X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=36f4ff64eb7b0352d81ed78dc91ac9cc5f8d8e85;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=4f383a0b22dea2bac633d13893306cd04086526e;hpb=60f2d6c034560415fd0139c8bc7df0c19cae1186;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 4f383a0..36f4ff6 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -166,9 +166,11 @@ public class Jalview
 
     String file = null, protocol = null, format = null, data = null;
     jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
-    Vector getFeatures = null; // vector of das source nicknames to fetch features from
+    Vector getFeatures = null; // vector of das source nicknames to fetch
+                                // features from
     // loading is done.
-    String groovyscript = null; // script to execute after all loading is completed one way or another
+    String groovyscript = null; // script to execute after all loading is
+                                // completed one way or another
     // extract groovy argument and execute if necessary
     groovyscript = aparser.getValue("groovy");
     file = aparser.getValue("open");
@@ -268,31 +270,36 @@ public class Jalview
         }
       }
       getFeatures = checkDasArguments(aparser);
-      if (af != null && getFeatures!=null)
+      if (af != null && getFeatures != null)
       {
-        startFeatureFetching(getFeatures); 
+        startFeatureFetching(getFeatures);
         // need to block until fetching is complete.
         while (af.operationInProgress())
         {
           // wait around until fetching is finished.
-          try {
+          try
+          {
             Thread.sleep(10);
           } catch (Exception e)
           {
-            
+
           }
         }
       }
-      if (groovyscript!=null)
+      if (groovyscript != null)
       {
-        // Execute the groovy script after we've  done all the rendering stuff
+        // Execute the groovy script after we've done all the rendering stuff
         // and before any images or figures are generated.
         if (jalview.bin.Cache.groovyJarsPresent())
         {
-          System.out.println("Executing script "+groovyscript);
+          System.out.println("Executing script " + groovyscript);
           executeGroovyScript(groovyscript, desktop);
-        } else {
-          System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript);
+        }
+        else
+        {
+          System.err
+                  .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+                          + groovyscript);
         }
         groovyscript = null;
       }
@@ -372,128 +379,156 @@ public class Jalview
       // extract groovy arguments before anything else.
     }
     // Once all loading is done. Retrieve features.
-    if (getFeatures!=null)
+    if (getFeatures != null)
     {
-      if (startUpAlframe!=null)
+      if (startUpAlframe != null)
       {
         startFeatureFetching(getFeatures);
       }
     }
-    if (groovyscript!=null)
+    if (groovyscript != null)
     {
       if (jalview.bin.Cache.groovyJarsPresent())
       {
-        System.out.println("Executing script "+groovyscript);
+        System.out.println("Executing script " + groovyscript);
         executeGroovyScript(groovyscript, desktop);
-      } else {
-        System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript);
+      }
+      else
+      {
+        System.err
+                .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+                        + groovyscript);
       }
     }
 
     // Once all other stuff is done, execute any groovy scripts (in order)
   }
+
   /**
    * Locate the given string as a file and pass it to the groovy interpreter.
-   * @param groovyscript the script to execute
-   * @param jalviewContext the Jalview Desktop object passed in to the groovy binding as the 'Jalview' object.
+   * 
+   * @param groovyscript
+   *                the script to execute
+   * @param jalviewContext
+   *                the Jalview Desktop object passed in to the groovy binding
+   *                as the 'Jalview' object.
    */
-  private static void executeGroovyScript(String groovyscript, Object jalviewContext)
+  private static void executeGroovyScript(String groovyscript,
+          Object jalviewContext)
   {
-    if (jalviewContext==null)
+    if (jalviewContext == null)
     {
-      System.err.println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
+      System.err
+              .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
     }
     File sfile = null;
     if (groovyscript.trim().equals("STDIN"))
     {
       // read from stdin into a tempfile and execute it
-      try {
+      try
+      {
         sfile = File.createTempFile("jalview", "groovy");
-        PrintWriter outfile = new PrintWriter(new OutputStreamWriter(new FileOutputStream(sfile)));
-        BufferedReader br = new BufferedReader(new java.io.InputStreamReader(System.in));
-        String line=null;
-        while ((line=br.readLine())!=null)
+        PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
+                new FileOutputStream(sfile)));
+        BufferedReader br = new BufferedReader(
+                new java.io.InputStreamReader(System.in));
+        String line = null;
+        while ((line = br.readLine()) != null)
         {
-          outfile.write(line+"\n");
+          outfile.write(line + "\n");
         }
         br.close();
         outfile.flush();
         outfile.close();
-        
+
       } catch (Exception ex)
       {
-        System.err.println("Failed to read from STDIN into tempfile "+((sfile==null) ? "(tempfile wasn't created)" : sfile.toString()));
+        System.err.println("Failed to read from STDIN into tempfile "
+                + ((sfile == null) ? "(tempfile wasn't created)" : sfile
+                        .toString()));
         ex.printStackTrace();
         return;
       }
-    } else {
+    }
+    else
+    {
       sfile = new File(groovyscript);
     }
     if (!sfile.exists())
     {
-      System.err.println("File '"+groovyscript+"' does not exist.");
+      System.err.println("File '" + groovyscript + "' does not exist.");
       return;
     }
     if (!sfile.canRead())
     {
-      System.err.println("File '"+groovyscript+"' cannot be read.");
+      System.err.println("File '" + groovyscript + "' cannot be read.");
       return;
     }
-    if (sfile.length()<1)
+    if (sfile.length() < 1)
     {
-      System.err.println("File '"+groovyscript+"' is empty.");
+      System.err.println("File '" + groovyscript + "' is empty.");
       return;
     }
     boolean success = false;
-    try {
-      /* The following code performs the GroovyScriptEngine invocation using reflection,
-       * and is equivalent to this fragment from the embedding groovy documentation on 
-       * the groovy site:
-       * <code>
-         import groovy.lang.Binding;
-         import groovy.util.GroovyScriptEngine;
-        
-         String[] roots = new String[] { "/my/groovy/script/path" };
-         GroovyScriptEngine gse = new GroovyScriptEngine(roots);
-         Binding binding = new Binding();
-         binding.setVariable("input", "world");
-         gse.run("hello.groovy", binding);
-         * </code>
-         */
-        ClassLoader cl = jalviewContext.getClass().getClassLoader();
-        Class   gbindingc = cl.loadClass("groovy.lang.Binding");
-        Constructor gbcons = gbindingc.getConstructor(null);
-        Object gbinding = gbcons.newInstance(null);
-        java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable", new Class[] { String.class, Object.class} );
-        setvar.invoke(gbinding, new Object[] { "Jalview", jalviewContext});
-        Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
-        Constructor gseccons = gsec.getConstructor(new Class[] { URL[].class } ); // String[].class });
-        Object gse = gseccons.newInstance(new Object[] { new URL[] { sfile.toURL() } }); // .toString() } });
-        java.lang.reflect.Method run = gsec.getMethod("run", new Class[]{ String.class, gbindingc });
-        run.invoke(gse, new Object[] { sfile.getName(), gbinding });
-        success = true;
+    try
+    {
+      /*
+       * The following code performs the GroovyScriptEngine invocation using
+       * reflection, and is equivalent to this fragment from the embedding
+       * groovy documentation on the groovy site: <code> import
+       * groovy.lang.Binding; import groovy.util.GroovyScriptEngine;
+       * 
+       * String[] roots = new String[] { "/my/groovy/script/path" };
+       * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding =
+       * new Binding(); binding.setVariable("input", "world");
+       * gse.run("hello.groovy", binding); </code>
+       */
+      ClassLoader cl = jalviewContext.getClass().getClassLoader();
+      Class gbindingc = cl.loadClass("groovy.lang.Binding");
+      Constructor gbcons = gbindingc.getConstructor(null);
+      Object gbinding = gbcons.newInstance(null);
+      java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable",
+              new Class[]
+              { String.class, Object.class });
+      setvar.invoke(gbinding, new Object[]
+      { "Jalview", jalviewContext });
+      Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
+      Constructor gseccons = gsec.getConstructor(new Class[]
+      { URL[].class }); // String[].class });
+      Object gse = gseccons.newInstance(new Object[]
+      { new URL[]
+      { sfile.toURL() } }); // .toString() } });
+      java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
+      { String.class, gbindingc });
+      run.invoke(gse, new Object[]
+      { sfile.getName(), gbinding });
+      success = true;
     } catch (Exception e)
     {
-      System.err.println("Exception Whilst trying to execute file "+sfile+" as a groovy script.");
+      System.err.println("Exception Whilst trying to execute file " + sfile
+              + " as a groovy script.");
       e.printStackTrace(System.err);
-      
+
     }
     if (success && groovyscript.equals("STDIN"))
     {
-      // delete temp file that we made - but only if it was successfully executed
+      // delete temp file that we made - but only if it was successfully
+      // executed
       sfile.delete();
     }
   }
+
   /**
    * Check commandline for any das server definitions or any fetchfrom switches
+   * 
    * @return vector of DAS source nicknames to retrieve from
    */
   private static Vector checkDasArguments(ArgsParser aparser)
   {
-    Vector source=null;
+    Vector source = null;
     String data;
     String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
-    while ((data = aparser.getValue("dasserver"))!=null)
+    while ((data = aparser.getValue("dasserver")) != null)
     {
       String nickname = null;
       String url = null;
@@ -509,32 +544,35 @@ public class Jalview
         {
           nickname = url;
         }
-        if (locsources==null)
+        if (locsources == null)
+        {
+          locsources = "";
+        }
+        else
         {
-          locsources="";
-        } else {
-          locsources+="\t";
+          locsources += "\t";
         }
-        locsources=locsources+nickname+"|"+url;
+        locsources = locsources + nickname + "|" + url;
         System.err
                 .println("NOTE! dasserver parameter not yet really supported (got args of "
                         + nickname + "|" + url);
-        if (source==null)
+        if (source == null)
         {
           source = new Vector();
         }
         source.addElement(nickname);
       }
     } // loop until no more server entries are found.
-    if (locsources!=null && locsources.indexOf('|')>-1)
+    if (locsources != null && locsources.indexOf('|') > -1)
     {
-      Cache.log.debug("Setting local source list in properties file to:\n"+locsources);
+      Cache.log.debug("Setting local source list in properties file to:\n"
+              + locsources);
       Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
     }
-    while ((data = aparser.getValue("fetchfrom"))!=null)
+    while ((data = aparser.getValue("fetchfrom")) != null)
     {
-      System.out.println("adding source '"+data+"'");
-      if (source==null)
+      System.out.println("adding source '" + data + "'");
+      if (source == null)
       {
         source = new Vector();
       }
@@ -542,24 +580,27 @@ public class Jalview
     }
     return source;
   }
+
   /**
    * start a feature fetcher for every alignment frame
+   * 
    * @param dasSources
    */
   private static void startFeatureFetching(final Vector dasSources)
   {
     AlignFrame afs[] = Desktop.getAlignframes();
-    if (afs==null || afs.length==0)
+    if (afs == null || afs.length == 0)
     {
       return;
     }
-    for (int i = 0; i<afs.length; i++)
+    for (int i = 0; i < afs.length; i++)
     {
       final AlignFrame af = afs[i];
-      SwingUtilities.invokeLater(new Runnable() {
+      SwingUtilities.invokeLater(new Runnable()
+      {
 
         public void run()
-        { 
+        {
           af.featureSettings_actionPerformed(null);
           af.featureSettings.fetchDasFeatures(dasSources);
         }
@@ -581,11 +622,12 @@ public class Jalview
 
 /**
  * Notes: this argParser does not distinguish between parameter switches,
- * parameter values and argument text. If an argument happens to be identical
- * to a parameter, it will be taken as such (even though it didn't have a '-' prefixing it).
+ * parameter values and argument text. If an argument happens to be identical to
+ * a parameter, it will be taken as such (even though it didn't have a '-'
+ * prefixing it).
  * 
  * @author Andrew Waterhouse and JBP documented.
- *
+ * 
  */
 class ArgsParser
 {
@@ -604,8 +646,10 @@ class ArgsParser
       vargs.addElement(arg);
     }
   }
+
   /**
    * check for and remove first occurence of arg+parameter in arglist.
+   * 
    * @param arg
    * @return return the argument following the given arg if arg was in list.
    */
@@ -621,8 +665,10 @@ class ArgsParser
     }
     return ret;
   }
+
   /**
    * check for and remove first occurence of arg in arglist.
+   * 
    * @param arg
    * @return true if arg was present in argslist.
    */