JAL-629 parse SubVals once with ArgValue. Ensure SubVals exists. Change to setprops...

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 9ff95e3..4a70bd9 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -399,7 +399,7 @@ public class Commands
         for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
         {
           String val = av.getValue();
-          SubVals subId = new SubVals(val);
+          SubVals subId = av.getSubVals();
           SequenceI seq = getSpecifiedSequence(af, subId);
           if (seq == null)
           {
@@ -494,7 +494,7 @@ public class Commands
         for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
         {
           String val = av.getValue();
-          SubVals subVals = ArgParser.getSubVals(val);
+          SubVals subVals = av.getSubVals();
           String paeLabel = subVals.get("label");
           File paeFile = new File(subVals.getContent());
           String paePath = null;
@@ -507,10 +507,14 @@ public class Commands
             Console.warn(
                     "Problem with the PAE file path: '" + paePath + "'");
           }
-          String structid = null;
-          String structfile = null;
-          int seqindex = SubVals.NOTSET;
-          if (subVals.notSet())
+          String structid = subVals.get("structid");
+          String structfile = subVals.get("structfile");
+          String seqid = subVals.get("seqid");
+          int seqindex = subVals.getIndex();
+
+          // let's find a structure
+          if (structfile == null && structid == null && seqid == null
+                  && seqindex == SubVals.NOTSET)
           {
             ArgValue likelyStructure = avm
                     .getClosestPreviousArgValueOfArg(av, Arg.STRUCTURE);
@@ -530,41 +534,39 @@ public class Commands
               }
             }
           }
-          else if (subVals.has("structfile"))
-          {
-            structfile = subVals.get("structfile");
-          }
-          else if (subVals.has("structid"))
-          {
-            structid = subVals.get("structid");
-          }
+
           if (structfile != null)
           {
-            Console.info("##### Attaching paeFile '" + paePath + "' to "
+            Console.debug("##### Attaching paeFile '" + paePath + "' to "
                     + "structfile=" + structfile);
             EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
                     paeFile, seqindex, structfile, true, false, paeLabel);
           }
           else if (structid != null)
           {
-            Console.info("##### Attaching paeFile '" + paePath + "' to "
+            Console.debug("##### Attaching paeFile '" + paePath + "' to "
                     + "structid=" + structid);
             EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
-                    paeFile, seqindex, subVals.get("structid"), true, true,
-                    paeLabel);
+                    paeFile, seqindex, structid, true, true, paeLabel);
           }
-          else
+          else if (seqid != null)
+          {
+            Console.debug("##### Attaching paeFile '" + paePath + "' to "
+                    + "seqid=" + seqid);
+            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+                    paeFile, seqindex, seqid, false, false, paeLabel);
+          }
+          else if (seqindex >= 0)
           {
-            seqindex = subVals.getIndex();
             Console.debug("##### Attaching paeFile '" + paePath
                     + "' to sequence index " + seqindex);
             EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
                     paeFile, seqindex, null, false, false, paeLabel);
-            // required to readjust the height and position of the PAE
-            // annotation
           }
           for (AlignmentViewPanel ap : af.getAlignPanels())
           {
+            // required to readjust the height and position of the PAE
+            // annotation
             ap.adjustAnnotationHeight();
           }
         }
@@ -605,7 +607,7 @@ public class Commands
       for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
       {
         String val = av.getValue();
-        SubVals subVal = new SubVals(val);
+        SubVals subVal = av.getSubVals();
         String type = "png"; // default
         String fileName = subVal.getContent();
         File file = new File(fileName);

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 951578a..44494e2 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -526,7 +526,7 @@ public class Jalview
         }
         // DISABLED FOR SECURITY REASONS
         // TODO: add a property to allow properties to be overriden by cli args
-        // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
+        // Cache.setProperty(setprop.substring(0,p), setprop.substring(p+1));
       }
     }
     if (System.getProperty("java.awt.headless") != null

diff --git a/src/jalview/bin/argparser/ArgValue.java b/src/jalview/bin/argparser/ArgValue.java
index 28cead9..c9e86b8 100644 (file)
--- a/src/jalview/bin/argparser/ArgValue.java
+++ b/src/jalview/bin/argparser/ArgValue.java
@@ -11,19 +11,19 @@ public class ArgValue
 
   private String id;
 
-  private SubVals subVals = null;
+  private SubVals subVals;
 
   protected ArgValue(SubVals sv, String content, int argIndex)
   {
     this.value = content;
     this.argIndex = argIndex;
-    this.subVals = sv;
+    this.subVals = sv == null ? new SubVals("") : sv;
   }
 
   protected ArgValue(String value, int argIndex)
   {
     this.argIndex = argIndex;
-    this.subVals = ArgParser.getSubVals(value);
+    this.subVals = new SubVals(value);
     this.value = getSubVals().getContent();
   }
 

diff --git a/src/jalview/bin/argparser/ArgValues.java b/src/jalview/bin/argparser/ArgValues.java
index 27d52ba..c166da0 100644 (file)
--- a/src/jalview/bin/argparser/ArgValues.java
+++ b/src/jalview/bin/argparser/ArgValues.java
@@ -123,7 +123,7 @@ public class ArgValues
     {
       argValueList = new ArrayList<ArgValue>();
     }
-    SubVals sv = ArgParser.getSubVals(av.getValue());
+    SubVals sv = new SubVals(av.getValue());
     if (sv.has(ID))
     {
       String id = sv.get(ID);

diff --git a/src/jalview/bin/argparser/SubVals.java b/src/jalview/bin/argparser/SubVals.java
index 3c7ba7c..6708cf9 100644 (file)
--- a/src/jalview/bin/argparser/SubVals.java
+++ b/src/jalview/bin/argparser/SubVals.java
@@ -19,7 +19,7 @@ public class SubVals
 
   private int index = NOTSET;
 
-  private Map<String, String> subVals = null;
+  private Map<String, String> subValMap;
 
   private static char SEPARATOR = ';';
 
@@ -27,18 +27,24 @@ public class SubVals
 
   private String content = null;
 
-  public SubVals(SubVals sv, String c)
+  protected SubVals(SubVals sv, String c)
   {
-    if (sv != null)
+    if (sv == null)
     {
-      this.subVals = sv.getSubValsMap();
+      this.subValMap = new HashMap<>();
+    }
+    else
+    {
+      this.subValMap = sv == null ? new HashMap<>() : sv.getSubValMap();
       this.index = sv.getIndex();
     }
     this.content = c;
   }
 
-  public SubVals(String item)
+  protected SubVals(String item)
   {
+    if (subValMap == null)
+      subValMap = new HashMap<>();
     this.parseVals(item);
   }
 
@@ -56,8 +62,6 @@ public class SubVals
       for (String subvalString : subvalsString
               .split(Character.toString(SEPARATOR)))
       {
-        if (subVals == null)
-          subVals = new HashMap<>();
         int equals = subvalString.indexOf(EQUALS);
         if (equals > -1)
         {
@@ -73,7 +77,7 @@ public class SubVals
           } catch (NumberFormatException e)
           {
             // store this non-numeric key as a "true" value
-            subVals.put(subvalString, "true");
+            this.put(subvalString, "true");
           }
         }
       }
@@ -91,25 +95,23 @@ public class SubVals
 
   protected void put(String key, String val)
   {
-    if (subVals == null)
-      subVals = new HashMap<>();
-    subVals.put(key, val);
+    subValMap.put(key, val);
   }
 
   public boolean notSet()
   {
     // notSet is true if content present but nonsensical
-    return index == NOTSET && subVals == null;
+    return index == NOTSET && (subValMap == null || subValMap.size() == 0);
   }
 
   public String get(String key)
   {
-    return subVals == null ? null : subVals.get(key);
+    return subValMap.get(key);
   }
 
   public boolean has(String key)
   {
-    return subVals == null ? false : subVals.containsKey(key);
+    return subValMap.containsKey(key);
   }
 
   public int getIndex()
@@ -122,19 +124,19 @@ public class SubVals
     return content;
   }
 
-  protected Map<String, String> getSubValsMap()
+  protected Map<String, String> getSubValMap()
   {
-    return subVals;
+    return subValMap;
   }
 
   public String toString()
   {
-    if (subVals == null && getIndex() == NOTSET)
+    if (subValMap == null && getIndex() == NOTSET)
       return "";
 
     StringBuilder sb = new StringBuilder();
     List<String> entries = new ArrayList<>();
-    subVals.entrySet().stream().forEachOrdered(
+    subValMap.entrySet().stream().forEachOrdered(
             m -> entries.add(m.getValue().equals("true") ? m.getKey()
                     : new StringBuilder().append(m.getKey()).append(EQUALS)
                             .append(m.getValue()).toString()));