Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112
[jalview.git] / src / jalview / gui / AlignViewport.java
index 70eae9d..6024cf9 100644 (file)
@@ -22,7 +22,6 @@ package jalview.gui;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureColourI;
@@ -36,11 +35,11 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.renderer.ResidueShader;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
@@ -49,6 +48,7 @@ import jalview.schemes.UserColourScheme;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
+import jalview.util.ColorUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.params.AutoCalcSetting;
@@ -60,8 +60,8 @@ import java.awt.FontMetrics;
 import java.awt.Rectangle;
 import java.util.ArrayList;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
-import java.util.Vector;
 
 import javax.swing.JInternalFrame;
 
@@ -76,15 +76,13 @@ public class AlignViewport extends AlignmentViewport
 {
   Font font;
 
-  TreeModel currentTree = null;
-
   boolean cursorMode = false;
 
   boolean antiAlias = false;
 
-  private Rectangle explodedGeometry;
+  private Rectangle explodedGeometry = null;
 
-  String viewName;
+  private String viewName = null;
 
   /*
    * Flag set true on the view that should 'gather' multiple views of the same
@@ -211,7 +209,7 @@ public class AlignViewport extends AlignmentViewport
    */
   private void applyViewProperties()
   {
-    antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+    antiAlias = Cache.getDefault("ANTI_ALIAS", true);
 
     viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
     setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
@@ -259,14 +257,13 @@ public class AlignViewport extends AlignmentViewport
 
     setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
 
-    alignment
-            .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+               alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
 
     // We must set conservation and consensus before setting colour,
     // as Blosum and Clustal require this to be done
-    if (hconsensus == null && !isDataset)
+               if (hconsensus == null && !isDataset)
     {
-      if (!alignment.isNucleotide())
+                       if (!alignment.isNucleotide())
       {
         showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
         showQuality = Cache.getDefault("SHOW_QUALITY", true);
@@ -278,16 +275,19 @@ public class AlignViewport extends AlignmentViewport
       showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
       normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
               false);
+      // for now, use consensus options for Information till it gets its own
+      setShowHMMSequenceLogo(showSequenceLogo);
+      setNormaliseHMMSequenceLogo(normaliseSequenceLogo);
+      setShowInformationHistogram(showConsensusHistogram);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
       showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
 
       showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
     }
     initAutoAnnotation();
-    initInformation();
-
+    // initInformation();
 
-    String colourProperty = alignment.isNucleotide()
+               String colourProperty = alignment.isNucleotide()
             ? Preferences.DEFAULT_COLOUR_NUC
             : Preferences.DEFAULT_COLOUR_PROT;
     String schemeName = Cache.getProperty(colourProperty);
@@ -298,7 +298,7 @@ public class AlignViewport extends AlignmentViewport
               ResidueColourScheme.NONE);
     }
     ColourSchemeI colourScheme = ColourSchemeProperty
-            .getColourScheme(alignment, schemeName);
+            .getColourScheme(this, alignment, schemeName);
     residueShading = new ResidueShader(colourScheme);
 
     if (colourScheme instanceof UserColourScheme)
@@ -310,10 +310,11 @@ public class AlignViewport extends AlignmentViewport
 
     if (residueShading != null)
     {
-      residueShading.setConsensus(hconsensus);
+                       residueShading.setConsensus(hconsensus);
     }
+    setColourAppliesToAllGroups(true);
   }
-
+  
   boolean validCharWidth;
 
   /**
@@ -398,7 +399,7 @@ public class AlignViewport extends AlignmentViewport
     /*
      * replace mappings on our alignment
      */
-    if (alignment != null && align != null)
+               if (alignment != null && align != null)
     {
       alignment.setCodonFrames(align.getCodonFrames());
     }
@@ -451,38 +452,17 @@ public class AlignViewport extends AlignmentViewport
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param tree
-   *          DOCUMENT ME!
-   */
-  public void setCurrentTree(TreeModel tree)
-  {
-    currentTree = tree;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public TreeModel getCurrentTree()
-  {
-    return currentTree;
-  }
-
-  /**
-   * returns the visible column regions of the alignment
+   * Returns an iterator over the visible column regions of the alignment
    * 
    * @param selectedRegionOnly
    *          true to just return the contigs intersecting with the selected
    *          area
    * @return
    */
-  public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+  public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
   {
-    int[] viscontigs = null;
-    int start = 0, end = 0;
+    int start = 0;
+    int end = 0;
     if (selectedRegionOnly && selectionGroup != null)
     {
       start = selectionGroup.getStartRes();
@@ -492,8 +472,9 @@ public class AlignViewport extends AlignmentViewport
     {
       end = alignment.getWidth();
     }
-    viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end);
-    return viscontigs;
+
+    return (alignment.getHiddenColumns().getVisContigsIterator(start,
+            end, false));
   }
 
   /**
@@ -543,7 +524,7 @@ public class AlignViewport extends AlignmentViewport
   }
 
   public boolean followSelection = true;
-
+  
   /**
    * @return true if view selection should always follow the selections
    *         broadcast by other selection sources
@@ -608,75 +589,19 @@ public class AlignViewport extends AlignmentViewport
     return StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance);
   }
-
-  /**
-   * 
-   * @param pdbEntries
-   * @return an array of SequenceI arrays, one for each PDBEntry, listing which
-   *         sequences in the alignment hold a reference to it
-   */
-  public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
-  {
-    List<SequenceI[]> seqvectors = new ArrayList<>();
-    for (PDBEntry pdb : pdbEntries)
-    {
-      List<SequenceI> choosenSeqs = new ArrayList<>();
-      for (SequenceI sq : alignment.getSequences())
-      {
-        Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
-                .getAllPDBEntries();
-        if (pdbRefEntries == null)
-        {
-          continue;
-        }
-        for (PDBEntry pdbRefEntry : pdbRefEntries)
-        {
-          if (pdbRefEntry.getId().equals(pdb.getId()))
-          {
-            if (pdbRefEntry.getChainCode() != null
-                    && pdb.getChainCode() != null)
-            {
-              if (pdbRefEntry.getChainCode().equalsIgnoreCase(
-                      pdb.getChainCode()) && !choosenSeqs.contains(sq))
-              {
-                choosenSeqs.add(sq);
-                continue;
-              }
-            }
-            else
-            {
-              if (!choosenSeqs.contains(sq))
-              {
-                choosenSeqs.add(sq);
-                continue;
-              }
-            }
-
-          }
-        }
-      }
-      seqvectors
-              .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
-    }
-    return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
-  }
-
+  
   @Override
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
   }
 
-
-  public void setNormaliseSequenceLogo(boolean state)
+  @Override
+public void setNormaliseSequenceLogo(boolean state)
   {
     normaliseSequenceLogo = state;
   }
 
-  public void setNormaliseHMMSequenceLogo(boolean state)
-  {
-    normaliseHMMSequenceLogo = state;
-  }
 
   /**
    * 
@@ -687,7 +612,7 @@ public class AlignViewport extends AlignmentViewport
   {
     return validCharWidth;
   }
-
+  
   private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
 
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
@@ -794,16 +719,20 @@ public class AlignViewport extends AlignmentViewport
     {
       if (AlignmentUtils.isMappable(toAdd, getAlignment()))
       {
-        if (openLinkedAlignment(toAdd, title))
-        {
-          return;
-        }
+        openLinkedAlignment(toAdd, title);
+        return;
       }
     }
+    addDataToAlignment(toAdd);
+  }
 
-    /*
-     * No mappings, or offer declined - add sequences to this alignment
-     */
+  /**
+   * adds sequences to this alignment
+   * 
+   * @param toAdd
+   */
+  void addDataToAlignment(AlignmentI toAdd)
+  {
     // TODO: JAL-407 regardless of above - identical sequences (based on ID and
     // provenance) should share the same dataset sequence
 
@@ -825,7 +754,7 @@ public class AlignViewport extends AlignmentViewport
       }
     }
 
-    ranges.setEndSeq(getAlignment().getHeight());
+    ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
     firePropertyChange("alignment", null, getAlignment().getSequences());
   }
 
@@ -838,30 +767,58 @@ public class AlignViewport extends AlignmentViewport
    * @param al
    * @param title
    */
-  protected boolean openLinkedAlignment(AlignmentI al, String title)
+  protected void openLinkedAlignment(AlignmentI al, String title)
   {
     String[] options = new String[] { MessageManager.getString("action.no"),
         MessageManager.getString("label.split_window"),
         MessageManager.getString("label.new_window"), };
     final String question = JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.open_split_window?"));
-    int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
+    final AlignViewport us = this;
+    
+    /*
+     * options No, Split Window, New Window correspond to
+     * dialog responses 0, 1, 2 (even though JOptionPane shows them
+     * in reverse order)
+     */
+    JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
+            .setResponseHandler(0, new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                  addDataToAlignment(al);
+              }
+            }).setResponseHandler(1, new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                us.openLinkedAlignmentAs(al, title, true);
+              }
+            }).setResponseHandler(2, new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                us.openLinkedAlignmentAs(al, title, false);
+              }
+            });
+       dialog.showDialog(question,
             MessageManager.getString("label.open_split_window"),
             JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
             options, options[0]);
+  }
 
-    if (response != 1 && response != 2)
+  protected void openLinkedAlignmentAs(AlignmentI al, String title,
+          boolean newWindowOrSplitPane)
     {
-      return false;
-    }
-    final boolean openSplitPane = (response == 1);
-    final boolean openInNewWindow = (response == 2);
-
     /*
      * Identify protein and dna alignments. Make a copy of this one if opening
      * in a new split pane.
      */
-    AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
+    AlignmentI thisAlignment = newWindowOrSplitPane
+            ? new Alignment(getAlignment())
             : getAlignment();
     AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
     final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
@@ -882,7 +839,7 @@ public class AlignViewport extends AlignmentViewport
     AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
             AlignFrame.DEFAULT_HEIGHT);
     newAlignFrame.setTitle(title);
-    newAlignFrame.statusBar.setText(MessageManager
+    newAlignFrame.setStatus(MessageManager
             .formatMessage("label.successfully_loaded_file", new Object[]
             { title }));
 
@@ -893,7 +850,7 @@ public class AlignViewport extends AlignmentViewport
     // alignFrame.setFileName(file, format);
     // }
 
-    if (openInNewWindow)
+    if (!newWindowOrSplitPane)
     {
       Desktop.addInternalFrame(newAlignFrame, title,
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
@@ -907,13 +864,11 @@ public class AlignViewport extends AlignmentViewport
     {
     }
 
-    if (openSplitPane)
+    if (newWindowOrSplitPane)
     {
       al.alignAs(thisAlignment);
       protein = openSplitFrame(newAlignFrame, thisAlignment);
     }
-
-    return true;
   }
 
   /**
@@ -975,10 +930,9 @@ public class AlignViewport extends AlignmentViewport
     if (ap != null)
     {
       // modify GUI elements to reflect geometry change
-      Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
-              .getPreferredSize();
+      Dimension idw = ap.getIdPanel().getIdCanvas().getPreferredSize();
       idw.width = i;
-      getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
+      ap.getIdPanel().getIdCanvas().setPreferredSize(idw);
     }
   }
 
@@ -1067,19 +1021,60 @@ public class AlignViewport extends AlignmentViewport
   @Override
   public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
   {
+    transferFeaturesStyles(featureSettings, false);
+  }
+
+  /**
+   * Applies the supplied feature settings descriptor to currently known features.
+   * This supports an 'initial configuration' of feature colouring based on a
+   * preset or user favourite. This may then be modified in the usual way using
+   * the Feature Settings dialogue.
+   * 
+   * @param featureSettings
+   */
+  @Override
+  public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
+  {
+    transferFeaturesStyles(featureSettings, true);
+  }
+
+  /**
+   * when mergeOnly is set, then group and feature visibility or feature colours
+   * are not modified for features and groups already known to the feature
+   * renderer. Feature ordering is always adjusted, and transparency is always set
+   * regardless.
+   * 
+   * @param featureSettings
+   * @param mergeOnly
+   */
+  private void transferFeaturesStyles(FeatureSettingsModelI featureSettings,
+          boolean mergeOnly)
+  {
     if (featureSettings == null)
     {
       return;
     }
-
+    
     FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
             .getFeatureRenderer();
+    List<String> origRenderOrder = new ArrayList(),
+            origGroups = new ArrayList();
+    // preserve original render order - allows differentiation between user configured colours and autogenerated ones
+    origRenderOrder.addAll(fr.getRenderOrder());
+    origGroups.addAll(fr.getFeatureGroups());
+
     fr.findAllFeatures(true);
     List<String> renderOrder = fr.getRenderOrder();
     FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
-    displayed.clear();
+    if (!mergeOnly)
+    {
+      // only clear displayed features if we are mergeing
+      displayed.clear();
+    }
     // TODO this clears displayed.featuresRegistered - do we care?
-
+    //
+    // JAL-3330 - JBP - yes we do - calling applyFeatureStyle to a view where
+    // feature visibility has already been configured is not very friendly
     /*
      * set feature colour if specified by feature settings
      * set visibility of all features
@@ -1088,13 +1083,32 @@ public class AlignViewport extends AlignmentViewport
     {
       FeatureColourI preferredColour = featureSettings
               .getFeatureColour(type);
-      if (preferredColour != null)
-      {
-        fr.setColour(type, preferredColour);
-      }
-      if (featureSettings.isFeatureDisplayed(type))
+      FeatureMatcherSetI preferredFilters = featureSettings
+              .getFeatureFilters(type);
+
+      FeatureColourI origColour = fr.getFeatureStyle(type);
+      if (!mergeOnly || (!origRenderOrder.contains(type)
+              || origColour == null
+              || (!origColour.isGraduatedColour()
+                      && origColour.getColour() != null
+                      && origColour.getColour().equals(
+                              ColorUtils.createColourFromName(type)))))
       {
-        displayed.setVisible(type);
+        // if we are merging, only update if there wasn't already a colour defined for
+        // this type
+        if (preferredColour != null)
+        {
+          fr.setColour(type, preferredColour);
+        }
+        if (preferredFilters != null
+                && (!mergeOnly || fr.getFeatureFilter(type) != null))
+        {
+          fr.setFeatureFilter(type, preferredFilters);
+        }
+        if (featureSettings.isFeatureDisplayed(type))
+        {
+          displayed.setVisible(type);
+        }
       }
     }
 
@@ -1103,7 +1117,12 @@ public class AlignViewport extends AlignmentViewport
      */
     for (String group : fr.getFeatureGroups())
     {
-      fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
+      if (!mergeOnly || !origGroups.contains(group))
+      {
+        // when merging, display groups only if the aren't already marked as not visible
+        fr.setGroupVisibility(group,
+                featureSettings.isGroupDisplayed(group));
+      }
     }
 
     /*
@@ -1120,12 +1139,13 @@ public class AlignViewport extends AlignmentViewport
     fr.setTransparency(featureSettings.getTransparency());
   }
 
-  @Override
-  public boolean isNormaliseHMMSequenceLogo()
+  public String getViewName()
   {
-    return normaliseHMMSequenceLogo;
+    return viewName;
   }
 
-
-
+  public void setViewName(String viewName)
+  {
+    this.viewName = viewName;
+  }
 }