JAL-3746 apply copyright to source

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

diff --git a/src/jalview/structure/StructureCommandsBase.java b/src/jalview/structure/StructureCommandsBase.java
index e688b64..0b5874a 100644 (file)
--- a/src/jalview/structure/StructureCommandsBase.java
+++ b/src/jalview/structure/StructureCommandsBase.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.structure;
 
 import java.awt.Color;
@@ -6,9 +26,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.SequenceI;
-
 /**
  * A base class holding methods useful to all classes that implement commands
  * for structure viewers
@@ -18,6 +35,8 @@ import jalview.datamodel.SequenceI;
  */
 public abstract class StructureCommandsBase implements StructureCommandsI
 {
+  public static final String NAMESPACE_PREFIX = "jv_";
+
   private static final String CMD_SEPARATOR = ";";
 
   /**
@@ -25,20 +44,11 @@ public abstract class StructureCommandsBase implements StructureCommandsI
    * 
    * @return
    */
-  protected static String getCommandSeparator()
+  protected String getCommandSeparator()
   {
     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
    * 
@@ -51,8 +61,9 @@ public abstract class StructureCommandsBase implements StructureCommandsI
   }
 
   /**
-   * Helper method to add one contiguous range to the AtomSpec model for the given
-   * value (creating the model if necessary). As used by Jalview, {@code value} is
+   * Helper method to add one contiguous range to the AtomSpec model for the
+   * given value (creating the model if necessary). As used by Jalview,
+   * {@code value} is
    * <ul>
    * <li>a colour, when building a 'colour structure by sequence' command</li>
    * <li>a feature value, when building a 'set Chimera attributes from features'
@@ -79,11 +90,33 @@ public abstract class StructureCommandsBase implements StructureCommandsI
       atomSpec = new AtomSpecModel();
       map.put(value, atomSpec);
     }
-  
+
     atomSpec.addRange(model, startPos, endPos, chain);
   }
 
   /**
+   * 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.
@@ -129,8 +162,8 @@ public abstract class StructureCommandsBase implements StructureCommandsI
   protected StructureCommandI getColourCommand(AtomSpecModel atomSpecModel,
           Color colour)
   {
-    String atomSpec = getAtomSpec(atomSpecModel, false);
-    return getColourCommand(atomSpec, colour);
+    String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
+    return colourResidues(atomSpec, colour);
   }
 
   /**
@@ -141,7 +174,7 @@ public abstract class StructureCommandsBase implements StructureCommandsI
    * @param colour
    * @return
    */
-  protected abstract StructureCommandI getColourCommand(String atomSpec,
+  protected abstract StructureCommandI colourResidues(String atomSpec,
           Color colour);
 
   @Override
@@ -159,7 +192,7 @@ 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);
   }
 
   /**
@@ -204,4 +237,42 @@ 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;
+  }
 }