JAL-629 Change behaviour of --open GLOB to increment defaultLinkedId to allow --allfr...

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

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index fc2ee1a..f33202d 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -2,16 +2,15 @@ package jalview.bin;
 
 import java.io.File;
 import java.io.IOException;
-import java.util.AbstractMap;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.EnumSet;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
-import java.util.Map.Entry;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.bin.argparser.Arg;
@@ -82,11 +81,11 @@ public class Commands
     headless = h;
     boolean theseArgsWereParsed = false;
 
-    if (argParser != null && argParser.linkedIds() != null)
+    if (argParser != null && argParser.getLinkedIds() != null)
     {
-      for (String id : argParser.linkedIds())
+      for (String id : argParser.getLinkedIds())
       {
-        ArgValuesMap avm = argParser.linkedArgs(id);
+        ArgValuesMap avm = argParser.getLinkedArgs(id);
         theseArgsWereParsed = true;
         if (id == null)
         {
@@ -139,7 +138,7 @@ public class Commands
   protected boolean processLinked(String id)
   {
     boolean theseArgsWereParsed = false;
-    ArgValuesMap avm = argParser.linkedArgs(id);
+    ArgValuesMap avm = argParser.getLinkedArgs(id);
     if (avm == null)
       return true;
 
@@ -150,7 +149,7 @@ public class Commands
      * m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null;
      * DataSourceType protocol = null;
      */
-    if (avm.containsArg(Arg.OPEN) || avm.containsArg(Arg.OPENNEW))
+    if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
     {
       commandArgsProvided = true;
       long progress = -1;
@@ -158,21 +157,17 @@ public class Commands
       boolean first = true;
       boolean progressBarSet = false;
       AlignFrame af;
-      // Combine the OPEN and OPENNEW files into one list, along with whether it
-      // was OPEN or OPENNEW
-      List<Entry<Arg, ArgValue>> openAvList = new ArrayList<>();
-      avm.getArgValueList(Arg.OPEN).stream()
-              .forEachOrdered(av -> openAvList.add(
-                      new AbstractMap.SimpleEntry<Arg, ArgValue>(Arg.OPEN,
-                              av)));
-      avm.getArgValueList(Arg.OPENNEW).stream()
-              .forEachOrdered(av -> openAvList
-                      .add(new AbstractMap.SimpleEntry<Arg, ArgValue>(
-                              Arg.OPENNEW, av)));
-      for (Entry<Arg, ArgValue> aav : openAvList)
+      // Combine the APPEND and OPEN files into one list, along with whether it
+      // was APPEND or OPEN
+      List<ArgValue> openAvList = new ArrayList<>();
+      openAvList.addAll(avm.getArgValueList(Arg.OPEN));
+      openAvList.addAll(avm.getArgValueList(Arg.APPEND));
+      // sort avlist based on av.getArgIndex()
+      Collections.sort(openAvList);
+      for (ArgValue av : openAvList)
       {
-        Arg a = aav.getKey();
-        ArgValue av = aav.getValue();
+        Arg a = av.getArg();
+        SubVals sv = av.getSubVals();
         String openFile = av.getValue();
         if (openFile == null)
           continue;
@@ -220,8 +215,9 @@ public class Commands
         }
 
         af = afMap.get(id);
+        // When to open a new AlignFrame
         if (af == null || "true".equals(av.getSubVal("new"))
-                || a == Arg.OPENNEW || format == FileFormat.Jalview)
+                || a == Arg.OPEN || format == FileFormat.Jalview)
         {
           /*
            * this approach isn't working yet // get default annotations before opening
@@ -251,20 +247,24 @@ public class Commands
           af.setAnnotationsVisibility(showAnnotations, false, true);
 
           // wrap alignment?
-          if (avm.getBoolean(Arg.WRAP))
-          {
-            af.getCurrentView().setWrapAlignment(true);
-          }
+          boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
+                  null, "WRAP_ALIGNMENT", false);
+          af.getCurrentView().setWrapAlignment(wrap);
 
           // colour aligment?
-          if (avm.containsArg(Arg.COLOUR))
+          String colour = ArgParser.getFromSubValArgOrPref(avm, Arg.COLOUR,
+                  sv, null, "DEFAULT_COLOUR_PROT", "");
+
+          if ("" != colour)
           {
-            af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
+            af.changeColour_actionPerformed(colour);
           }
 
           // change alignment frame title
-          if (avm.containsArg(Arg.TITLE))
-            af.setTitle(avm.getValue(Arg.TITLE));
+          String title = ArgParser.getFromSubValArgOrPref(avm, Arg.TITLE,
+                  sv, null, null, null);
+          if (title != null)
+            af.setTitle(title);
 
           // show secondary structure annotations?
           boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
@@ -337,10 +337,15 @@ public class Commands
         {
           Console.debug(
                   "Opening '" + openFile + "' in existing alignment frame");
-          af.getCurrentView().addFile(new File(openFile), format, false);
+          DataSourceType dst = HttpUtils.startsWithHttpOrHttps(openFile)
+                  ? DataSourceType.URL
+                  : DataSourceType.FILE;
+          FileLoader fileLoader = new FileLoader(!headless);
+          fileLoader.LoadFile(af.getCurrentView(), openFile, dst, null,
+                  false);
         }
 
-        Console.debug("Command " + Arg.OPEN + " executed successfully!");
+        Console.debug("Command " + Arg.APPEND + " executed successfully!");
 
       }
       if (first) // first=true means nothing opened
@@ -566,7 +571,7 @@ public class Commands
 
   protected boolean processImages(String id)
   {
-    ArgValuesMap avm = argParser.linkedArgs(id);
+    ArgValuesMap avm = argParser.getLinkedArgs(id);
     AlignFrame af = afMap.get(id);
 
     if (af == null)