JAL-629 Fixed appending URLs

[jalview.git] / src / jalview / bin / argparser / ArgParser.java

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 70ed5d1..e08ae03 100644 (file)
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -37,6 +37,7 @@ import jalview.bin.Console;
 import jalview.bin.Jalview;
 import jalview.bin.argparser.Arg.Opt;
 import jalview.util.FileUtils;
+import jalview.util.HttpUtils;
 
 public class ArgParser
 {
@@ -55,11 +56,12 @@ public class ArgParser
   // the substitution string used to use the defaultLinkedIdCounter
   private static final String DEFAULTLINKEDIDCOUNTER = "{}";
 
-  // the counter added to the default linked id prefix
-  private int opennewLinkedIdCounter = 0;
+  // the counter added to the default linked id prefix. NOW using
+  // linkedIdAutoCounter
+  // private int openLinkedIdCounter = 0;
 
-  // the linked id prefix used for --opennew files
-  protected static final String OPENNEWLINKEDIDPREFIX = "OPENNEW:";
+  // the linked id prefix used for --open files. NOW the same as DEFAULT
+  protected static final String OPENLINKEDIDPREFIX = DEFAULTLINKEDIDPREFIX;
 
   // the counter used for {n} substitutions
   private int linkedIdAutoCounter = 0;
@@ -71,12 +73,12 @@ public class ArgParser
   // the linked id substitution string used to use the idCounter
   private static final String LINKEDIDAUTOCOUNTER = "{n}";
 
-  // the linked id substitution string used to use the base filename of --open
-  // or --opennew
+  // the linked id substitution string used to use the base filename of --append
+  // or --open
   private static final String LINKEDIDBASENAME = "{basename}";
 
-  // the linked id substitution string used to use the dir path of --open
-  // or --opennew
+  // the linked id substitution string used to use the dir path of --append
+  // or --open
   private static final String LINKEDIDDIRNAME = "{dirname}";
 
   // the current argfile
@@ -141,7 +143,7 @@ public class ArgParser
     // Make a mutable new ArrayList so that shell globbing parser works.
     // (When shell file globbing is used, there are a sequence of non-Arg
     // arguments (which are the expanded globbed filenames) that need to be
-    // consumed by the --open/--argfile/etc Arg which is most easily done by
+    // consumed by the --append/--argfile/etc Arg which is most easily done by
     // removing these filenames from the list one at a time. This can't be done
     // with an ArrayList made with only Arrays.asList(String[] args). )
     this(new ArrayList<>(Arrays.asList(args)), initsubstitutions);
@@ -155,7 +157,8 @@ public class ArgParser
   public ArgParser(List<String> args, boolean initsubstitutions,
           boolean allowPrivate)
   {
-    // do nothing if there are no "--" args and some "-" args
+    // do nothing if there are no "--" args and (some "-" args || >0 arg is
+    // "open")
     boolean d = false;
     boolean dd = false;
     for (String arg : args)
@@ -165,7 +168,7 @@ public class ArgParser
         dd = true;
         break;
       }
-      else if (arg.startsWith("-"))
+      else if (arg.startsWith("-") || arg.equals("open"))
       {
         d = true;
       }
@@ -195,9 +198,10 @@ public class ArgParser
       // single arg[i] and increment the defaultLinkedIdCounter so that each of
       // these files is opened separately.
       if (openEachInitialFilenames && !arg.startsWith(DOUBLEDASH)
-              && !arg.startsWith("-") && new File(arg).exists())
+              && !arg.startsWith("-") && (new File(arg).exists()
+                      || HttpUtils.startsWithHttpOrHttps(arg)))
       {
-        arg = Arg.OPENNEW.argString();
+        arg = Arg.OPEN.argString();
       }
       else
       {
@@ -329,7 +333,7 @@ public class ArgParser
 
         // make NOACTION adjustments
         // default and auto counter increments
-        if (a == Arg.INCREMENT)
+        if (a == Arg.NEWFRAME)
         {
           defaultLinkedIdCounter++;
         }
@@ -360,13 +364,14 @@ public class ArgParser
         {
           if (linkedId == null)
           {
-            if (a == Arg.OPENNEW)
+            if (a == Arg.OPEN)
             {
-              // use the next default prefixed OPENNEWLINKEDID
-              linkedId = new StringBuilder(OPENNEWLINKEDIDPREFIX)
-                      .append(Integer.toString(opennewLinkedIdCounter))
+              // use the next default prefixed OPENLINKEDID
+              // NOW using the linkedIdAutoCounter
+              defaultLinkedIdCounter++;
+              linkedId = new StringBuilder(OPENLINKEDIDPREFIX)
+                      .append(Integer.toString(defaultLinkedIdCounter))
                       .toString();
-              opennewLinkedIdCounter++;
             }
             else
             {