X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=e9205f638e3ca3e5761ce60ae9e96ff9dae571ee;hb=a14b9e1a4dd98235f72acfbcffa71554a4fceaeb;hp=16e8cddef26dd2df9c8c835ba7d8aac0c74a3c0d;hpb=670c6ccb4d070850b8ba3af2a99f600459a61bbe;p=jalview.git

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 16e8cdd..e9205f6 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -1,47 +1,101 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.controller;
 
-import java.awt.Color;
-
+import jalview.analysis.AlignmentSorter;
+import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.commands.OrderCommand;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FeaturesFile;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.List;
 
 public class AlignViewController implements AlignViewControllerI
 {
-  AlignViewportI viewport=null;
-  AlignmentViewPanel alignPanel=null;
-  @Override
-  protected void finalize() throws Throwable {
-    viewport = null;
-    alignPanel = null;
-  };
-  
-  public AlignViewController(AlignViewportI viewport,
-          AlignmentViewPanel alignPanel)
+  AlignViewportI viewport = null;
+
+  AlignmentViewPanel alignPanel = null;
+
+  /**
+   * the GUI container that is handling interactions with the user
+   */
+  private AlignViewControllerGuiI avcg;
+
+  public AlignViewController(AlignViewControllerGuiI alignFrame,
+          AlignViewportI vp, AlignmentViewPanel ap)
   {
-    this.viewport=viewport;
-    this.alignPanel = alignPanel;
+    this.avcg = alignFrame;
+    this.viewport = vp;
+    this.alignPanel = ap;
   }
+
   @Override
-  public void setViewportAndAlignmentPanel(AlignViewportI viewport,AlignmentViewPanel alignPanel)
+  public void setViewportAndAlignmentPanel(AlignViewportI vp,
+          AlignmentViewPanel ap)
   {
-    this.alignPanel = alignPanel;
-    this.viewport = viewport;
-    
+    this.alignPanel = ap;
+    this.viewport = vp;
   }
+
   @Override
   public boolean makeGroupsFromSelection()
   {
-
-    if (viewport.getSelectionGroup() != null)
+    SequenceGroup sg = viewport.getSelectionGroup();
+    ColumnSelection cs = viewport.getColumnSelection();
+    SequenceGroup[] gps = null;
+    if (sg != null && (cs == null || cs.isEmpty()))
     {
-      SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
+      gps = jalview.analysis.Grouping.makeGroupsFrom(
               viewport.getSequenceSelection(),
-              viewport.getAlignmentView(true).getSequenceStrings(
-                      viewport.getGapCharacter()), viewport.getAlignment()
-                      .getGroups());
+              viewport.getAlignmentView(true)
+                      .getSequenceStrings(viewport.getGapCharacter()),
+              viewport.getAlignment().getGroups());
+    }
+    else
+    {
+      if (cs != null)
+      {
+        gps = jalview.analysis.Grouping.makeGroupsFromCols(
+                (sg == null) ? viewport.getAlignment().getSequencesArray()
+                        : sg.getSequences().toArray(new SequenceI[0]),
+                cs, viewport.getAlignment().getGroups());
+      }
+    }
+    if (gps != null)
+    {
       viewport.getAlignment().deleteAllGroups();
       viewport.clearSequenceColours();
       viewport.setSelectionGroup(null);
@@ -55,46 +109,442 @@ public class AlignViewController implements AlignViewControllerI
                 (int) (Math.random() * 255), (int) (Math.random() * 255));
         col = col.brighter();
         for (SequenceI sq : gps[g].getSequences(null))
+        {
           viewport.setSequenceColour(sq, col);
+        }
       }
       return true;
     }
     return false;
-}
+  }
+
   @Override
   public boolean createGroup()
   {
 
     SequenceGroup sg = viewport.getSelectionGroup();
-    if (sg!=null)
+    if (sg != null)
     {
-        viewport.getAlignment().addGroup(sg);
-        return true;
-      } 
+      viewport.getAlignment().addGroup(sg);
+      return true;
+    }
     return false;
   }
+
   @Override
   public boolean unGroup()
   {
     SequenceGroup sg = viewport.getSelectionGroup();
-    if (sg!=null)
+    if (sg != null)
     {
-        viewport.getAlignment().deleteGroup(sg);
-        return true;
+      viewport.getAlignment().deleteGroup(sg);
+      return true;
     }
     return false;
   }
+
   @Override
   public boolean deleteGroups()
   {
-    if (viewport.getAlignment().getGroups()!=null && viewport.getAlignment().getGroups().size()>0)
+    if (viewport.getAlignment().getGroups() != null
+            && viewport.getAlignment().getGroups().size() > 0)
     {
-    viewport.getAlignment().deleteAllGroups();
-    viewport.clearSequenceColours();
-    viewport.setSelectionGroup(null);
-    return true;
+      viewport.getAlignment().deleteAllGroups();
+      viewport.clearSequenceColours();
+      viewport.setSelectionGroup(null);
+      return true;
     }
     return false;
   }
-    
+
+  @Override
+  public boolean markColumnsContainingFeatures(boolean invert,
+          boolean extendCurrent, boolean toggle, String featureType)
+  {
+    // JBPNote this routine could also mark rows, not just columns.
+    // need a decent query structure to allow all types of feature searches
+    BitSet bs = new BitSet();
+    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
+            || extendCurrent) ? viewport.getAlignment()
+                    : viewport.getSelectionGroup();
+
+    int nseq = findColumnsWithFeature(featureType, sqcol, bs);
+
+    ColumnSelection cs = viewport.getColumnSelection();
+    if (cs == null)
+    {
+      cs = new ColumnSelection();
+    }
+
+    if (bs.cardinality() > 0 || invert)
+    {
+      boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+              sqcol.getEndRes(), invert, extendCurrent, toggle);
+      if (changed)
+      {
+        viewport.setColumnSelection(cs);
+        alignPanel.paintAlignment(false, false);
+        int columnCount = invert
+                ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+                        - bs.cardinality()
+                : bs.cardinality();
+        avcg.setStatus(MessageManager.formatMessage(
+                "label.view_controller_toggled_marked", new String[]
+                { toggle ? MessageManager.getString("label.toggled")
+                        : MessageManager.getString("label.marked"),
+                    String.valueOf(columnCount),
+                    invert ? MessageManager
+                            .getString("label.not_containing")
+                            : MessageManager.getString("label.containing"),
+                    featureType, Integer.valueOf(nseq).toString() }));
+        return true;
+      }
+    }
+    else
+    {
+      avcg.setStatus(MessageManager
+              .formatMessage("label.no_feature_of_type_found", new String[]
+              { featureType }));
+      if (!extendCurrent)
+      {
+        cs.clear();
+        alignPanel.paintAlignment(false, false);
+      }
+    }
+    return false;
   }
+
+  /**
+   * Sets a bit in the BitSet for each column (base 0) in the sequence
+   * collection which includes a visible feature of the specified feature type.
+   * Returns the number of sequences which have the feature visible in the
+   * selected range.
+   * 
+   * @param featureType
+   * @param sqcol
+   * @param bs
+   * @return
+   */
+  int findColumnsWithFeature(String featureType,
+          SequenceCollectionI sqcol, BitSet bs)
+  {
+    FeatureRenderer fr = alignPanel == null ? null : alignPanel
+            .getFeatureRenderer();
+
+    final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
+    final int endColumn = sqcol.getEndRes() + 1;
+    List<SequenceI> seqs = sqcol.getSequences();
+    int nseq = 0;
+    for (SequenceI sq : seqs)
+    {
+      if (sq != null)
+      {
+        // int ist = sq.findPosition(sqcol.getStartRes());
+        List<SequenceFeature> sfs = sq.findFeatures(startColumn,
+                endColumn, featureType);
+
+        boolean found = false;
+        for (SequenceFeature sf : sfs)
+        {
+          if (fr.getColour(sf) == null)
+          {
+            continue;
+          }
+          if (!found)
+          {
+            nseq++;
+          }
+          found = true;
+
+          int sfStartCol = sq.findIndex(sf.getBegin());
+          int sfEndCol = sq.findIndex(sf.getEnd());
+
+          if (sf.isContactFeature())
+          {
+            /*
+             * 'contact' feature - check for 'start' or 'end'
+             * position within the selected region
+             */
+            if (sfStartCol >= startColumn && sfStartCol <= endColumn)
+            {
+              bs.set(sfStartCol - 1);
+            }
+            if (sfEndCol >= startColumn && sfEndCol <= endColumn)
+            {
+              bs.set(sfEndCol - 1);
+            }
+            continue;
+          }
+
+          /*
+           * contiguous feature - select feature positions (if any) 
+           * within the selected region
+           */
+          if (sfStartCol < startColumn)
+          {
+            sfStartCol = startColumn;
+          }
+          // not sure what the point of this is
+          // if (sfStartCol < ist)
+          // {
+          // sfStartCol = ist;
+          // }
+          if (sfEndCol > endColumn)
+          {
+            sfEndCol = endColumn;
+          }
+          for (; sfStartCol <= sfEndCol; sfStartCol++)
+          {
+            bs.set(sfStartCol - 1); // convert to base 0
+          }
+        }
+      }
+    }
+    return nseq;
+  }
+
+  @Override
+  public void sortAlignmentByFeatureDensity(List<String> typ)
+  {
+    sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+  }
+
+  protected void sortBy(List<String> typ, String methodText,
+          final String method)
+  {
+    FeatureRenderer fr = alignPanel.getFeatureRenderer();
+    if (typ == null && fr != null)
+    {
+      typ = fr.getDisplayedFeatureTypes();
+    }
+    List<String> gps = null;
+    if (fr != null)
+    {
+      gps = fr.getDisplayedFeatureGroups();
+    }
+    AlignmentI al = viewport.getAlignment();
+
+    int start, stop;
+    SequenceGroup sg = viewport.getSelectionGroup();
+    if (sg != null)
+    {
+      start = sg.getStartRes();
+      stop = sg.getEndRes();
+    }
+    else
+    {
+      start = 0;
+      stop = al.getWidth();
+    }
+    SequenceI[] oldOrder = al.getSequencesArray();
+    AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
+    avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
+            viewport.getAlignment()));
+    alignPanel.paintAlignment(true, false);
+
+  }
+
+  @Override
+  public void sortAlignmentByFeatureScore(List<String> typ)
+  {
+    sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
+  }
+
+  @Override
+  public boolean parseFeaturesFile(String file, DataSourceType protocol,
+          boolean relaxedIdMatching)
+  {
+    boolean featuresAdded = false;
+    FeatureRenderer fr = alignPanel.getFeatureRenderer();
+    try
+    {
+      featuresAdded = new FeaturesFile(false, file, protocol).parse(
+              viewport.getAlignment().getDataset(), fr.getFeatureColours(),
+              fr.getFeatureFilters(), false, relaxedIdMatching);
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    if (featuresAdded)
+    {
+      avcg.refreshFeatureUI(true);
+      if (fr != null)
+      {
+        // update the min/max ranges where necessary
+        fr.findAllFeatures(true);
+      }
+      if (avcg.getFeatureSettingsUI() != null)
+      {
+        avcg.getFeatureSettingsUI().discoverAllFeatureData();
+      }
+      alignPanel.paintAlignment(true, true);
+    }
+
+    return featuresAdded;
+
+  }
+
+  /**
+   * 
+   * Add highlighted sequences to selected rows. Exclude highlighted sequences
+   * from selected rows. toggle inclusion or exclusion of highlighted sequences.
+   * or add/exclude/toggle for sequences not highlighted.
+   * 
+   * @param invert
+   *          - when true, sequences that are not highlighted are used to modify
+   *          selection
+   * @param extendCurrent
+   *          - normally true , the current selected group is modified.
+   * @param toggle
+   *          - if a select
+   * @return
+   */
+  public boolean selectHighlightedSequences(boolean invert,
+          boolean extendCurrent, boolean toggle)
+  {
+    List<SequenceI> results = alignPanel.getAlignViewport()
+            .getHighlightedSeqs();
+
+    SequenceGroup sq = (extendCurrent
+            && viewport.getSelectionGroup() != null)
+                    ? viewport.getSelectionGroup()
+                    : new SequenceGroup();
+
+    SearchResultsI searchResults = viewport.getSearchResults();
+    if (invert)
+    {
+      List<SequenceI> nothighlighted = new ArrayList();
+      for (SequenceI seq : alignPanel.getAlignViewport().getAlignment()
+              .getSequences())
+      {
+        if (!results.contains(seq) && (searchResults == null
+                || !searchResults.involvesSequence(seq)))
+        {
+          nothighlighted.add(seq);
+        }
+      }
+      results = nothighlighted;
+    }
+    else
+    {
+      // copy list and add in search results
+      results = new ArrayList(results);
+      if (searchResults != null)
+      {
+        for (SequenceI seq : alignPanel.getAlignViewport().getAlignment()
+                .getSequences())
+        {
+          if (searchResults.involvesSequence(seq))
+          {
+            results.add(seq);
+          }
+        }
+      }
+    }
+
+    if (results == null || results.size() == 0)
+    {
+      // do nothing if no selection exists
+      // unless toggle ??
+      return false;
+    }
+
+    boolean changed = false;
+
+    for (SequenceI seq : results)
+    {
+      int size = sq.getSize();
+      if (toggle)
+      {
+        sq.addOrRemove(seq, false);
+      }
+      else
+      {
+        sq.addSequence(seq, false);
+      }
+      changed |= size != sq.getSize();
+    }
+
+    if (sq.getSize() == 0)
+    {
+      viewport.setSelectionGroup(null);
+    }
+    else
+    {
+      if (sq != viewport.getSelectionGroup())
+    {
+      sq.setStartRes(0);
+      sq.setEndRes(viewport.getRanges().getAbsoluteAlignmentWidth());
+    }
+      viewport.setSelectionGroup(sq);
+    }
+
+    alignPanel.paintAlignment(false, false);
+
+    return changed;
+  }
+
+  @Override
+  public boolean markHighlightedColumns(boolean invert,
+          boolean extendCurrent, boolean toggle)
+  {
+    if (!viewport.hasSearchResults())
+    {
+      // do nothing if no selection exists
+      return false;
+    }
+    // JBPNote this routine could also mark rows, not just columns.
+    BitSet bs = new BitSet();
+    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
+            || extendCurrent) ? viewport.getAlignment()
+                    : viewport.getSelectionGroup();
+
+    // this could be a lambda... - the remains of the method is boilerplate,
+    // except for the different messages for reporting selection.
+    int nseq = viewport.getSearchResults().markColumns(sqcol, bs);
+
+    ColumnSelection cs = viewport.getColumnSelection();
+    if (cs == null)
+    {
+      cs = new ColumnSelection();
+    }
+
+    if (bs.cardinality() > 0 || invert)
+    {
+      boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+              sqcol.getEndRes(), invert, extendCurrent, toggle);
+      if (changed)
+      {
+        viewport.setColumnSelection(cs);
+        alignPanel.paintAlignment(false, false);
+        int columnCount = invert
+                ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+                        - bs.cardinality()
+                : bs.cardinality();
+        avcg.setStatus(MessageManager.formatMessage(
+                "label.view_controller_toggled_marked", new String[]
+                { toggle ? MessageManager.getString("label.toggled")
+                        : MessageManager.getString("label.marked"),
+                    String.valueOf(columnCount),
+                    invert ? MessageManager
+                            .getString("label.not_containing")
+                            : MessageManager.getString("label.containing"),
+                    "Highlight", Integer.valueOf(nseq).toString() }));
+        return true;
+      }
+    }
+    else
+    {
+      avcg.setStatus(MessageManager
+              .formatMessage("No highlighted regions marked"));
+      if (!extendCurrent)
+      {
+        cs.clear();
+        alignPanel.paintAlignment(false, false);
+      }
+    }
+    return false;
+  }
+
+}