JAL-3518 pull up [get|list]ResidueAttributes to StructureCommandsI

[jalview.git] / src / jalview / structure / StructureCommandsBase.java

diff --git a/src/jalview/structure/StructureCommandsBase.java b/src/jalview/structure/StructureCommandsBase.java
index 8c6ea4e..57544b7 100644 (file)
--- a/src/jalview/structure/StructureCommandsBase.java
+++ b/src/jalview/structure/StructureCommandsBase.java
@@ -1,8 +1,5 @@
 package jalview.structure;
 
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.SequenceI;
-
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.List;
@@ -18,6 +15,8 @@ import java.util.Map.Entry;
  */
 public abstract class StructureCommandsBase implements StructureCommandsI
 {
+  public static final String NAMESPACE_PREFIX = "jv_";
+
   private static final String CMD_SEPARATOR = ";";
 
   /**
@@ -30,15 +29,6 @@ public abstract class StructureCommandsBase implements StructureCommandsI
     return CMD_SEPARATOR;
   }
 
-  @Override
-  public List<StructureCommandI> setAttributesForFeatures(
-          StructureSelectionManager ssm,
-          String[] files, SequenceI[][] sequence, AlignmentViewPanel avp)
-  {
-    // default does nothing, override where this is implemented
-    return null;
-  }
-
   /**
    * Returns the lowest model number used by the structure viewer
    * 
@@ -84,9 +74,34 @@ public abstract class StructureCommandsBase implements StructureCommandsI
   }
 
   /**
+   * Makes a structure viewer attribute name for a Jalview feature type by
+   * prefixing it with "jv_", and replacing any non-alphanumeric characters with
+   * an underscore
+   * 
+   * @param featureType
+   * @return
+   */
+  protected String makeAttributeName(String featureType)
+  {
+    StringBuilder sb = new StringBuilder();
+    if (featureType != null)
+    {
+      for (char c : featureType.toCharArray())
+      {
+        sb.append(Character.isLetterOrDigit(c) ? c : '_');
+      }
+    }
+    String attName = NAMESPACE_PREFIX + sb.toString();
+    return attName;
+  }
+
+  /**
    * Traverse the map of colours/models/chains/positions to construct a list of
    * 'color' commands (one per distinct colour used). The format of each command
    * is specific to the structure viewer.
+   * <p>
+   * The default implementation returns a single command containing one command
+   * per colour, concatenated.
    * 
    * @param colourMap
    * @return
@@ -95,18 +110,23 @@ public abstract class StructureCommandsBase implements StructureCommandsI
   public List<StructureCommandI> colourBySequence(
           Map<Object, AtomSpecModel> colourMap)
   {
-    /*
-     * default implementation creates one command per colour;
-     * override to concatenate colour commands if wanted
-     */
     List<StructureCommandI> commands = new ArrayList<>();
+    StringBuilder sb = new StringBuilder(colourMap.size() * 20);
+    boolean first = true;
     for (Object key : colourMap.keySet())
     {
       Color colour = (Color) key;
       final AtomSpecModel colourData = colourMap.get(colour);
-      commands.add(getColourCommand(colourData, colour));
+      StructureCommandI command = getColourCommand(colourData, colour);
+      if (!first)
+      {
+        sb.append(getCommandSeparator());
+      }
+      first = false;
+      sb.append(command.getCommand());
     }
 
+    commands.add(new StructureCommand(sb.toString()));
     return commands;
   }
 
@@ -122,7 +142,7 @@ public abstract class StructureCommandsBase implements StructureCommandsI
           Color colour)
   {
     String atomSpec = getAtomSpec(atomSpecModel, false);
-    return getColourCommand(atomSpec, colour);
+    return colourResidues(atomSpec, colour);
   }
 
   /**
@@ -133,7 +153,7 @@ public abstract class StructureCommandsBase implements StructureCommandsI
    * @param colour
    * @return
    */
-  protected abstract StructureCommandI getColourCommand(String atomSpec,
+  protected abstract StructureCommandI colourResidues(String atomSpec,
           Color colour);
 
   @Override
@@ -151,7 +171,7 @@ public abstract class StructureCommandsBase implements StructureCommandsI
   private StructureCommandI colourResidue(String resName, Color col)
   {
     String atomSpec = getResidueSpec(resName);
-    return getColourCommand(atomSpec, col);
+    return colourResidues(atomSpec, col);
   }
 
   /**
@@ -196,4 +216,42 @@ public abstract class StructureCommandsBase implements StructureCommandsI
    * @return
    */
   protected abstract String getResidueSpec(String residue);
+
+  @Override
+  public List<StructureCommandI> setAttributes(
+          Map<String, Map<Object, AtomSpecModel>> featureValues)
+  {
+    // default does nothing, override where this is implemented
+    return null;
+  }
+
+  @Override
+  public List<StructureCommandI> startNotifications(String uri)
+  {
+    return null;
+  }
+
+  @Override
+  public List<StructureCommandI> stopNotifications()
+  {
+    return null;
+  }
+
+  @Override
+  public StructureCommandI getSelectedResidues()
+  {
+    return null;
+  }
+
+  @Override
+  public StructureCommandI listResidueAttributes()
+  {
+    return null;
+  }
+
+  @Override
+  public StructureCommandI getResidueAttributes(String attName)
+  {
+    return null;
+  }
 }