From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 5 Aug 2019 14:24:11 +0000 (+0100)
Subject: JAL-3390 new View menu option to hide hidden regions in structure
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=e34c8452beda2cf80c2a3224f236d3096db69ae9

JAL-3390 new View menu option to hide hidden regions in structure
---

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index d2d8e88..c54e414 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1400,3 +1400,5 @@ label.pca = PCA
 label.create_image_of = Create {0} image of {1}
 label.click_to_edit = Click to edit, right-click for menu
 label.by_annotation_tooltip = Annotation Colour is configured from the main Colour menu
+label.show_alignment_only = Show alignment only
+label.hide_hidden_regions = Hide hidden columns / sequences
\ No newline at end of file
diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index e9e18ce..a99d3bb 100644
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -311,7 +311,8 @@ label.copied_sequences_to_clipboard = Copiadas {0} secuencias en el portapapeles
 label.check_file_matches_sequence_ids_alignment = Comprobar que el fichero coincide con el ID de la secuencia en el alineamiento.
 label.problem_reading_tcoffee_score_file = Problema de lectura del fichero de puntuaciones T-COFFEE
 label.source_to_target = {0} a {1}
-label.per_sequence_only= Sólo por secuencia
+label.per_sequence_
+= Sólo por secuencia
 label.to_file = a fichero
 label.to_textbox = a cuadro de texto
 label.jalview = Jalview
@@ -1401,3 +1402,5 @@ label.pca = ACP
 label.create_image_of = Crear imagen {0} de {1}
 label.click_to_edit = Haga clic para editar, clic en el botón derecho para ver el menú  
 label.by_annotation_tooltip = El color de anotación se configura desde el menú principal de colores
+label.show_alignment_only = Mostrar solo alineamiento
+label.hide_hidden_regions = Ocultar columnas / secuencias ocultas
\ No newline at end of file
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index e5a1733..d317722 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -23,7 +23,6 @@ package jalview.ext.jmol;
 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.PDBEntry;
@@ -510,16 +509,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   /**
    * @param files
-   * @param sr
    * @param viewPanel
    * @return
    */
   @Override
   protected StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
+          String[] files, AlignmentViewPanel viewPanel)
   {
     return JmolCommands.getColourBySequenceCommand(getSsm(), files,
-            getSequence(), sr, viewPanel);
+            this, viewPanel);
   }
 
   /**
diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 8fb0de6..c981165 100644
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -31,6 +31,7 @@ import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
 
 import java.awt.Color;
 import java.util.ArrayList;
@@ -55,6 +56,15 @@ public class JmolCommands
    */
   public static StructureMappingcommandSet[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
+          AAStructureBindingModel binding, AlignmentViewPanel viewPanel)
+  {
+    SequenceRenderer sr = binding.getSequenceRenderer(viewPanel);
+    SequenceI[][] sequence = binding.getSequence();
+    return getColourBySequenceCommand(ssm, files, sequence, sr, viewPanel);
+  }
+
+  public static StructureMappingcommandSet[] getColourBySequenceCommand(
+          StructureSelectionManager ssm, String[] files,
           SequenceI[][] sequence, SequenceRenderer sr,
           AlignmentViewPanel viewPanel)
   {
@@ -63,14 +73,14 @@ public class JmolCommands
     AlignViewportI viewport = viewPanel.getAlignViewport();
     HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
     AlignmentI al = viewport.getAlignment();
-    List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
+    List<StructureMappingcommandSet> cset = new ArrayList<>();
 
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
       StringBuffer command = new StringBuffer();
       StructureMappingcommandSet smc;
-      ArrayList<String> str = new ArrayList<String>();
+      ArrayList<String> str = new ArrayList<>();
 
       if (mapping == null || mapping.length < 1)
       {
diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index ec94e7d..dc53c2b 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -32,6 +32,7 @@ import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.ColorUtils;
 import jalview.util.Comparison;
 
@@ -68,11 +69,24 @@ public class ChimeraCommands
    */
   public static StructureMappingcommandSet[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
+          AAStructureBindingModel binding, AlignmentViewPanel viewPanel)
+  {
+    SequenceRenderer sr = binding.getSequenceRenderer(viewPanel);
+    SequenceI[][] sequence = binding.getSequence();
+    boolean hideHiddenRegions = binding.isShowAlignmentOnly()
+            && binding.isHideHiddenRegions();
+
+    return getColourBySequenceCommand(ssm, files, sequence, sr,
+            hideHiddenRegions, viewPanel);
+  }
+
+  static StructureMappingcommandSet[] getColourBySequenceCommand(
+          StructureSelectionManager ssm, String[] files,
           SequenceI[][] sequence, SequenceRenderer sr,
-          AlignmentViewPanel viewPanel)
+          boolean hideHiddenRegions, AlignmentViewPanel viewPanel)
   {
     Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
-            sequence, sr, viewPanel);
+            sequence, sr, hideHiddenRegions, viewPanel);
 
     List<String> colourCommands = buildColourCommands(colourMap);
 
@@ -175,20 +189,31 @@ public class ChimeraCommands
   }
 
   /**
-   * <pre>
-   * Build a data structure which records contiguous subsequences for each colour. 
+   * Build a data structure which records contiguous subsequences for each colour.
    * From this we can easily generate the Chimera command for colour by sequence.
+   * 
+   * <pre>
    * 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>
+   * 
+   * Ordering is by order of addition (for colours and positions), natural
+   * ordering (for models and chains)
+   * 
+   * @param ssm
+   * @param files
+   * @param sequence
+   * @param sr
+   * @param hideHiddenRegions
+   * @param viewPanel
+   * @return
    */
   protected static Map<Object, AtomSpecModel> buildColoursMap(
           StructureSelectionManager ssm, String[] files,
           SequenceI[][] sequence, SequenceRenderer sr,
-          AlignmentViewPanel viewPanel)
+          boolean hideHiddenRegions, AlignmentViewPanel viewPanel)
   {
     FeatureRenderer fr = viewPanel.getFeatureRenderer();
     FeatureColourFinder finder = new FeatureColourFinder(fr);
@@ -235,12 +260,18 @@ public class ChimeraCommands
               Color colour = sr.getResidueColour(seq, r, finder);
 
               /*
-               * hidden regions are shown gray
-               * todo: iterate over visible columns only
+               * hidden regions are shown gray or, optionally, ignored
                */
               if (!cs.isVisible(r))
               {
-                continue; // colour = Color.GRAY;
+                if (hideHiddenRegions)
+                {
+                  continue;
+                }
+                else
+                {
+                  colour = Color.GRAY;
+                }
               }
 
               final String chain = mapping[m].getChain();
diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 1731a05..fc6dd26 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -22,7 +22,6 @@ package jalview.ext.rbvi.chimera;
 
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
-import jalview.api.SequenceRenderer;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
@@ -667,16 +666,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   /**
    * @param files
-   * @param sr
    * @param viewPanel
    * @return
    */
   @Override
   protected StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
+          String[] files, AlignmentViewPanel viewPanel)
   {
     return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
-            getSequence(), sr, viewPanel);
+            this, viewPanel);
   }
 
   /**
@@ -1350,7 +1348,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
               continue;
             }
             Iterator<int[]> visible;
-            if (isShowAlignmentOnly())
+            if (isShowAlignmentOnly() && isHideHiddenRegions())
             {
               visible = alignment.getHiddenColumns()
                     .getVisContigsIterator(0, width, true);
diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index cc431ac..ec51943 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -711,12 +711,14 @@ public abstract class StructureViewerBase extends GStructureViewer
             });
     viewMenu.add(seqColourBy);
 
-    showAlignmentOnly = new JCheckBoxMenuItem("Visible alignment only");
+    showAlignmentOnly = new JCheckBoxMenuItem(
+            MessageManager.getString("label.show_alignment_only"));
     showAlignmentOnly.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
+        hideHiddenRegions.setEnabled(showAlignmentOnly.isSelected());
         getBinding().setShowAlignmentOnly(showAlignmentOnly.isSelected());
         getBinding().showStructures(getAlignmentPanel().getAlignViewport(),
                 true);
@@ -724,6 +726,21 @@ public abstract class StructureViewerBase extends GStructureViewer
     });
     viewMenu.add(showAlignmentOnly);
 
+    hideHiddenRegions = new JCheckBoxMenuItem(
+            MessageManager.getString("label.hide_hidden_regions"));
+    hideHiddenRegions.setEnabled(false);
+    hideHiddenRegions.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        getBinding().setHideHiddenRegions(hideHiddenRegions.isSelected());
+        getBinding().showStructures(getAlignmentPanel().getAlignViewport(),
+                false);
+      }
+    });
+    viewMenu.add(hideHiddenRegions);
+
     final ItemListener handler = new ItemListener()
     {
       @Override
diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 418e413..66cd8f2 100644
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -59,6 +59,8 @@ public abstract class GStructureViewer extends JInternalFrame
 
   protected JCheckBoxMenuItem showAlignmentOnly;
 
+  protected JCheckBoxMenuItem hideHiddenRegions;
+
   protected JMenuItem fitToWindow;
 
   protected JRadioButtonMenuItem seqColour;
diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 1fc59ed..ef4fed3 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -104,6 +104,8 @@ public abstract class AAStructureBindingModel
   // TODO make private once showStructures() deals with this
   protected List<String> chainsToShow;
 
+  private boolean hideHiddenRegions;
+
   /**
    * Data bean class to simplify parameterisation in superposeStructures
    */
@@ -785,7 +787,7 @@ public abstract class AAStructureBindingModel
   public abstract void setBackgroundColour(Color col);
 
   protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, AlignmentViewPanel avp);
+          String[] files, AlignmentViewPanel avp);
 
   /**
    * returns the current sequenceRenderer that should be used to colour the
@@ -829,10 +831,8 @@ public abstract class AAStructureBindingModel
     }
     String[] files = getStructureFiles();
 
-    SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
     StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
-            files, sr, alignmentv);
+            files, alignmentv);
     colourBySequence(colourBySequenceCommands);
   }
 
@@ -856,8 +856,8 @@ public abstract class AAStructureBindingModel
   }
 
   /**
-   * Answers true if only mapped visible residues in the alignment should be
-   * visible in the structure viewer, else false
+   * Answers true if only residues mapped to the alignment should be shown in the
+   * structure viewer, else false
    * 
    * @return
    */
@@ -867,6 +867,30 @@ public abstract class AAStructureBindingModel
   }
 
   /**
+   * Sets the flag for hiding regions of structure which are hidden in the
+   * alignment (only applies when the structure viewer is restricted to the
+   * alignment only)
+   * 
+   * @param b
+   */
+  public void setHideHiddenRegions(boolean b)
+  {
+    hideHiddenRegions = b;
+  }
+
+  /**
+   * Answers true if regions hidden in the alignment should also be hidden in the
+   * structure viewer, else false (only applies when the structure viewer is
+   * restricted to the alignment only)
+   * 
+   * @return
+   */
+  public boolean isHideHiddenRegions()
+  {
+    return hideHiddenRegions;
+  }
+
+  /**
    * Shows the structures in the viewer, without changing their colouring. This is
    * to support toggling of whether the whole structure is shown, or only residues
    * mapped to visible regions of the alignment.
diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
index 2c973ca..fbfe33c 100644
--- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
@@ -59,7 +59,7 @@ public class ChimeraCommandsTest
   public void testBuildColourCommands()
   {
 
-    Map<Object, AtomSpecModel> map = new LinkedHashMap<Object, AtomSpecModel>();
+    Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
     ChimeraCommands.addColourRange(map, Color.blue, 0, 2, 5, "A");
     ChimeraCommands.addColourRange(map, Color.blue, 0, 7, 7, "B");
     ChimeraCommands.addColourRange(map, Color.blue, 0, 9, 23, "A");
@@ -72,10 +72,11 @@ public class ChimeraCommandsTest
 
     // Colours should appear in the Chimera command in the order in which
     // they were added; within colour, by model, by chain, ranges in start order
+    // all prefixed with #808080 to colour hidden regions (if shown) gray
     String command = ChimeraCommands.buildColourCommands(map).get(0);
     assertEquals(
             command,
-            "color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B; color #ffff00 #1:3-5.A,8.A; color #ff0000 #0:3-9.A");
+            "color #808080; color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B; color #ffff00 #1:3-5.A,8.A; color #ff0000 #0:3-9.A");
   }
 
   @Test(groups = { "Functional" })
@@ -84,8 +85,8 @@ public class ChimeraCommandsTest
     /*
      * make a map of { featureType, {featureValue, {residue range specification } } }
      */
-    Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
-    Map<Object, AtomSpecModel> featureValues = new HashMap<Object, AtomSpecModel>();
+    Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
+    Map<Object, AtomSpecModel> featureValues = new HashMap<>();
     
     /*
      * start with just one feature/value...
@@ -189,7 +190,7 @@ public class ChimeraCommandsTest
     /*
      * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
      */
-    HashMap<Integer, int[]> map = new HashMap<Integer, int[]>();
+    HashMap<Integer, int[]> map = new HashMap<>();
     for (int pos = 1; pos <= seq1.getLength(); pos++)
     {
       map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
@@ -202,7 +203,8 @@ public class ChimeraCommandsTest
     ssm.addStructureMapping(sm2);
 
     StructureMappingcommandSet[] commands = ChimeraCommands
-            .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
+            .getColourBySequenceCommand(ssm, files, seqs, sr, false,
+                    af.alignPanel);
     assertEquals(1, commands.length);
     assertEquals(1, commands[0].commands.length);
     String theCommand = commands[0].commands[0];
diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java
index af02d5e..dde7d14 100644
--- a/test/jalview/structures/models/AAStructureBindingModelTest.java
+++ b/test/jalview/structures/models/AAStructureBindingModelTest.java
@@ -202,7 +202,7 @@ public class AAStructureBindingModelTest
       
       @Override
       protected StructureMappingcommandSet[] getColourBySequenceCommands(
-              String[] files, SequenceRenderer sr, AlignmentViewPanel avp)
+              String[] files, AlignmentViewPanel avp)
       {
         // TODO Auto-generated method stub
         return null;
@@ -329,7 +329,7 @@ public class AAStructureBindingModelTest
 
       @Override
       protected StructureMappingcommandSet[] getColourBySequenceCommands(
-              String[] files, SequenceRenderer sr, AlignmentViewPanel avp)
+              String[] files, AlignmentViewPanel avp)
       {
         return null;
       }