JAL-1445 extend functionality to select or toggle selection for columns containing...

[jalview.git] / src / jalview / controller / AlignViewController.java

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 16e8cdd..329267e 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -1,10 +1,18 @@
 package jalview.controller;
 
 import java.awt.Color;
+import java.util.BitSet;
+import java.util.List;
 
+import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
@@ -12,15 +20,21 @@ public class AlignViewController implements AlignViewControllerI
 {
   AlignViewportI viewport=null;
   AlignmentViewPanel alignPanel=null;
+  /**
+   * the GUI container that is handling interactions with the user
+   */
+  private AlignViewControllerGuiI avcg;
   @Override
   protected void finalize() throws Throwable {
     viewport = null;
     alignPanel = null;
+    avcg = null;
   };
   
-  public AlignViewController(AlignViewportI viewport,
+  public AlignViewController(AlignViewControllerGuiI alignFrame, AlignViewportI viewport,
           AlignmentViewPanel alignPanel)
   {
+    this.avcg = alignFrame;
     this.viewport=viewport;
     this.alignPanel = alignPanel;
   }
@@ -96,5 +110,148 @@ public class AlignViewController implements AlignViewControllerI
     }
     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();
+    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);
+              }
+            }
+          }
+        }
+
+        if (tfeat > 0)
+        {
+          nseq++;
+        }
+      }
+    }
+    ColumnSelection cs = viewport.getColumnSelection();
+    if (bs.cardinality() > 0 || invert)
+    {
+      if (cs == null)
+      {
+        cs = new ColumnSelection();
+      } else {
+        if (!extendCurrent)
+        {
+          cs.clear();
+        }
+      }
+      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((toggle ? "Toggled ": "Marked ")
+              + (invert ? (alw-alStart) - bs.cardinality() : bs.cardinality())
+              + " columns "+(invert ? "not " : "") + "containing features of type " + featureType
+              + " across " + nseq + " sequence(s)");
+      return true;
+    }
+    else
+    {
+      avcg.setStatus("No features of type " + featureType + " found.");
+      if (!extendCurrent && cs!=null)
+      {
+        cs.clear();
+        alignPanel.paintAlignment(true);
+      }
+      return false;
+    }
   }
+}