              StringBuilder sb = new StringBuilder().append("Cannot set --")
-                      .append(Arg.TEMPFAC.getName()).append(" to '")
+              StringBuilder sb = new StringBuilder().append("Cannot set ")
+                      .append(Arg.TEMPFAC.argString()).append(" to '")
                       .append(tempfacType)
                       .append("', ignoring.  Valid values are: ");
               Iterator<StructureImportSettings.TFType> it = Arrays
@@ -342,9 +325,10 @@ public class Commands
                     false, false);
           }
           else
-          /* comment out hacky approach up to here and add this line:
-           if (showTemperatureFactor)
-             */
+          /*
+           * comment out hacky approach up to here and add this line: if
+           * (showTemperatureFactor)
+           */
           {
             if (avm.containsArg(Arg.TEMPFAC_LABEL))
             {
@@ -419,8 +403,8 @@ public class Commands
           SequenceI seq = getSpecifiedSequence(af, subId);
           if (seq == null)
           {
-            Console.warn("Could not find sequence for argument --"
-                    + Arg.STRUCTURE + "=" + val);
+            Console.warn("Could not find sequence for argument "
+                    + Arg.STRUCTURE.argString() + "=" + val);
             // you probably want to continue here, not break
             // break;
             continue;
@@ -436,15 +420,13 @@ public class Commands
 
           // TRY THIS
           /*
-           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-                  .associatePdbWithSeq(selectedPdbFileName,
-                          DataSourceType.FILE, selectedSequence, true,
-                          Desktop.instance);
-                          
-           sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
-                  ap, new SequenceI[]
-                  { selectedSequence });
-          
+           * 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 */
@@ -487,12 +469,12 @@ public class Commands
 
           // get tft, paeFilename, label?
           /*
-          ArgValue tftAv = avm.getArgValuesReferringTo("structid", structId,
-                  Arg.TEMPFAC);
+           * ArgValue tftAv = avm.getArgValuesReferringTo("structid", structId,
+           * Arg.TEMPFAC);
            */
           StructureChooser.openStructureFileForSequence(null, null, ap, seq,
                   false, structureFile.getAbsolutePath(), null, null); // tft,
-                                                                       // paeFilename);
+          // paeFilename);
         }
       }
     }
@@ -549,7 +531,7 @@ public class Commands
           }
           if (structfile != null)
           {
-            Console.info("***** Attaching paeFile '" + paePath + "' to "
+            Console.info("##### Attaching paeFile '" + paePath + "' to "
                     + "structfile=" + subVals.get("structfile"));
             EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
                     paeFile, subVals.getIndex(), subVals.get("structfile"),
@@ -557,7 +539,7 @@ public class Commands
           }
           else if (structid != null)
           {
-            Console.info("***** Attaching paeFile '" + paePath + "' to "
+            Console.info("##### Attaching paeFile '" + paePath + "' to "
                     + "structid=" + subVals.get("structid"));
             EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
                     paeFile, subVals.getIndex(), subVals.get("structid"),
@@ -565,7 +547,7 @@ public class Commands
           }
           else
           {
-            Console.debug("***** Attaching paeFile '" + paePath
+            Console.debug("##### Attaching paeFile '" + paePath
                     + "' to sequence index " + subVals.getIndex());
             EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
                     paeFile, subVals.getIndex(), null, false, false,
@@ -653,7 +635,8 @@ public class Commands
           htmlSVG.exportHTML(fileName);
           break;
         default:
-          Console.warn("--image type '" + type + "' not known. Ignoring");
+          Console.warn(Arg.IMAGE.argString() + " type '" + type
+                  + "' not known. Ignoring");
           break;
         }
       }

diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index 8207996..7eaac09 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -26,7 +26,7 @@ public enum Arg
   {
     HELP.setOptions(Opt.UNARY);
     CALCULATION.setOptions(true, Opt.BOOLEAN); // default "true" implies only
-                                               // expecting "--nocalculation"
+    // expecting "--nocalculation"
     MENUBAR.setOptions(true, Opt.BOOLEAN);
     STATUS.setOptions(true, Opt.BOOLEAN);
     SHOWOVERVIEW.setOptions(Opt.UNARY, Opt.LINKED);
@@ -119,6 +119,12 @@ public enum Arg
       System.arraycopy(names, 0, this.argNames, 1, names.length);
   }
 
+  public String argString()
+  {
+    return new StringBuilder(ArgParser.DOUBLEDASH).append(getName())
+            .toString();
+  }
+
   public String toLongString()
   {
     StringBuilder sb = new StringBuilder();

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 7d4f187..ff238da 100644 (file)
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -29,7 +29,6 @@ import java.util.Arrays;
 import java.util.EnumSet;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Locale;
 import java.util.Map;
 
 import jalview.bin.Console;
@@ -107,7 +106,8 @@ public class ArgParser
         if (argMap.containsKey(argName))
         {
           Console.warn("Trying to add argument name multiple times: '"
-                  + argName + "'"); // RESTORE THIS WHEN MERGED
+                  + argName + "'"); // RESTORE THIS WHEN
+          // MERGED
           if (argMap.get(argName) != a)
           {
             Console.error(
@@ -189,7 +189,7 @@ public class ArgParser
       if (openEachInitialFilenames && !arg.startsWith(DOUBLEDASH)
               && !arg.startsWith("-") && new File(arg).exists())
       {
-        arg = DOUBLEDASH + Arg.OPENNEW.getName();
+        arg = Arg.OPENNEW.argString();
       }
       else
       {
@@ -242,8 +242,8 @@ public class ArgParser
         }
         if (a.hasOption(Opt.PRIVATE) && !allowPrivate)
         {
-          Console.error("Argument '" + DOUBLEDASH + argName
-                  + "' is private. Ignoring.");
+          Console.error(
+                  "Argument '" + a.argString() + "' is private. Ignoring.");
           continue;
         }
         if (!a.hasOption(Opt.BOOLEAN) && negated)
@@ -256,7 +256,7 @@ public class ArgParser
         if (!a.hasOption(Opt.STRING) && equalPos > -1)
         {
           // set --argname=value when arg does not accept values
-          Console.error("Argument '" + DOUBLEDASH + argName
+          Console.error("Argument '" + a.argString()
                   + "' does not expect a value (given as '" + arg
                   + "').  Ignoring.");
           continue;
@@ -264,7 +264,7 @@ public class ArgParser
         if (!a.hasOption(Opt.LINKED) && linkedId != null)
         {
           // set --argname[linkedId] when arg does not use linkedIds
-          Console.error("Argument '" + DOUBLEDASH + argName
+          Console.error("Argument '" + a.argString()
                   + "' does not expect a linked id (given as '" + arg
                   + "'). Ignoring.");
           continue;
@@ -403,7 +403,7 @@ public class ArgParser
         // not dealing with both NODUPLICATEVALUES and GLOB
         if (a.hasOption(Opt.NODUPLICATEVALUES) && avm.hasValue(a, val))
         {
-          Console.error("Argument '" + DOUBLEDASH + argName
+          Console.error("Argument '" + a.argString()
                   + "' cannot contain a duplicate value ('" + val
                   + "'). Ignoring this and subsequent occurrences.");
           continue;
@@ -414,7 +414,7 @@ public class ArgParser
         String id = idsv.get(ArgValues.ID);
         if (id != null && avm.hasId(a, id))
         {
-          Console.error("Argument '" + DOUBLEDASH + argName
+          Console.error("Argument '" + a.argString()
                   + "' has a duplicate id ('" + id + "'). Ignoring.");
           continue;
         }
@@ -534,12 +534,11 @@ public class ArgParser
   /*
    * A helper method to take a list of String args where we're expecting
    * {"--previousargs", "--arg", "file1", "file2", "file3", "--otheroptionsornot"}
-   * and the index of the globbed arg, here 1.  It returns a
-   * List<String> {"file1", "file2", "file3"}
-   * *and remove these from the original list object* so that processing
-   * can continue from where it has left off, e.g. args has become
-   * {"--previousargs", "--arg", "--otheroptionsornot"}
-   * so the next increment carries on from the next --arg if available.
+   * and the index of the globbed arg, here 1. It returns a List<String> {"file1",
+   * "file2", "file3"} *and remove these from the original list object* so that
+   * processing can continue from where it has left off, e.g. args has become
+   * {"--previousargs", "--arg", "--otheroptionsornot"} so the next increment
+   * carries on from the next --arg if available.
    */
   protected static List<String> getShellGlobbedFilenameValues(Arg a,
           List<String> args, int i)
@@ -658,25 +657,22 @@ public class ArgParser
     {
       if (!argFile.exists())
       {
-        String message = DOUBLEDASH
-                + Arg.ARGFILE.name().toLowerCase(Locale.ROOT) + EQUALS
-                + "\"" + argFile.getPath() + "\": File does not exist.";
+        String message = Arg.ARGFILE.argString() + EQUALS + "\""
+                + argFile.getPath() + "\": File does not exist.";
         Jalview.exit(message, 2);
       }
       try
       {
-        String setargfile = new StringBuilder(ArgParser.DOUBLEDASH)
-                .append(Arg.SETARGFILE.getName()).append(EQUALS)
-                .append(argFile.getCanonicalPath()).toString();
+        String setargfile = new StringBuilder(Arg.SETARGFILE.argString())
+                .append(EQUALS).append(argFile.getCanonicalPath())
+                .toString();
         argsList.add(setargfile);
         argsList.addAll(Files.readAllLines(Paths.get(argFile.getPath())));
-        argsList.add(new StringBuilder(ArgParser.DOUBLEDASH)
-                .append(Arg.UNSETARGFILE.getName()).toString());
+        argsList.add(Arg.UNSETARGFILE.argString());
       } catch (IOException e)
       {
-        String message = DOUBLEDASH
-                + Arg.ARGFILE.name().toLowerCase(Locale.ROOT) + "=\""
-                + argFile.getPath() + "\": File could not be read.";
+        String message = Arg.ARGFILE.argString() + "=\"" + argFile.getPath()
+                + "\": File could not be read.";
         Jalview.exit(message, 3);
       }
     }