X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureCommandsBase.java;h=ec6032de9c38c6e8a1b0e71ff8b789c0065ca2ea;hb=9bfda76754fb426a471e1c12c9f0ca0c4c1784bc;hp=44764db439a872510de274500ccda446153ca556;hpb=fea6f8ed76719fd78b600adfea8891dafb8c9d12;p=jalview.git

diff --git a/src/jalview/structure/StructureCommandsBase.java b/src/jalview/structure/StructureCommandsBase.java
index 44764db..ec6032d 100644
--- a/src/jalview/structure/StructureCommandsBase.java
+++ b/src/jalview/structure/StructureCommandsBase.java
@@ -1,22 +1,33 @@
+/*
+ * 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 jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
-import jalview.util.Comparison;
-
 import java.awt.Color;
 import java.util.ArrayList;
-import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 
+import jalview.bin.Console;
+
 /**
  * A base class holding methods useful to all classes that implement commands
  * for structure viewers
@@ -26,6 +37,8 @@ import java.util.Map.Entry;
  */
 public abstract class StructureCommandsBase implements StructureCommandsI
 {
+  public static final String NAMESPACE_PREFIX = "jv_";
+
   private static final String CMD_SEPARATOR = ";";
 
   /**
@@ -33,19 +46,11 @@ public abstract class StructureCommandsBase implements StructureCommandsI
    * 
    * @return
    */
-  protected static String getCommandSeparator()
+  protected String getCommandSeparator()
   {
     return CMD_SEPARATOR;
   }
 
-  @Override
-  public String[] 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
    * 
@@ -58,8 +63,9 @@ 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'
@@ -74,8 +80,8 @@ public abstract class StructureCommandsBase implements StructureCommandsI
    * @param chain
    */
   public static final void addAtomSpecRange(Map<Object, AtomSpecModel> map,
-          Object value,
-          int model, int startPos, int endPos, String chain)
+          Object value, String model, int startPos, int endPos,
+          String chain)
   {
     /*
      * Get/initialize map of data for the colour
@@ -86,43 +92,65 @@ 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.
+   * <p>
+   * The default implementation returns a single command containing one command
+   * per colour, concatenated.
    * 
    * @param colourMap
    * @return
    */
   @Override
-  public String[] colourBySequence(Map<Object, AtomSpecModel> colourMap)
+  public List<StructureCommandI> colourBySequence(
+          Map<Object, AtomSpecModel> colourMap)
   {
-    /*
-     * This version concatenates all commands into a single String (semi-colon
-     * delimited). If length limit issues arise, refactor to return one color
-     * command per colour.
-     */
-    List<String> commands = new ArrayList<>();
-    StringBuilder sb = new StringBuilder(256);
-    boolean firstColour = true;
+    List<StructureCommandI> commands = new ArrayList<>();
+    StringBuilder sb = new StringBuilder(colourMap.size() * 20);
+    boolean first = true;
     for (Object key : colourMap.keySet())
     {
       Color colour = (Color) key;
-      if (!firstColour)
+      final AtomSpecModel colourData = colourMap.get(colour);
+      StructureCommandI command = getColourCommand(colourData, colour);
+      if (!first)
       {
-        sb.append(getCommandSeparator()).append(" ");
+        sb.append(getCommandSeparator());
       }
-      firstColour = false;
-      final AtomSpecModel colourData = colourMap.get(colour);
-      sb.append(getColourCommand(colourData, colour));
+      first = false;
+      sb.append(command.getCommand());
     }
-    commands.add(sb.toString());
 
-    return commands.toArray(new String[commands.size()]);
+    commands.add(new StructureCommand(sb.toString()));
+    return commands;
   }
 
   /**
@@ -133,10 +161,11 @@ public abstract class StructureCommandsBase implements StructureCommandsI
    * @param colour
    * @return
    */
-  protected String getColourCommand(AtomSpecModel atomSpecModel, Color colour)
+  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);
   }
 
   /**
@@ -147,21 +176,25 @@ public abstract class StructureCommandsBase implements StructureCommandsI
    * @param colour
    * @return
    */
-  protected abstract String getColourCommand(String atomSpec, Color colour);
+  protected abstract StructureCommandI colourResidues(String atomSpec,
+          Color colour);
 
   @Override
-  public String colourByResidues(Map<String, Color> colours)
+  public List<StructureCommandI> colourByResidues(
+          Map<String, Color> colours)
   {
-    StringBuilder cmd = new StringBuilder(12 * colours.size());
-  
+    List<StructureCommandI> commands = new ArrayList<>();
     for (Entry<String, Color> entry : colours.entrySet())
     {
-      String residue = entry.getKey();
-      String atomSpec = getResidueSpec(residue);
-      cmd.append(getColourCommand(atomSpec, entry.getValue()));
-      cmd.append(getCommandSeparator());
+      commands.add(colourResidue(entry.getKey(), entry.getValue()));
     }
-    return cmd.toString();
+    return commands;
+  }
+
+  private StructureCommandI colourResidue(String resName, Color col)
+  {
+    String atomSpec = getResidueSpec(resName);
+    return colourResidues(atomSpec, col);
   }
 
   /**
@@ -206,4 +239,48 @@ 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;
+  }
+
+  @Override
+  public StructureCommandI restoreSession(String filePath)
+  {
+    return loadFile(filePath);
+  }
 }