JAL-629 Allow multiple structure images for multiple structure files for the one...

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 9a85f1e..737c9eb 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -456,35 +456,31 @@ public class Commands
                     + Arg.STRUCTURE.argString() + "=" + val);
             continue;
           }
+          String structureFilename = null;
           File structureFile = null;
           if (subVals.getContent() != null
                   && subVals.getContent().length() != 0)
           {
-            structureFile = new File(subVals.getContent());
+            structureFilename = subVals.getContent();
             Console.debug("Using structure file (from argument) '"
-                    + structureFile.getAbsolutePath() + "'");
+                    + structureFilename + "'");
+            structureFile = new File(structureFilename);
           }
-          // TRY THIS
-          /*
-           * PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-           * .associatePdbWithSeq(selectedPdbFileName, DataSourceType.FILE,
-           * selectedSequence, true, Desktop.instance);
-           * 
-           * sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, new
-           * SequenceI[] { selectedSequence });
-           * 
-           */
           /* THIS DOESN'T WORK */
           else if (seq.getAllPDBEntries() != null
                   && seq.getAllPDBEntries().size() > 0)
           {
             structureFile = new File(
                     seq.getAllPDBEntries().elementAt(0).getFile());
-            Console.debug("Using structure file (from sequence) '"
-                    + structureFile.getAbsolutePath() + "'");
+            if (structureFile != null)
+            {
+              Console.debug("Using structure file (from sequence) '"
+                      + structureFile.getAbsolutePath() + "'");
+            }
+            structureFilename = structureFile.getAbsolutePath();
           }
 
-          if (structureFile == null)
+          if (structureFilename == null || structureFile == null)
           {
             addWarn("Not provided structure file with '" + val + "'");
             continue;
@@ -500,6 +496,8 @@ public class Commands
           Console.debug("Using structure file "
                   + structureFile.getAbsolutePath());
 
+          argParser.setStructureFilename(structureFilename);
+
           // open structure view
           AlignmentPanel ap = af.alignPanel;
           if (headless)
@@ -634,8 +632,8 @@ public class Commands
             for (ArgValue structureImageArgValue : avm
                     .getArgValueList(Arg.STRUCTUREIMAGE))
             {
-              String structureImageFilename = structureImageArgValue
-                      .getValue();
+              String structureImageFilename = argParser.makeSubstitutions(
+                      structureImageArgValue.getValue(), id, true);
               if (structureViewer != null && structureImageFilename != null)
               {
                 SubVals structureImageSubVals = null;
@@ -682,6 +680,10 @@ public class Commands
                 this.colourAlignFrame(af, imageColour);
 
                 List<String> extraCommands = new ArrayList<>();
+                // these don't actually do anything to the output image since we
+                // renderScreenImage
+                // extraCommands.add("set antialiasImages on");
+                // extraCommands.add("set antialiasTranslucent on");
 
                 String bgcolour = avm.getValueFromSubValOrArg(
                         structureImageArgValue, Arg.BGCOLOUR,

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index fd42bb2..1b8e6ad 100644 (file)
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -119,6 +119,46 @@ public class ArgParser
   private static final String LINKEDIDDIRNAME = "{dirname}";
 
   /**
+   * On-the-fly substitution (not made at argument parsing time)! the current
+   * structure filename extension
+   */
+  private static final String STRUCTUREEXTENSION = "{structureextension}";
+
+  /**
+   * On-the-fly substitution (not made at argument parsing time)! the current
+   * structure filename base
+   */
+  private static final String STRUCTUREBASENAME = "{structurebasename}";
+
+  /**
+   * On-the-fly substitution (not made at argument parsing time)! the current
+   * structure filename dir path
+   */
+  private static final String STRUCTUREDIRNAME = "{structuredirname}";
+
+  /**
+   * On-the-fly substitution (not made at argument parsing time)! increment the
+   * on-the-fly counter and substitute the incremented value
+   */
+  private static final String INCREMENTONTHEFLYCOUNTER = "{++m}";
+
+  /**
+   * On-the-fly substitution (not made at argument parsing time)! the current
+   * substitute with the on-the-fly counter
+   */
+  private static final String ONTHEFLYCOUNTER = "{m}";
+
+  /**
+   * the string used for on-the-fly structure filename substitutions
+   */
+  private String currentStructureFilename = null;
+
+  /**
+   * the counter used for on-the-fly {m} substitutions
+   */
+  private int ontheflyCounter = 0;
+
+  /**
    * the current argfile
    */
   private String argFile = null;
@@ -724,6 +764,12 @@ public class ArgParser
 
   public String makeSubstitutions(String val, String linkedId)
   {
+    return makeSubstitutions(val, linkedId, false);
+  }
+
+  public String makeSubstitutions(String val, String linkedId,
+          boolean onthefly)
+  {
     if (!this.substitutions || val == null)
       return val;
 
@@ -743,14 +789,20 @@ public class ArgParser
       rest = val;
     }
     if (rest.contains(LINKEDIDAUTOCOUNTER))
+    {
       rest = rest.replace(LINKEDIDAUTOCOUNTER,
               String.valueOf(linkedIdAutoCounter));
+    }
     if (rest.contains(INCREMENTLINKEDIDAUTOCOUNTER))
+    {
       rest = rest.replace(INCREMENTLINKEDIDAUTOCOUNTER,
               String.valueOf(++linkedIdAutoCounter));
+    }
     if (rest.contains(DEFAULTLINKEDIDCOUNTER))
+    {
       rest = rest.replace(DEFAULTLINKEDIDCOUNTER,
               String.valueOf(defaultLinkedIdCounter));
+    }
     ArgValuesMap avm = linkedArgs.get(linkedId);
     if (avm != null)
     {
@@ -780,6 +832,32 @@ public class ArgParser
                 FileUtils.getDirname(new File(argFile)));
       }
     }
+    if (onthefly)
+    {
+      if (rest.contains(ONTHEFLYCOUNTER))
+      {
+        rest = rest.replace(ONTHEFLYCOUNTER,
+                String.valueOf(ontheflyCounter));
+      }
+      if (rest.contains(INCREMENTONTHEFLYCOUNTER))
+      {
+        rest = rest.replace(INCREMENTONTHEFLYCOUNTER,
+                String.valueOf(++ontheflyCounter));
+      }
+      if (currentStructureFilename != null)
+      {
+        if (rest.contains(STRUCTUREBASENAME))
+        {
+          rest = rest.replace(STRUCTUREBASENAME, FileUtils
+                  .getBasename(new File(currentStructureFilename)));
+        }
+        if (rest.contains(STRUCTUREDIRNAME))
+        {
+          rest = rest.replace(STRUCTUREDIRNAME,
+                  FileUtils.getDirname(new File(currentStructureFilename)));
+        }
+      }
+    }
 
     return new StringBuilder(subvals).append(rest).toString();
   }
@@ -1203,4 +1281,9 @@ public class ArgParser
     return mixedExamples;
   }
 
+  public void setStructureFilename(String s)
+  {
+    this.currentStructureFilename = s;
+  }
+
 }
\ No newline at end of file