X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=0bb2d038a817aa1c300c5669372300130ac5cc93;hb=0705acce562063909c4db16013b8b2a00001884b;hp=7b42a30e5f38e6c3196316be485deef3e2a1e6d8;hpb=95de746a08351b07696a0c455ef37d866c8104d2;p=jalview.git

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 7b42a30..0bb2d03 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -28,18 +28,17 @@ import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.commands.OrderCommand;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 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.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
 
 import java.awt.Color;
-import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.List;
 
@@ -54,58 +53,67 @@ public class AlignViewController implements AlignViewControllerI
    */
   private AlignViewControllerGuiI avcg;
 
-  @Override
-  protected void finalize() throws Throwable
-  {
-    viewport = null;
-    alignPanel = null;
-    avcg = null;
-  };
-
   public AlignViewController(AlignViewControllerGuiI alignFrame,
-          AlignViewportI viewport, AlignmentViewPanel alignPanel)
+          AlignViewportI vp, AlignmentViewPanel ap)
   {
     this.avcg = alignFrame;
-    this.viewport = viewport;
-    this.alignPanel = alignPanel;
+    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);
+      ColourSchemeI colours = viewport.getGlobalColourScheme();
       // set view properties for each group
       for (int g = 0; g < gps.length; g++)
       {
         // gps[g].setShowunconserved(viewport.getShowUnconserved());
         gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
         viewport.getAlignment().addGroup(gps[g]);
-        Color col = new Color((int) (Math.random() * 255),
-                (int) (Math.random() * 255), (int) (Math.random() * 255));
-        col = col.brighter();
-        for (SequenceI sq : gps[g].getSequences(null))
+        if (colours != null)
         {
-          viewport.setSequenceColour(sq, col);
+          gps[g].setColourScheme(colours.getInstance(viewport, gps[g]));
         }
+        Color col = new Color((int) (Math.random() * 255),
+                (int) (Math.random() * 255), (int) (Math.random() * 255));
+        gps[g].idColour = col;
+        viewport.setUpdateStructures(true);
+        viewport.addSequenceGroup(gps[g]);
       }
       return true;
     }
@@ -158,279 +166,183 @@ public class AlignViewController implements AlignViewControllerI
     // 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();
-    int alw, alStart;
-    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport
-            .getAlignment() : viewport.getSelectionGroup());
-    alStart = sqcol.getStartRes();
-    alw = sqcol.getEndRes() + 1;
-    List<SequenceI> seqs = sqcol.getSequences();
-    int nseq = 0;
-    for (SequenceI sq : seqs)
-    {
-      int tfeat = 0;
-      if (sq != null)
-      {
-        SequenceI dsq = sq.getDatasetSequence();
-        while (dsq.getDatasetSequence() != null)
-        {
-          dsq = dsq.getDatasetSequence();
-        }
-        ;
-        SequenceFeature[] sf = dsq.getSequenceFeatures();
-        if (sf != null)
-        {
-          int ist = sq.findIndex(sq.getStart());
-          int iend = sq.findIndex(sq.getEnd());
-          if (iend < alStart || ist > alw)
-          {
-            // sequence not in region
-            continue;
-          }
-          for (SequenceFeature sfpos : sf)
-          {
-            // future functionalty - featureType == null means mark columns
-            // containing all displayed features
-            if (sfpos != null && (featureType.equals(sfpos.getType())))
-            {
-              tfeat++;
-              // optimisation - could consider 'spos,apos' like cursor argument
-              // - findIndex wastes time by starting from first character and
-              // counting
-
-              int i = sq.findIndex(sfpos.getBegin());
-              int j = sq.findIndex(sfpos.getEnd());
-              if (j < alStart || i > alw)
-              {
-                // feature is outside selected region
-                continue;
-              }
-              if (i < alStart)
-              {
-                i = alStart;
-              }
-              if (i < ist)
-              {
-                i = ist;
-              }
-              if (j > alw)
-              {
-                j = alw;
-              }
-              for (; i <= j; i++)
-              {
-                bs.set(i - 1);
-              }
-            }
-          }
-        }
+    boolean searchSelection = viewport.getSelectionGroup() != null
+            && !extendCurrent;
+    SequenceCollectionI sqcol = searchSelection ? viewport
+            .getSelectionGroup() : viewport.getAlignment();
+
+    int nseq = findColumnsWithFeature(featureType, sqcol, bs);
 
-        if (tfeat > 0)
-        {
-          nseq++;
-        }
-      }
-    }
     ColumnSelection cs = viewport.getColumnSelection();
+    if (cs == null)
+    {
+      cs = new ColumnSelection();
+    }
+
     if (bs.cardinality() > 0 || invert)
     {
-      if (cs == null)
-      {
-        cs = new ColumnSelection();
-      }
-      else
+      boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+              sqcol.getEndRes(), invert, extendCurrent, toggle);
+      if (changed)
       {
-        if (!extendCurrent)
-        {
-          cs.clear();
-        }
+        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;
       }
-      if (invert)
-      {
-        // invert only in the currently selected sequence region
-        for (int i = bs.nextClearBit(alStart), ibs = bs.nextSetBit(alStart); i >= alStart
-                && i < (alw);)
-        {
-          if (ibs < 0 || i < ibs)
-          {
-            if (toggle && cs.contains(i))
-            {
-              cs.removeElement(i++);
-            }
-            else
-            {
-              cs.addElement(i++);
-            }
-          }
-          else
-          {
-            i = bs.nextClearBit(ibs);
-            ibs = bs.nextSetBit(i);
-          }
-        }
-      }
-      else
-      {
-        for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
-                .nextSetBit(i + 1))
-        {
-          if (toggle && cs.contains(i))
-          {
-            cs.removeElement(i);
-          }
-          else
-          {
-            cs.addElement(i);
-          }
-        }
-      }
-      viewport.setColumnSelection(cs);
-      alignPanel.paintAlignment(true);
-      avcg.setStatus(MessageManager.formatMessage("label.view_controller_toggled_marked",
-    		  new String[]{
-    	  			(toggle ? MessageManager.getString("label.toggled") : MessageManager.getString("label.marked")),
-    	  			(invert ? (Integer.valueOf((alw - alStart) - bs.cardinality()).toString()):(Integer.valueOf(bs.cardinality()).toString())),
-    	  			featureType, Integer.valueOf(nseq).toString()
-      		 	}));
-      return true;
     }
     else
     {
-      avcg.setStatus(MessageManager.formatMessage("label.no_feature_of_type_found", new String[]{featureType}));
-      if (!extendCurrent && cs != null)
+      String key = searchSelection ? "label.no_feature_found_selection"
+              : "label.no_feature_of_type_found";
+      avcg.setStatus(MessageManager.formatMessage(key,
+              new String[] { featureType }));
+      if (!extendCurrent)
       {
         cs.clear();
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(false, false);
       }
-      return false;
     }
+    return false;
   }
 
-  public static boolean filterAnnotations(Annotation[] annotations,
-          AnnotationFilterParameter filterParams, ColumnSelection cs)
+  /**
+   * 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)
   {
-    cs.revealAllHiddenColumns();
-    cs.clear();
-    int count = 0;
-    do
+    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 (annotations[count] != null)
+      if (sq != null)
       {
+        // int ist = sq.findPosition(sqcol.getStartRes());
+        List<SequenceFeature> sfs = sq.findFeatures(startColumn,
+                endColumn, featureType);
 
-        boolean itemMatched = false;
-
-        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
-                && annotations[count].value > filterParams
-                        .getThresholdValue())
-        {
-          itemMatched = true;
-        }
-        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
-                && annotations[count].value < filterParams
-                        .getThresholdValue())
+        boolean found = false;
+        for (SequenceFeature sf : sfs)
         {
-          itemMatched = true;
-        }
-
-        if (filterParams.isFilterAlphaHelix()
-                && annotations[count].secondaryStructure == 'H')
-        {
-          itemMatched = true;
-        }
+          if (fr.getColour(sf) == null)
+          {
+            continue;
+          }
+          if (!found)
+          {
+            nseq++;
+          }
+          found = true;
 
-        if (filterParams.isFilterBetaSheet()
-                && annotations[count].secondaryStructure == 'E')
-        {
-          itemMatched = true;
-        }
+          int sfStartCol = sq.findIndex(sf.getBegin());
+          int sfEndCol = sq.findIndex(sf.getEnd());
 
-        if (filterParams.isFilterTurn()
-                && annotations[count].secondaryStructure == 'S')
-        {
-          itemMatched = true;
-        }
-
-        String regexSearchString = filterParams.getRegexString();
-        if (regexSearchString != null
-                && !filterParams.getRegexSearchFields().isEmpty())
-        {
-          List<SearchableAnnotationField> fields = filterParams
-                  .getRegexSearchFields();
-          try
+          if (sf.isContactFeature())
           {
-            if (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
-                    && annotations[count].displayCharacter
-                            .matches(regexSearchString))
+            /*
+             * 'contact' feature - check for 'start' or 'end'
+             * position within the selected region
+             */
+            if (sfStartCol >= startColumn && sfStartCol <= endColumn)
             {
-              itemMatched = true;
+              bs.set(sfStartCol - 1);
             }
-          } catch (java.util.regex.PatternSyntaxException pse)
-          {
-            if (annotations[count].displayCharacter
-                    .equals(regexSearchString))
+            if (sfEndCol >= startColumn && sfEndCol <= endColumn)
             {
-              itemMatched = true;
+              bs.set(sfEndCol - 1);
             }
+            continue;
+          }
+
+          /*
+           * contiguous feature - select feature positions (if any) 
+           * within the selected region
+           */
+          if (sfStartCol < startColumn)
+          {
+            sfStartCol = startColumn;
           }
-          if (fields.contains(SearchableAnnotationField.DESCRIPTION)
-                  && annotations[count].description != null
-                  && annotations[count].description
-                          .matches(regexSearchString))
+          // not sure what the point of this is
+          // if (sfStartCol < ist)
+          // {
+          // sfStartCol = ist;
+          // }
+          if (sfEndCol > endColumn)
           {
-            itemMatched = true;
+            sfEndCol = endColumn;
+          }
+          for (; sfStartCol <= sfEndCol; sfStartCol++)
+          {
+            bs.set(sfStartCol - 1); // convert to base 0
           }
-        }
-
-        if (itemMatched)
-        {
-          cs.addElement(count);
         }
       }
-      count++;
-    } while (count < annotations.length);
-    return false;
+    }
+    return nseq;
   }
 
   @Override
-  public void sortAlignmentByFeatureDensity(String[] typ)
+  public void sortAlignmentByFeatureDensity(List<String> typ)
   {
-    sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+    String methodText = MessageManager.getString("label.sort_by_density");
+    sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_DENSITY);
   }
 
-  protected void sortBy(String[] typ, String methodText, final String method)
+  /**
+   * Sorts the alignment (or current selection) by either average score or density
+   * of the specified feature types, and adds to the command history. If
+   * {@code types} is null, all visible feature types are used for the sort. If no
+   * feature types apply, does nothing.
+   * 
+   * @param types
+   * @param methodText
+   *                     - text shown in Undo/Redo command
+   * @param method
+   *                     - passed to
+   *                     jalview.analysis.AlignmentSorter.sortByFeatures()
+   */
+  protected void sortByFeatures(List<String> types, String methodText,
+          final String method)
   {
     FeatureRenderer fr = alignPanel.getFeatureRenderer();
-    if (typ == null)
+    if (types == null && fr != null)
     {
-      typ = fr==null ? null : fr.getDisplayedFeatureTypes();
+      types = fr.getDisplayedFeatureTypes();
     }
-    String gps[] = null;
-    gps = fr==null ? null : fr.getDisplayedFeatureGroups();
-    if (typ != null)
+    if (types.isEmpty())
     {
-      ArrayList types = new ArrayList();
-      for (int i = 0; i < typ.length; i++)
-      {
-        if (typ[i] != null)
-        {
-          types.add(typ[i]);
-        }
-        typ = new String[types.size()];
-        types.toArray(typ);
-      }
+      return; // nothing to do
     }
-    if (gps != null)
+    List<String> gps = null;
+    if (fr != null)
     {
-      ArrayList grps = new ArrayList();
-
-      for (int i = 0; i < gps.length; i++)
-      {
-        if (gps[i] != null)
-        {
-          grps.add(gps[i]);
-        }
-      }
-      gps = new String[grps.size()];
-      grps.toArray(gps);
+      gps = fr.getDisplayedFeatureGroups();
     }
     AlignmentI al = viewport.getAlignment();
 
@@ -447,16 +359,115 @@ public class AlignViewController implements AlignViewControllerI
       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);
+    AlignmentSorter.sortByFeature(types, gps, start, stop, al, method);
+    avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
+            viewport.getAlignment()));
+    alignPanel.paintAlignment(true, false);
+
+  }
+
+  @Override
+  public void sortAlignmentByFeatureScore(List<String> typ)
+  {
+    String methodText = MessageManager.getString("label.sort_by_score");
+    sortByFeatures(typ, methodText, 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;
 
   }
 
   @Override
-  public void sortAlignmentByFeatureScore(String[] typ)
+  public boolean markHighlightedColumns(boolean invert,
+          boolean extendCurrent, boolean toggle)
   {
-    sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
+    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;
   }
+
 }