X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureCommandsBase.java;h=57544b750838c2709e775110768c96e4323ac4a1;hb=d87b55e45cc1e6a5b7df3865ded1b87a0e3dc7ff;hp=921c9cde88b8dafe1982b45b07a4e416509cce81;hpb=9c1a9d682a2664d525bfd0f38bae861292dc3921;p=jalview.git

diff --git a/src/jalview/structure/StructureCommandsBase.java b/src/jalview/structure/StructureCommandsBase.java
index 921c9cd..57544b7 100644
--- a/src/jalview/structure/StructureCommandsBase.java
+++ b/src/jalview/structure/StructureCommandsBase.java
@@ -1,18 +1,7 @@
 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;
@@ -26,6 +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 = ";";
 
   /**
@@ -38,14 +29,6 @@ public abstract class StructureCommandsBase implements StructureCommandsI
     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
    * 
@@ -58,118 +41,6 @@ public abstract class StructureCommandsBase implements StructureCommandsI
   }
 
   /**
-   * <pre>
-   * Build a data structure which records contiguous subsequences for each colour. 
-   * From this we can easily generate the viewer command for colour by sequence.
-   * Color
-   *     Model number
-   *         Chain
-   *             list of start/end ranges
-   * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
-   * </pre>
-   * 
-   * @param ssm
-   * @param files
-   * @param sequence
-   * @param sr
-   * @param viewPanel
-   * @return
-   */
-  protected Map<Object, AtomSpecModel> buildColoursMap(
-          StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr, AlignmentViewPanel viewPanel)
-  {
-    FeatureRenderer fr = viewPanel.getFeatureRenderer();
-    FeatureColourFinder finder = new FeatureColourFinder(fr);
-    AlignViewportI viewport = viewPanel.getAlignViewport();
-    HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
-    AlignmentI al = viewport.getAlignment();
-    Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<>();
-    Color lastColour = null;
-  
-    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
-    {
-      final int modelNumber = pdbfnum + getModelStartNo();
-      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-  
-      if (mapping == null || mapping.length < 1)
-      {
-        continue;
-      }
-  
-      int startPos = -1, lastPos = -1;
-      String lastChain = "";
-      for (int s = 0; s < sequence[pdbfnum].length; s++)
-      {
-        for (int sp, m = 0; m < mapping.length; m++)
-        {
-          final SequenceI seq = sequence[pdbfnum][s];
-          if (mapping[m].getSequence() == seq
-                  && (sp = al.findIndex(seq)) > -1)
-          {
-            SequenceI asp = al.getSequenceAt(sp);
-            for (int r = 0; r < asp.getLength(); r++)
-            {
-              // no mapping to gaps in sequence
-              if (Comparison.isGap(asp.getCharAt(r)))
-              {
-                continue;
-              }
-              int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-  
-              if (pos < 1 || pos == lastPos)
-              {
-                continue;
-              }
-  
-              Color colour = sr.getResidueColour(seq, r, finder);
-  
-              /*
-               * darker colour for hidden regions
-               */
-              if (!cs.isVisible(r))
-              {
-                colour = Color.GRAY;
-              }
-  
-              final String chain = mapping[m].getChain();
-  
-              /*
-               * Just keep incrementing the end position for this colour range
-               * _unless_ colour, PDB model or chain has changed, or there is a
-               * gap in the mapped residue sequence
-               */
-              final boolean newColour = !colour.equals(lastColour);
-              final boolean nonContig = lastPos + 1 != pos;
-              final boolean newChain = !chain.equals(lastChain);
-              if (newColour || nonContig || newChain)
-              {
-                if (startPos != -1)
-                {
-                  addAtomSpecRange(colourMap, lastColour, modelNumber,
-                          startPos, lastPos, lastChain);
-                }
-                startPos = pos;
-              }
-              lastColour = colour;
-              lastPos = pos;
-              lastChain = chain;
-            }
-            // final colour range
-            if (lastColour != null)
-            {
-              addAtomSpecRange(colourMap, lastColour, modelNumber, startPos,
-                      lastPos, lastChain);
-            }
-            // break;
-          }
-        }
-      }
-    }
-    return colourMap;
-  }
-
-  /**
    * 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>
@@ -186,8 +57,8 @@ 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
@@ -203,44 +74,59 @@ public abstract class StructureCommandsBase implements StructureCommandsI
   }
 
   /**
-   * Returns a colour formatted suitable for use in viewer command syntax
+   * 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 colour
+   * @param featureType
    * @return
    */
-  protected abstract String getColourString(Color colour);
+  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
    */
-  public List<String> buildColourCommands(
+  @Override
+  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());
+
+    commands.add(new StructureCommand(sb.toString()));
     return commands;
   }
 
@@ -252,10 +138,11 @@ 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);
+    return colourResidues(atomSpec, colour);
   }
 
   /**
@@ -266,21 +153,25 @@ 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);
   }
 
   /**
@@ -325,4 +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;
+  }
 }