JAL-1788 added help documentation for biojson

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index e184db7..177d56f 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -109,7 +109,14 @@ public class Jalview
       System.setProperty("java.awt.headless", "true");
       headless = true;
     }
-    Cache.loadProperties(aparser.getValue("props")); // must do this before
+    String usrPropsFile = aparser.getValue("props");
+    Cache.loadProperties(usrPropsFile); // must do this before
+    if (usrPropsFile != null)
+    {
+      System.out.println("CMD [-props " + usrPropsFile
+              + "] executed successfully!");
+    }
+
     // anything else!
 
     final String jabawsUrl = aparser.getValue("jabaws");
@@ -118,6 +125,8 @@ public class Jalview
       try
       {
         Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+        System.out.println("CMD [-jabaws " + jabawsUrl
+                + "] executed successfully!");
       } catch (MalformedURLException e)
       {
         System.err.println("Invalid jabaws parameter: " + jabawsUrl
@@ -195,6 +204,11 @@ public class Jalview
       {
         startUsageStats(desktop);
       }
+      else
+      {
+        System.err.println("CMD [-nousagestats] executed successfully!");
+      }
+
       if (!aparser.contains("noquestionnaire"))
       {
         String url = aparser.getValue("questionnaire");
@@ -204,6 +218,8 @@ public class Jalview
           // questionnaire
           Cache.log.debug("Starting questionnaire url at " + url);
           desktop.checkForQuestionnaire(url);
+          System.out.println("CMD questionnaire[-" + url
+                  + "] executed successfully!");
         }
         else
         {
@@ -222,14 +238,21 @@ public class Jalview
           }
         }
       }
+      else
+      {
+        System.err
+.println("CMD [-noquestionnaire] executed successfully!");
+      }
       desktop.checkForNews();
     }
 
-    BioJsHTMLOutput bjs = new BioJsHTMLOutput(null, null);
-    bjs.updateBioJS();
+    if (!isHeadlessMode())
+    {
+      BioJsHTMLOutput.updateBioJS();
+    }
 
     String file = null, protocol = null, format = null, data = null;
-    jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
+    jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless);
     Vector getFeatures = null; // vector of das source nicknames to fetch
     // features from
     // loading is done.
@@ -338,7 +361,7 @@ public class Jalview
         desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"),
                 progress = System.currentTimeMillis());
       }
-      System.out.println("Opening file: " + file);
+      System.out.println("CMD [-open " + file + "] executed successfully!");
 
       if (!file.startsWith("http://"))
       {
@@ -380,8 +403,11 @@ public class Jalview
             ucs.parseAppletParameter(data);
             cs = ucs;
           }
-
-          System.out.println("colour is " + data);
+          else
+          {
+            System.out.println("CMD [-color " + data
+                    + "] executed successfully!");
+          }
           af.changeColour(cs);
         }
 
@@ -391,34 +417,55 @@ public class Jalview
         {
           af.parseFeaturesFile(data,
                   jalview.io.AppletFormatAdapter.checkProtocol(data));
-          System.out.println("Added " + data);
+          // System.out.println("Added " + data);
+          System.out.println("CMD groups[-" + data
+                  + "]  executed successfully!");
         }
         data = aparser.getValue("features", true);
         if (data != null)
         {
           af.parseFeaturesFile(data,
                   jalview.io.AppletFormatAdapter.checkProtocol(data));
-          System.out.println("Added " + data);
+          // System.out.println("Added " + data);
+          System.out.println("CMD [-features " + data
+                  + "]  executed successfully!");
         }
 
         data = aparser.getValue("annotations", true);
         if (data != null)
         {
           af.loadJalviewDataFile(data, null, null, null);
-          System.out.println("Added " + data);
+          // System.out.println("Added " + data);
+          System.out.println("CMD [-annotations " + data
+                  + "] executed successfully!");
         }
         // set or clear the sortbytree flag.
         if (aparser.contains("sortbytree"))
         {
           af.getViewport().setSortByTree(true);
+          if (af.getViewport().getSortByTree())
+          {
+            System.out
+.println("CMD [-sortbytree] executed successfully!");
+          }
         }
         if (aparser.contains("no-annotation"))
         {
           af.getViewport().setShowAnnotation(false);
+          if (!af.getViewport().isShowAnnotation())
+          {
+            System.out
+.println("CMD no-annotation executed successfully!");
+          }
         }
         if (aparser.contains("nosortbytree"))
         {
           af.getViewport().setSortByTree(false);
+          if (!af.getViewport().getSortByTree())
+          {
+            System.out
+                    .println("CMD [-nosortbytree] executed successfully!");
+          }
         }
         data = aparser.getValue("tree", true);
         if (data != null)
@@ -426,13 +473,14 @@ public class Jalview
           jalview.io.NewickFile fin = null;
           try
           {
+            System.out.println("CMD [-tree " + data
+                    + "] executed successfully!");
             fin = new jalview.io.NewickFile(data,
                     jalview.io.AppletFormatAdapter.checkProtocol(data));
             if (fin != null)
             {
               af.getViewport().setCurrentTree(
                       af.ShowNewickTree(fin, data).getTree());
-              System.out.println("Added tree " + data);
             }
           } catch (IOException ex)
           {
@@ -473,6 +521,9 @@ public class Jalview
             System.out.println("Executing script " + groovyscript);
             executeGroovyScript(groovyscript, new Object[]
             { desktop, af });
+
+            System.out.println("CMD groovy[" + groovyscript
+                    + "] executed successfully!");
           }
           else
           {
@@ -519,8 +570,10 @@ public class Jalview
           }
           else if (format.equalsIgnoreCase("eps"))
           {
-            System.out.println("Creating EPS file: " + file);
-            af.createEPS(new java.io.File(file));
+            File outputFile = new java.io.File(file);
+            System.out.println("Creating EPS file: "
+                    + outputFile.getAbsolutePath());
+            af.createEPS(outputFile);
             continue;
           }
 
@@ -640,6 +693,7 @@ public class Jalview
                     + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
                     + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
                     + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
+                    + "-json FILE\tCreate alignment file FILE in JSON format.\n"
                     + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
                     + "-png FILE\tCreate PNG image FILE from alignment.\n"
                     + "-svg FILE\tCreate SVG image FILE from alignment.\n"
@@ -926,6 +980,8 @@ public class Jalview
         }
         source.addElement(nickname);
       }
+      System.out.println("CMD [-dasserver " + data
+              + "] executed successfully!");
     } // loop until no more server entries are found.
     if (locsources != null && locsources.indexOf('|') > -1)
     {
@@ -964,6 +1020,16 @@ public class Jalview
     }
     return ff;
   }
+
+  public static boolean isHeadlessMode()
+  {
+    String isheadless = System.getProperty("java.awt.headless");
+    if (isheadless != null && isheadless.equalsIgnoreCase("true"))
+    {
+      return true;
+    }
+    return false;
+  }
 }
 
 /**
@@ -1132,4 +1198,4 @@ class FeatureFetcher
     return queued == 0 && running == 0;
   }
 
-};
+}