JAL-3518 more pull up / test coverage of structure command generation

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

diff --git a/src/jalview/structure/StructureCommandsBase.java b/src/jalview/structure/StructureCommandsBase.java
index 921c9cd..44764db 100644 (file)
--- a/src/jalview/structure/StructureCommandsBase.java
+++ b/src/jalview/structure/StructureCommandsBase.java
@@ -58,118 +58,6 @@ 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>
@@ -203,14 +91,6 @@ public abstract class StructureCommandsBase implements StructureCommandsI
   }
 
   /**
-   * Returns a colour formatted suitable for use in viewer command syntax
-   * 
-   * @param colour
-   * @return
-   */
-  protected abstract String getColourString(Color colour);
-
-  /**
    * 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.
@@ -218,8 +98,8 @@ public abstract class StructureCommandsBase implements StructureCommandsI
    * @param colourMap
    * @return
    */
-  public List<String> buildColourCommands(
-          Map<Object, AtomSpecModel> colourMap)
+  @Override
+  public String[] colourBySequence(Map<Object, AtomSpecModel> colourMap)
   {
     /*
      * This version concatenates all commands into a single String (semi-colon
@@ -241,7 +121,8 @@ public abstract class StructureCommandsBase implements StructureCommandsI
       sb.append(getColourCommand(colourData, colour));
     }
     commands.add(sb.toString());
-    return commands;
+
+    return commands.toArray(new String[commands.size()]);
   }
 
   /**