X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;fp=src%2Fjalview%2Fgui%2FAlignViewport.java;h=5e477c7f8cd29991a627c5fe73eae606f029b551;hb=ed2283c5f54da377a2a2fdbdb7aec75ed7041714;hp=d84d3a38cb457a876edf3afef8ed1b77fd307b92;hpb=86c580ce122275898f6ecb1a3d70d32fd79d5815;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index d84d3a3..5e477c7 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -44,7 +44,6 @@ import java.awt.Font;
 import java.awt.Rectangle;
 import java.util.ArrayList;
 import java.util.Hashtable;
-import java.util.List;
 import java.util.Set;
 import java.util.Vector;
 
@@ -62,7 +61,6 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.Sequence;
@@ -74,8 +72,6 @@ import jalview.structure.CommandListener;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
-import jalview.util.Comparison;
-import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.params.AutoCalcSetting;
@@ -89,14 +85,6 @@ import jalview.ws.params.AutoCalcSetting;
 public class AlignViewport extends AlignmentViewport implements
         SelectionSource, AlignViewportI, CommandListener
 {
-  int startRes;
-
-  int endRes;
-
-  int startSeq;
-
-  int endSeq;
-
   Font font;
 
   NJTree currentTree = null;
@@ -371,112 +359,6 @@ public class AlignViewport extends AlignmentViewport implements
     return sq;
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public int getStartRes()
-  {
-    return startRes;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public int getEndRes()
-  {
-    return endRes;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public int getStartSeq()
-  {
-    return startSeq;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param res
-   *          DOCUMENT ME!
-   */
-  public void setStartRes(int res)
-  {
-    this.startRes = res;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param seq
-   *          DOCUMENT ME!
-   */
-  public void setStartSeq(int seq)
-  {
-    this.startSeq = seq;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param res
-   *          DOCUMENT ME!
-   */
-  public void setEndRes(int res)
-  {
-    if (res > (alignment.getWidth() - 1))
-    {
-      // log.System.out.println(" Corrected res from " + res + " to maximum " +
-      // (alignment.getWidth()-1));
-      res = alignment.getWidth() - 1;
-    }
-
-    if (res < 0)
-    {
-      res = 0;
-    }
-
-    this.endRes = res;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param seq
-   *          DOCUMENT ME!
-   */
-  public void setEndSeq(int seq)
-  {
-    if (seq > alignment.getHeight())
-    {
-      seq = alignment.getHeight();
-    }
-
-    if (seq < 0)
-    {
-      seq = 0;
-    }
-
-    this.endSeq = seq;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public int getEndSeq()
-  {
-    return endSeq;
-  }
-
   boolean validCharWidth;
 
   /**
@@ -674,21 +556,6 @@ public class AlignViewport extends AlignmentViewport implements
     return false;
   }
 
-  /**
-   * when set, view will scroll to show the highlighted position
-   */
-  public boolean followHighlight = true;
-
-  /**
-   * @return true if view should scroll to show the highlighted region of a
-   *         sequence
-   * @return
-   */
-  public boolean getFollowHighlight()
-  {
-    return followHighlight;
-  }
-
   public boolean followSelection = true;
 
   /**
@@ -1139,70 +1006,22 @@ public class AlignViewport extends AlignmentViewport implements
   /**
    * If this viewport has a (Protein/cDNA) complement, then scroll the
    * complementary alignment to match this one.
-   * 
-   * @param horizontal
-   *          true for horizontal scroll event, false for vertical
    */
-  public void scrollComplementaryAlignment(boolean horizontal)
+  public void scrollComplementaryAlignment()
   {
     /*
-     * If no complement, or it is not following scrolling, do nothing.
+     * Populate a SearchResults object with the mapped location to scroll to. If
+     * there is no complement, or it is not following highlights, or no mapping
+     * is found, the result will be empty.
      */
-    // TODO pull up followHighlight to AlignmentViewport/AlignViewportI
-    final AlignViewport codingComplement = (AlignViewport) getCodingComplement();
-    if (codingComplement == null || !codingComplement.followHighlight)
-    {
-      return;
-    }
-    boolean iAmProtein = !getAlignment().isNucleotide();
-    AlignmentI proteinAlignment = iAmProtein ? getAlignment()
-            : codingComplement.getAlignment();
-    if (proteinAlignment == null)
+    SearchResults sr = new SearchResults();
+    int seqOffset = findComplementScrollTarget(sr);
+    if (!sr.isEmpty())
     {
-      return;
-    }
-    final Set<AlignedCodonFrame> mappings = proteinAlignment
-            .getCodonFrames();
-
-    /*
-     * Heuristic: find the first mapped sequence (if any) with a non-gapped
-     * residue in the middle column of the visible region. Scroll the
-     * complementary alignment to line up the corresponding residue.
-     */
-    int seqOffset = 0;
-    SequenceI sequence = null;
-    int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
-    final HiddenSequences hiddenSequences = getAlignment()
-            .getHiddenSequences();
-    for (int seqNo = getStartSeq(); seqNo < getEndSeq(); seqNo++, seqOffset++)
-    {
-      sequence = getAlignment().getSequenceAt(seqNo);
-      if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
-      {
-        continue;
-      }
-      if (Comparison.isGap(sequence.getCharAt(middleColumn)))
-      {
-        continue;
-      }
-      List<AlignedCodonFrame> seqMappings = MappingUtils
-              .findMappingsForSequence(sequence, mappings);
-      if (!seqMappings.isEmpty())
-      {
-        break;
-      }
-    }
-
-    if (sequence == null)
-    {
-      /*
-       * No ungapped mapped sequence in middle column - do nothing
-       */
-      return;
+      // TODO would like next line without cast but needs more refactoring...
+      final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()).getAlignPanel();
+      complementPanel.setFollowingComplementScroll(true);
+      complementPanel.scrollToCentre(sr, seqOffset);
     }
-    SearchResults sr = MappingUtils.buildSearchResults(sequence,
-            sequence.findPosition(middleColumn), mappings);
-    codingComplement.getAlignPanel().scrollAsComplement(sr, seqOffset,
-            horizontal);
   }
 }