X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=99d0794f3c9adb3cfb933b54b31f7ac131fbd7ed;hb=c42fcf7bf5cfcf51e67dd0f683edb9ab6683d157;hp=481a657501204114037cf42065ec41e75555c0a7;hpb=245ddd4612033edc65de15acb93ac9c22912a828;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 481a657..99d0794 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -56,7 +56,7 @@ public class AlignViewport
   boolean conservationColourSelected = false;
   boolean abovePIDThreshold = false;
 
-  SequenceGroup selectionGroup = new SequenceGroup();
+  SequenceGroup selectionGroup;
 
   int charHeight;
   int charWidth;
@@ -79,7 +79,11 @@ public class AlignViewport
 
   // The following vector holds the features which are
  // currently visible, in the correct order or rendering
-  Hashtable featuresDisplayed = null;
+  Hashtable featuresDisplayed;
+
+  boolean hasHiddenColumns = false;
+  boolean hasHiddenRows = false;
+  boolean showHiddenMarkers = true;
 
 
   public Vector vconsensus;
@@ -95,8 +99,11 @@ public class AlignViewport
 
   boolean ignoreGapsInConsensusCalculation = false;
 
+  jalview.bin.JalviewLite applet;
+
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
+    this.applet = applet;
     setAlignment(al);
     this.startRes = 0;
     this.endRes = al.getWidth() - 1;
@@ -141,14 +148,34 @@ public class AlignViewport
     updateConservation();
     updateConsensus();
 
-    if (applet != null && applet.getParameter("defaultColour") != null)
+
+    if (applet != null)
     {
-      globalColourScheme = ColourSchemeProperty.getColour(alignment,
-          applet.getParameter("defaultColour"));
-      if (globalColourScheme != null)
+      String colour = applet.getParameter("defaultColour");
+
+      if(colour == null)
       {
-        globalColourScheme.setConsensus(vconsensus);
+        colour = applet.getParameter("userDefinedColour");
+        if(colour !=null)
+          colour = "User Defined";
       }
+
+      if(colour != null)
+      {
+        globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
+        if (globalColourScheme != null)
+        {
+          globalColourScheme.setConsensus(vconsensus);
+        }
+      }
+
+      if(applet.getParameter("userDefinedColour")!=null)
+      {
+        ((UserColourScheme)globalColourScheme).parseAppletParameter(
+            applet.getParameter("userDefinedColour"));
+      }
+
+
     }
   }
 
@@ -561,30 +588,11 @@ public class AlignViewport
     return increment;
   }
 
-  public int getIndex(int y)
+  public void setHiddenColumns(ColumnSelection colsel)
   {
-    int y1 = 0;
-    int starty = getStartSeq();
-    int endy = getEndSeq();
-
-    for (int i = starty; i <= endy; i++)
-    {
-      if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null)
-      {
-        int y2 = y1 + getCharHeight();
-
-        if (y >= y1 && y <= y2)
-        {
-          return i;
-        }
-        y1 = y2;
-      }
-      else
-      {
-        return -1;
-      }
-    }
-    return -1;
+    this.colSel = colsel;
+    if(colSel.getHiddenColumns()!=null)
+      hasHiddenColumns = true;
   }
 
   public ColumnSelection getColumnSelection()
@@ -719,6 +727,288 @@ public class AlignViewport
   {
     return ignoreGapsInConsensusCalculation;
   }
+  public void hideSelectedColumns()
+  {
+    if (colSel.size() < 1)
+      return;
+
+    colSel.hideSelectedColumns();
+    setSelectionGroup(null);
+
+    hasHiddenColumns = true;
+  }
+
+  public void invertColumnSelection()
+  {
+    int column;
+    for (int i = 0; i < alignment.getWidth(); i++)
+    {
+      column = i;
+
+      if (colSel.contains(column))
+        colSel.removeElement(column);
+      else
+        colSel.addElement(column);
+
+    }
+  }
+
+
+  public void hideColumns(int start, int end)
+  {
+    if(start==end)
+      colSel.hideColumns(start);
+    else
+      colSel.hideColumns(start, end);
+    setSelectionGroup(null);
+    hasHiddenColumns = true;
+  }
+
+  public void hideSequence(SequenceI seq)
+  {
+    if(seq!=null)
+    {
+      alignment.getHiddenSequences().hideSequence(seq);
+      hasHiddenRows = true;
+    }
+  }
+
+  public void showSequence(int index)
+  {
+    alignment.getHiddenSequences().showSequence(index);
+
+    if(alignment.getHiddenSequences().getSize()<1)
+      hasHiddenRows = false;
+  }
+
+  public void showColumn(int col)
+  {
+    colSel.revealHiddenColumns(col);
+    if(colSel.getHiddenColumns()==null)
+      hasHiddenColumns = false;
+  }
+
+  public void showAllHiddenColumns()
+  {
+    colSel.revealAllHiddenColumns();
+    hasHiddenColumns = false;
+  }
+
+  public void showAllHiddenSeqs()
+  {
+    if(alignment.getHiddenSequences().getSize()>0)
+    {
+      alignment.getHiddenSequences().showAll();
+      hasHiddenRows = false;
+    }
+  }
+
+  public int adjustForHiddenSeqs(int alignmentIndex)
+  {
+    return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+  }
+
+  /**
+   * This method returns the a new SequenceI [] with
+   * the selection sequence and start and end points adjusted
+   * @return String[]
+   */
+  public SequenceI[] getSelectionAsNewSequence()
+  {
+    SequenceI[] sequences;
+
+    if (selectionGroup == null)
+      sequences = alignment.getSequencesArray();
+    else
+      sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+
+    return sequences;
+  }
+
+  /**
+   * This method returns the visible alignment as text, as
+   * seen on the GUI, ie if columns are hidden they will not
+   * be returned in the result.
+   * Use this for calculating trees, PCA, redundancy etc on views
+   * which contain hidden columns.
+   * @return String[]
+   */
+  public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
+  {
+    CigarArray selection=null;
+    SequenceI [] seqs= null;
+    int i, iSize;
+    int start = 0, end = 0;
+    if(selectedRegionOnly && selectionGroup!=null)
+    {
+      iSize = selectionGroup.getSize(false);
+      seqs = selectionGroup.getSequencesInOrder(alignment);
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
+    }
+    else
+    {
+      iSize = alignment.getHeight();
+      seqs = alignment.getSequencesArray();
+      end = alignment.getWidth()-1;
+    }
+    SeqCigar[] selseqs = new SeqCigar[iSize];
+    for(i=0; i<iSize; i++)
+    {
+      selseqs[i] = new SeqCigar(seqs[i], start, end);
+    }
+    selection=new CigarArray(selseqs);
+    // now construct the CigarArray operations
+    if (hasHiddenColumns) {
+      Vector regions = colSel.getHiddenColumns();
+      int [] region;
+      int hideStart, hideEnd;
+      int last=start;
+      for (int j = 0; last<end & j < regions.size(); j++)
+      {
+        region = (int[]) regions.elementAt(j);
+        hideStart = region[0];
+        hideEnd = region[1];
+        // edit hidden regions to selection range
+        if(hideStart<last) {
+          if (hideEnd > last)
+          {
+            hideStart = last;
+          } else
+            continue;
+        }
+
+        if (hideStart>end)
+          break;
+
+        if (hideEnd>end)
+          hideEnd=end;
+
+        if (hideStart>hideEnd)
+          break;
+        /**
+         * form operations...
+         */
+        if (last<hideStart)
+          selection.addOperation(CigarArray.M, hideStart-last);
+        selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
+        last = hideEnd+1;
+      }
+      // Final match if necessary.
+      if (last<end)
+        selection.addOperation(CigarArray.M, end-last);
+    } else {
+      selection.addOperation(CigarArray.M, end-start);
+    }
+    return selection;
+  }
+  /**
+   * return a compact representation of the current alignment selection to
+   * pass to an analysis function
+   * @param selectedOnly boolean true to just return the selected view
+   * @return AlignmentView
+   */
+  jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {
+    // JBPNote:
+    // this is here because the AlignmentView constructor modifies the CigarArray
+    // object. Refactoring of Cigar and alignment view representation should
+    // be done to remove redundancy.
+    CigarArray aligview = getViewAsCigars(selectedOnly);
+    if (aligview!=null)
+      return new AlignmentView(aligview);
+    return null;
+  }
+  /**
+   * This method returns the visible alignment as text, as
+   * seen on the GUI, ie if columns are hidden they will not
+   * be returned in the result.
+   * Use this for calculating trees, PCA, redundancy etc on views
+   * which contain hidden columns.
+   * @return String[]
+   */
+  public String [] getViewAsString(boolean selectedRegionOnly)
+  {
+    String [] selection = null;
+    SequenceI [] seqs= null;
+    int i, iSize;
+    int start = 0, end = 0;
+    if(selectedRegionOnly && selectionGroup!=null)
+    {
+      iSize = selectionGroup.getSize(false);
+      seqs = selectionGroup.getSequencesInOrder(alignment);
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes()+1;
+    }
+    else
+    {
+      iSize = alignment.getHeight();
+      seqs = alignment.getSequencesArray();
+      end = alignment.getWidth();
+    }
+
+    selection = new String[iSize];
+
+
+    for(i=0; i<iSize; i++)
+    {
+      if (hasHiddenColumns)
+      {
+           StringBuffer visibleSeq = new StringBuffer();
+           Vector regions = colSel.getHiddenColumns();
+
+           int blockStart = start, blockEnd=end;
+           int [] region;
+           int hideStart, hideEnd;
+
+           for (int j = 0; j < regions.size(); j++)
+           {
+             region = (int[]) regions.elementAt(j);
+             hideStart = region[0];
+             hideEnd = region[1];
+
+             if(hideStart < start)
+             {
+               continue;
+             }
+
+             blockStart = Math.min(blockStart, hideEnd+1);
+             blockEnd = Math.min(blockEnd, hideStart);
+
+             if(blockStart>blockEnd)
+             {
+                break;
+             }
+
+
+             visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+
+             blockStart = hideEnd+1;
+             blockEnd = end;
+           }
+
+           if(end>blockStart)
+             visibleSeq.append(seqs[i].getSequence(blockStart, end));
+
+           selection[i] = visibleSeq.toString();
+      }
+      else
+      {
+        selection[i] = seqs[i].getSequence(start, end);
+      }
+    }
+
+    return selection;
+  }
+
+  public boolean getShowHiddenMarkers()
+  {
+    return showHiddenMarkers;
+  }
+
+  public void setShowHiddenMarkers(boolean show)
+  {
+    showHiddenMarkers = show;
+  }
 
 
 }