X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=2005b91757de11968e32e4cff50d0280d8f63a5f;hb=refs%2Fheads%2Ffeatures%2Fhmmer_statistics;hp=5944b806f65f9ce098d6c52a9feec9c0e6204977;hpb=9b3219d225131af5a165553f206ebf8da304ee23;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 5944b80..2005b91 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -18,31 +18,16 @@
  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
 package jalview.gui;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureSettingsModelI;
+import jalview.api.FeaturesDisplayedI;
 import jalview.api.ViewStyleI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
@@ -50,14 +35,18 @@ import jalview.datamodel.AlignedCodonFrame;
 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.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShader;
+import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.UserColourScheme;
-import jalview.structure.CommandListener;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
@@ -68,15 +57,14 @@ import jalview.ws.params.AutoCalcSetting;
 import java.awt.Container;
 import java.awt.Dimension;
 import java.awt.Font;
+import java.awt.FontMetrics;
 import java.awt.Rectangle;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
-import java.util.Set;
 import java.util.Vector;
 
 import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
 
 /**
  * DOCUMENT ME!
@@ -85,11 +73,11 @@ import javax.swing.JOptionPane;
  * @version $Revision: 1.141 $
  */
 public class AlignViewport extends AlignmentViewport implements
-        SelectionSource, CommandListener
+        SelectionSource
 {
   Font font;
 
-  NJTree currentTree = null;
+  TreeModel currentTree = null;
 
   boolean cursorMode = false;
 
@@ -118,7 +106,7 @@ public class AlignViewport extends AlignmentViewport implements
    */
   public AlignViewport(AlignmentI al)
   {
-    setAlignment(al);
+    super(al);
     init();
   }
 
@@ -136,6 +124,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   public AlignViewport(AlignmentI al, String seqsetid, String viewid)
   {
+    super(al);
     sequenceSetID = seqsetid;
     viewId = viewid;
     // TODO remove these once 2.4.VAMSAS release finished
@@ -148,8 +137,8 @@ public class AlignViewport extends AlignmentViewport implements
     {
       Cache.log.debug("Setting viewport's view id : " + viewId);
     }
-    setAlignment(al);
     init();
+
   }
 
   /**
@@ -160,12 +149,12 @@ public class AlignViewport extends AlignmentViewport implements
    * @param hiddenColumns
    *          ColumnSelection
    */
-  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
+  public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)
   {
-    setAlignment(al);
+    super(al);
     if (hiddenColumns != null)
     {
-      colSel = hiddenColumns;
+      al.setHiddenColumns(hiddenColumns);
     }
     init();
   }
@@ -178,7 +167,7 @@ public class AlignViewport extends AlignmentViewport implements
    * @param seqsetid
    *          (may be null)
    */
-  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+  public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
           String seqsetid)
   {
     this(al, hiddenColumns, seqsetid, null);
@@ -194,9 +183,10 @@ public class AlignViewport extends AlignmentViewport implements
    * @param viewid
    *          (may be null)
    */
-  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+  public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
           String seqsetid, String viewid)
   {
+    super(al);
     sequenceSetID = seqsetid;
     viewId = viewid;
     // TODO remove these once 2.4.VAMSAS release finished
@@ -209,10 +199,10 @@ public class AlignViewport extends AlignmentViewport implements
     {
       Cache.log.debug("Setting viewport's view id : " + viewId);
     }
-    setAlignment(al);
+
     if (hiddenColumns != null)
     {
-      colSel = hiddenColumns;
+      al.setHiddenColumns(hiddenColumns);
     }
     init();
   }
@@ -251,10 +241,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   void init()
   {
-    this.startRes = 0;
-    this.endRes = alignment.getWidth() - 1;
-    this.startSeq = 0;
-    this.endSeq = alignment.getHeight() - 1;
     applyViewProperties();
 
     String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
@@ -295,32 +281,33 @@ public class AlignViewport extends AlignmentViewport implements
               false);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
       showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+
+      showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
     }
     initAutoAnnotation();
     String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
             : Preferences.DEFAULT_COLOUR_PROT;
-    String propertyValue = Cache.getProperty(colourProperty);
-    if (propertyValue == null)
+    String schemeName = Cache.getProperty(colourProperty);
+    if (schemeName == null)
     {
-      // fall back on this property for backwards compatibility
-      propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR);
+      // only DEFAULT_COLOUR available in Jalview before 2.9
+      schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
+              ResidueColourScheme.NONE);
     }
-    if (propertyValue != null)
-    {
-      globalColourScheme = ColourSchemeProperty.getColour(alignment,
-              propertyValue);
+    ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
+            alignment, schemeName);
+    residueShading = new ResidueShader(colourScheme);
 
-      if (globalColourScheme instanceof UserColourScheme)
-      {
-        globalColourScheme = UserDefinedColours.loadDefaultColours();
-        ((UserColourScheme) globalColourScheme).setThreshold(0,
-                isIgnoreGapsConsensus());
-      }
+    if (colourScheme instanceof UserColourScheme)
+    {
+      residueShading = new ResidueShader(
+              UserDefinedColours.loadDefaultColours());
+      residueShading.setThreshold(0, isIgnoreGapsConsensus());
+    }
 
-      if (globalColourScheme != null)
-      {
-        globalColourScheme.setConsensus(hconsensus);
-      }
+    if (residueShading != null)
+    {
+      residueShading.setConsensus(hconsensus);
     }
   }
 
@@ -365,23 +352,19 @@ public class AlignViewport extends AlignmentViewport implements
   boolean validCharWidth;
 
   /**
-   * update view settings with the given font. You may need to call
-   * alignPanel.fontChanged to update the layout geometry
-   * 
-   * @param setGrid
-   *          when true, charWidth/height is set according to font mentrics
+   * {@inheritDoc}
    */
+  @Override
   public void setFont(Font f, boolean setGrid)
   {
     font = f;
 
     Container c = new Container();
 
-    java.awt.FontMetrics fm = c.getFontMetrics(font);
-    int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
-            .getCharHeight();
     if (setGrid)
     {
+      FontMetrics fm = c.getFontMetrics(font);
+      int ww = fm.charWidth('M');
       setCharHeight(fm.getHeight());
       setCharWidth(ww);
     }
@@ -398,7 +381,6 @@ public class AlignViewport extends AlignmentViewport implements
     super.setViewStyle(settingsForView);
     setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
             viewStyle.getFontSize()), false);
-
   }
 
   /**
@@ -417,10 +399,11 @@ public class AlignViewport extends AlignmentViewport implements
    * @param align
    *          DOCUMENT ME!
    */
+  @Override
   public void setAlignment(AlignmentI align)
   {
     replaceMappings(align);
-    this.alignment = align;
+    super.setAlignment(align);
   }
 
   /**
@@ -461,7 +444,7 @@ public class AlignViewport extends AlignmentViewport implements
     AlignmentI al = getAlignment();
     if (al != null)
     {
-      Set<AlignedCodonFrame> mappings = al.getCodonFrames();
+      List<AlignedCodonFrame> mappings = al.getCodonFrames();
       if (mappings != null)
       {
         StructureSelectionManager ssm = StructureSelectionManager
@@ -505,21 +488,10 @@ public class AlignViewport extends AlignmentViewport implements
   /**
    * DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
-   */
-  @Override
-  public ColumnSelection getColumnSelection()
-  {
-    return colSel;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @param tree
    *          DOCUMENT ME!
    */
-  public void setCurrentTree(NJTree tree)
+  public void setCurrentTree(TreeModel tree)
   {
     currentTree = tree;
   }
@@ -529,7 +501,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return DOCUMENT ME!
    */
-  public NJTree getCurrentTree()
+  public TreeModel getCurrentTree()
   {
     return currentTree;
   }
@@ -555,7 +527,7 @@ public class AlignViewport extends AlignmentViewport implements
     {
       end = alignment.getWidth();
     }
-    viscontigs = colSel.getVisibleContigs(start, end);
+    viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end);
     return viscontigs;
   }
 
@@ -625,7 +597,9 @@ public class AlignViewport extends AlignmentViewport implements
     jalview.structure.StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance).sendSelection(
                     new SequenceGroup(getSelectionGroup()),
-                    new ColumnSelection(getColumnSelection()), this);
+                    new ColumnSelection(getColumnSelection()),
+                    new HiddenColumns(getAlignment().getHiddenColumns()),
+                    this);
   }
 
   /**
@@ -661,39 +635,6 @@ public class AlignViewport extends AlignmentViewport implements
   }
 
   /**
-   * synthesize a column selection if none exists so it covers the given
-   * selection group. if wholewidth is false, no column selection is made if the
-   * selection group covers the whole alignment width.
-   * 
-   * @param sg
-   * @param wholewidth
-   */
-  public void expandColSelection(SequenceGroup sg, boolean wholewidth)
-  {
-    int sgs, sge;
-    if (sg != null
-            && (sgs = sg.getStartRes()) >= 0
-            && sg.getStartRes() <= (sge = sg.getEndRes())
-            && (colSel == null || colSel.getSelected() == null || colSel
-                    .getSelected().size() == 0))
-    {
-      if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
-      {
-        // do nothing
-        return;
-      }
-      if (colSel == null)
-      {
-        colSel = new ColumnSelection();
-      }
-      for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
-      {
-        colSel.addElement(cspos);
-      }
-    }
-  }
-
-  /**
    * Returns the (Desktop) instance of the StructureSelectionManager
    */
   @Override
@@ -711,30 +652,47 @@ public class AlignViewport extends AlignmentViewport implements
    */
   public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
   {
-    List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+    List<SequenceI[]> seqvectors = new ArrayList<>();
     for (PDBEntry pdb : pdbEntries)
     {
-      List<SequenceI> seqs = new ArrayList<SequenceI>();
+      List<SequenceI> choosenSeqs = new ArrayList<>();
       for (SequenceI sq : alignment.getSequences())
       {
-        Vector<PDBEntry> pdbs = sq.getDatasetSequence().getAllPDBEntries();
-        if (pdbs == null)
+        Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
+                .getAllPDBEntries();
+        if (pdbRefEntries == null)
         {
           continue;
         }
-        for (PDBEntry p1 : pdbs)
+        for (PDBEntry pdbRefEntry : pdbRefEntries)
         {
-          if (p1.getId().equals(pdb.getId()))
+          if (pdbRefEntry.getId().equals(pdb.getId()))
           {
-            if (!seqs.contains(sq))
+            if (pdbRefEntry.getChainCode() != null
+                    && pdb.getChainCode() != null)
             {
-              seqs.add(sq);
-              continue;
+              if (pdbRefEntry.getChainCode().equalsIgnoreCase(
+                      pdb.getChainCode())
+                      && !choosenSeqs.contains(sq))
+              {
+                choosenSeqs.add(sq);
+                continue;
+              }
             }
+            else
+            {
+              if (!choosenSeqs.contains(sq))
+              {
+                choosenSeqs.add(sq);
+                continue;
+              }
+            }
+
           }
         }
       }
-      seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+      seqvectors
+              .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
     }
     return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
   }
@@ -750,6 +708,11 @@ public class AlignViewport extends AlignmentViewport implements
     normaliseSequenceLogo = state;
   }
 
+  public void setNormaliseHMMSequenceLogo(boolean state)
+  {
+    normaliseHMMSequenceLogo = state;
+  }
+
   /**
    * 
    * @return true if alignment characters should be displayed
@@ -760,7 +723,7 @@ public class AlignViewport extends AlignmentViewport implements
     return validCharWidth;
   }
 
-  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
 
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
   {
@@ -855,7 +818,7 @@ public class AlignViewport extends AlignmentViewport implements
      * Check if any added sequence could be the object of a mapping or
      * cross-reference; if so, make the mapping explicit 
      */
-    realiseMappings(getAlignment(), toAdd);
+    getAlignment().realiseMappings(toAdd.getSequences());
 
     /*
      * If any cDNA/protein mappings exist or can be made between the alignments, 
@@ -863,17 +826,6 @@ public class AlignViewport extends AlignmentViewport implements
      */
     if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
     {
-      // if (toAdd.getDataset() == null)
-      // {
-      // // need to create ds seqs
-      // for (SequenceI sq : toAdd.getSequences())
-      // {
-      // if (sq.getDatasetSequence() == null)
-      // {
-      // sq.createDatasetSequence();
-      // }
-      // }
-      // }
       if (AlignmentUtils.isMappable(toAdd, getAlignment()))
       {
         if (openLinkedAlignment(toAdd, title))
@@ -889,61 +841,26 @@ public class AlignViewport extends AlignmentViewport implements
     // TODO: JAL-407 regardless of above - identical sequences (based on ID and
     // provenance) should share the same dataset sequence
 
+    AlignmentI al = getAlignment();
+    String gap = String.valueOf(al.getGapCharacter());
     for (int i = 0; i < toAdd.getHeight(); i++)
     {
-      getAlignment().addSequence(toAdd.getSequenceAt(i));
-    }
-
-    setEndSeq(getAlignment().getHeight());
-    firePropertyChange("alignment", null, getAlignment().getSequences());
-  }
-
-  /**
-   * Check if any added sequence could be the object of a mapping or
-   * cross-reference; if so, make the mapping explicit. Returns the count of
-   * mappings updated.
-   * 
-   * @param al
-   * @param toAdd
-   */
-  protected int realiseMappings(AlignmentI al, AlignmentI toAdd)
-  {
-    // TODO this is proof of concept
-    // we might want to give the user some choice here
-    int count = 0;
-    for (SequenceI seq : toAdd.getSequences())
-    {
-      count += realiseMappingsTo(al, seq);
-    }
-    return count;
-  }
-
-  /**
-   * If the alignment holds any mappings to a dummy (placeholder) sequence that
-   * matches the given sequence, then update the mapping to point to the
-   * sequence. Returns the number of mappings updated.
-   * 
-   * @param al
-   * @param seq
-   * @return
-   */
-  protected int realiseMappingsTo(AlignmentI al, SequenceI seq)
-  {
-    int count = 0;
-    Set<AlignedCodonFrame> mappings = al.getDataset().getCodonFrames();
-    // TODO are mappings on alignment or alignment dataset?!?
-    for (AlignedCodonFrame mapping : mappings)
-    {
+      SequenceI seq = toAdd.getSequenceAt(i);
       /*
-       * TODO could just go straight to realiseWith() here unless we want
-       * to give the user some choice before going ahead
+       * experimental!
+       * - 'align' any mapped sequences as per existing 
+       *    e.g. cdna to genome, domain hit to protein sequence
+       * very experimental! (need a separate menu option for this)
+       * - only add mapped sequences ('select targets from a dataset')
        */
-      if (mapping.isRealisableWith(seq))
+      if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/)
       {
-        count += mapping.realiseWith(seq);
+        al.addSequence(seq);
       }
     }
-    return count;
+
+    ranges.setEndSeq(getAlignment().getHeight());
+    firePropertyChange("alignment", null, getAlignment().getSequences());
   }
 
   /**
@@ -963,9 +880,9 @@ public class AlignViewport extends AlignmentViewport implements
         MessageManager.getString("label.new_window"), };
     final String question = JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.open_split_window?"));
-    int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
+    int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
             MessageManager.getString("label.open_split_window"),
-            JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
+            JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
             options, options[0]);
 
     if (response != 1 && response != 2)
@@ -1005,7 +922,7 @@ public class AlignViewport extends AlignmentViewport implements
 
     // TODO if we want this (e.g. to enable reload of the alignment from file),
     // we will need to add parameters to the stack.
-    // if (!protocol.equals(AppletFormatAdapter.PASTE))
+    // if (!protocol.equals(DataSourceType.PASTE))
     // {
     // alignFrame.setFileName(file, format);
     // }
@@ -1130,15 +1047,16 @@ public class AlignViewport extends AlignmentViewport implements
      * there is no complement, or it is not following highlights, or no mapping
      * is found, the result will be empty.
      */
-    SearchResults sr = new SearchResults();
+    SearchResultsI sr = new SearchResults();
     int verticalOffset = findComplementScrollTarget(sr);
     if (!sr.isEmpty())
     {
       // TODO would like next line without cast but needs more refactoring...
       final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
               .getAlignPanel();
-      complementPanel.setDontScrollComplement(true);
+      complementPanel.setToScrollComplementPanel(false);
       complementPanel.scrollToCentre(sr, verticalOffset);
+      complementPanel.setToScrollComplementPanel(true);
     }
   }
 
@@ -1172,4 +1090,75 @@ public class AlignViewport extends AlignmentViewport implements
     return true;
   }
 
+  /**
+   * 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 applyFeaturesStyle(FeatureSettingsModelI featureSettings)
+  {
+    if (featureSettings == null)
+    {
+      return;
+    }
+
+    FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
+            .getFeatureRenderer();
+    fr.findAllFeatures(true);
+    List<String> renderOrder = fr.getRenderOrder();
+    FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
+    displayed.clear();
+    // TODO this clears displayed.featuresRegistered - do we care?
+
+    /*
+     * set feature colour if specified by feature settings
+     * set visibility of all features
+     */
+    for (String type : renderOrder)
+    {
+      FeatureColourI preferredColour = featureSettings
+              .getFeatureColour(type);
+      if (preferredColour != null)
+      {
+        fr.setColour(type, preferredColour);
+      }
+      if (featureSettings.isFeatureDisplayed(type))
+      {
+        displayed.setVisible(type);
+      }
+    }
+
+    /*
+     * set visibility of feature groups
+     */
+    for (String group : fr.getFeatureGroups())
+    {
+      fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
+    }
+
+    /*
+     * order the features
+     */
+    if (featureSettings.optimiseOrder())
+    {
+      // TODO not supported (yet?)
+    }
+    else
+    {
+      fr.orderFeatures(featureSettings);
+    }
+    fr.setTransparency(featureSettings.getTransparency());
+  }
+
+  @Override
+  public boolean isNormaliseHMMSequenceLogo()
+  {
+    // TODO Auto-generated method stub
+    return normaliseHMMSequenceLogo;
+  }
+
 }