X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;fp=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=2d2223111c2bb0c75b1aa104ab76ba9e98059ebf;hb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;hp=0000000000000000000000000000000000000000;hpb=072fc418c393cbd2a40dfa1d3e46f90178b79572;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
new file mode 100644
index 0000000..2d22231
--- /dev/null
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -0,0 +1,728 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+import jalview.util.ShiftList;
+
+import java.util.*;
+
+/**
+ * NOTE: Columns are zero based.
+ */
+public class ColumnSelection
+{
+    Vector selected = new Vector();
+
+    //Vector of int [] {startCol, endCol}
+    Vector hiddenColumns;
+
+    /**
+     * Add a column to the selection
+     *
+     * @param col index of column
+     */
+    public void addElement(int col)
+    {
+        Integer column = new Integer(col);
+        if (!selected.contains(column))
+        {
+            selected.addElement(column);
+        }
+    }
+
+    /**
+     * clears column selection
+     */
+    public void clear()
+    {
+        selected.removeAllElements();
+    }
+
+    /**
+     * removes col from selection
+     *
+     * @param col index of column to be removed
+     */
+    public void removeElement(int col)
+    {
+        Integer colInt = new Integer(col);
+
+        if (selected.contains(colInt))
+        {
+            selected.removeElement(colInt);
+        }
+    }
+
+    /**
+     * removes a range of columns from the selection
+     * @param start int - first column in range to be removed
+     * @param end int - last col
+     */
+    public void removeElements(int start, int end)
+    {
+      Integer colInt;
+      for(int i=start; i<end; i++)
+      {
+        colInt = new Integer(i);
+        if (selected.contains(colInt))
+        {
+            selected.removeElement(colInt);
+        }
+      }
+    }
+    /**
+     *
+     * @return Vector containing selected columns as Integers
+     */
+    public Vector getSelected()
+    {
+      return selected;
+    }
+
+    /**
+     *
+     * @param col index to search for in column selection
+     *
+     * @return true if Integer(col) is in selection.
+     */
+    public boolean contains(int col)
+    {
+        return selected.contains(new Integer(col));
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int columnAt(int i)
+    {
+        return ((Integer) selected.elementAt(i)).intValue();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int size()
+    {
+        return selected.size();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getMax()
+    {
+        int max = -1;
+
+        for (int i = 0; i < selected.size(); i++)
+        {
+            if (columnAt(i) > max)
+            {
+                max = columnAt(i);
+            }
+        }
+
+        return max;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getMin()
+    {
+        int min = 1000000000;
+
+        for (int i = 0; i < selected.size(); i++)
+        {
+            if (columnAt(i) < min)
+            {
+                min = columnAt(i);
+            }
+        }
+
+        return min;
+    }
+
+
+    /**
+     * propagate shift in alignment columns to column selection
+     *
+     * @param start beginning of edit
+     * @param left shift in edit (+ve for removal, or -ve for inserts)
+     */
+    public void compensateForEdit(int start, int change)
+    {
+        for (int i = 0; i < size(); i++)
+        {
+            int temp = columnAt(i);
+
+            if (temp >= start)
+            {
+                selected.setElementAt(new Integer(temp - change), i);
+            }
+        }
+
+        if(hiddenColumns!=null)
+        {
+          for(int i=0; i<hiddenColumns.size(); i++)
+          {
+            int[] region = (int[]) hiddenColumns.elementAt(i);
+            if(region[0] > start)
+            {
+              region[0] -= change;
+              region[1] -= change;
+            }
+            if(region[0]<0)
+              region[0] = 0;
+            if(region[1] <0)
+             region[1] = 0;
+          }
+        }
+    }
+    /**
+     * propagate shift in alignment columns to column selection
+     * special version of compensateForEdit - allowing for edits within hidden regions
+     * @param start beginning of edit
+     * @param left shift in edit (+ve for removal, or -ve for inserts)
+     */
+    private void compensateForDelEdits(int start, int change)
+    {
+        for (int i = 0; i < size(); i++)
+        {
+            int temp = columnAt(i);
+
+            if (temp >= start)
+            {
+                selected.setElementAt(new Integer(temp - change), i);
+            }
+        }
+
+        if(hiddenColumns!=null)
+        {
+          for(int i=0; i<hiddenColumns.size(); i++)
+          {
+            int[] region = (int[]) hiddenColumns.elementAt(i);
+            if(region[0] >= start)
+            {
+              region[0] -= change;
+            }
+            if (region[1]>= start) {
+              region[1] -=change;
+            }
+            if (region[1]<region[0]) {
+              hiddenColumns.removeElementAt(i--);
+            }
+
+            if(region[0]<0)
+              region[0] = 0;
+            if(region[1] <0)
+             region[1] = 0;
+          }
+        }
+    }
+    /**
+     * Adjust hidden column boundaries based on a series of column
+     * additions or deletions in visible regions.
+     * @param shiftrecord
+     * @return
+     */
+    public ShiftList compensateForEdits(ShiftList shiftrecord) {
+      if (shiftrecord!=null) {
+        Vector shifts = shiftrecord.shifts;
+        if (shifts!=null && shifts.size()>0) {
+          int shifted=0;
+          for (int i=0,j=shifts.size(); i<j; i++) {
+            int[] sh = (int[]) shifts.elementAt(i);
+            //compensateForEdit(shifted+sh[0], sh[1]);
+            compensateForDelEdits(shifted+sh[0], sh[1]);
+            shifted-=sh[1];
+          }
+        }
+        return shiftrecord.getInverse();
+      }
+      return null;
+    }
+    /**
+     * removes intersection of position,length ranges in deletions
+     * from the start,end regions marked in intervals.
+     * @param deletions
+     * @param intervals
+     * @return
+     */
+    private boolean pruneIntervalVector(Vector deletions, Vector intervals) {
+      boolean pruned=false;
+      int i=0,j=intervals.size()-1, s=0, t=deletions.size()-1;
+      int hr[]=(int[]) intervals.elementAt(i);
+      int sr[]=(int[]) deletions.elementAt(s);
+      while (i<=j && s<=t) {
+        boolean trailinghn=hr[1]>=sr[0];
+        if (!trailinghn) {
+          if (i<j)
+            hr=(int[]) intervals.elementAt(++i);
+          else
+            i++;
+          continue;
+        }
+        int endshift=sr[0]+sr[1]; // deletion ranges - -ve means an insert
+        if (endshift<hr[0] || endshift<sr[0]) { // leadinghc disjoint or not a deletion
+          if (s<t)
+            sr=(int[]) deletions.elementAt(++s);
+          else
+            s++;
+          continue;
+        }
+        boolean leadinghn=hr[0]>=sr[0];
+        boolean leadinghc=hr[0]<endshift;
+        boolean trailinghc=hr[1]<endshift;
+        if (leadinghn) {
+          if (trailinghc) {// deleted hidden region.
+            intervals.removeElementAt(i);
+            pruned=true;
+            j--;
+            if (i<=j)
+              hr=(int[]) intervals.elementAt(i);
+            continue;
+          }
+          if (leadinghc) {
+            hr[0]=endshift; // clip c terminal region
+            leadinghn=!leadinghn;
+            pruned=true;
+          }
+        }
+        if (!leadinghn) {
+          if (trailinghc) {
+            if (trailinghn) {
+              hr[1]=sr[0]-1;
+              pruned=true;
+            }
+          } else {
+            // sr contained in hr
+            if (s<t)
+              sr=(int[]) deletions.elementAt(++s);
+            else
+              s++;
+            continue;
+          }
+        }
+      }
+      return pruned; // true if any interval was removed or modified by operations.
+    }
+    private boolean pruneColumnList(Vector deletion, Vector list) {
+      int s=0,t=deletion.size();
+      int[] sr=(int[])list.elementAt(s++);
+      boolean pruned=false;
+      int i=0, j=list.size();
+      while (i<j && s<=t) {
+        int c=((Integer)list.elementAt(i++)).intValue();
+        if (sr[0]<=c) {
+          if (sr[1]+sr[0]>=c) { // sr[1] -ve means inseriton.
+            list.removeElementAt(--i);
+            j--;
+          } else {
+            if (s<t)
+              sr = (int[])deletion.elementAt(s);
+            s++;
+          }
+        }
+      }
+      return pruned;
+    }
+    /**
+     * remove any hiddenColumns or selected columns and shift remaining
+     * based on a series of position, range deletions.
+     * @param deletions
+     */
+    public void pruneDeletions(ShiftList deletions) {
+      if (deletions!=null) {
+        Vector shifts=deletions.shifts;
+        if (shifts!=null && shifts.size()>0) {
+          // delete any intervals intersecting.
+          if (hiddenColumns!=null) {
+            pruneIntervalVector(shifts, hiddenColumns);
+            if (hiddenColumns!=null && hiddenColumns.size()==0) {
+              hiddenColumns=null;
+            }
+          }
+          if (selected!=null && selected.size()>0) {
+            pruneColumnList(shifts, selected);
+            if (selected!=null && selected.size()==0)
+              selected=null;
+          }
+          // and shift the rest.
+          this.compensateForEdits(deletions);
+        }
+      }
+    }
+    /**
+     * This Method is used to return all the HiddenColumn regions
+     * less than the given index.
+     * @param end int
+     * @return Vector
+     */
+    public Vector getHiddenColumns()
+    {
+      return hiddenColumns;
+    }
+    /**
+     * Return absolute column index for a visible column index
+     * @param column int column index in alignment view
+     * @return alignment column index for column
+     */
+    public int adjustForHiddenColumns(int column)
+    {
+      int result = column;
+      if (hiddenColumns != null)
+      {
+        for (int i = 0; i < hiddenColumns.size(); i++)
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(i);
+          if (result >= region[0])
+          {
+            result += region[1] - region[0] + 1;
+          }
+        }
+      }
+      return result;
+    }
+
+    /**
+     * Use this method to find out where a visible column is in the alignment
+     * when hidden columns exist
+     * @param hiddenColumn int
+     * @return int
+     */
+    public int findColumnPosition(int hiddenColumn)
+    {
+      int result = hiddenColumn;
+      if (hiddenColumns != null)
+      {
+        int index = 0;
+        int gaps = 0;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if (hiddenColumn > region[1])
+          {
+            result -= region[1]+1-region[0];
+          }
+          index++;
+        }
+        while (index < hiddenColumns.size());
+
+        result -= gaps;
+      }
+
+      return result;
+    }
+
+    /**
+     * Use this method to determine where the next hiddenRegion starts
+    */
+    public int findHiddenRegionPosition(int hiddenRegion)
+    {
+      int result = 0;
+      if (hiddenColumns != null)
+      {
+        int index = 0;
+        int gaps = 0;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if(hiddenRegion==0)
+          {
+            return region[0];
+          }
+
+            gaps +=  region[1] +1 - region[0];
+            result = region[1] +1;
+            index++;
+        }
+        while(index < hiddenRegion+1);
+
+        result -= gaps;
+      }
+
+      return result;
+    }
+
+    /**
+     * THis method returns the rightmost limit of a
+     * region of an alignment with hidden columns.
+     * In otherwords, the next hidden column.
+     * @param index int
+     */
+    public int getHiddenBoundaryRight(int alPos)
+    {
+      if (hiddenColumns != null)
+      {
+        int index = 0;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if(alPos < region[0])
+            return region[0];
+
+          index++;
+        }
+        while(index < hiddenColumns.size());
+      }
+
+      return alPos;
+
+    }
+    /**
+     * THis method returns the rightmost limit of a
+     * region of an alignment with hidden columns.
+     * In otherwords, the next hidden column.
+     * @param index int
+     */
+    public int getHiddenBoundaryLeft(int alPos)
+    {
+      if (hiddenColumns != null)
+      {
+        int index = hiddenColumns.size()-1;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if(alPos > region[1])
+            return region[1];
+
+          index--;
+        }
+        while(index >-1);
+      }
+
+      return alPos;
+
+    }
+
+    public void hideSelectedColumns()
+    {
+      while (size() > 0)
+      {
+        int column = ( (Integer) getSelected().firstElement()).intValue();
+        hideColumns(column);
+      }
+
+    }
+
+    public void hideColumns(int start, int end)
+    {
+      if(hiddenColumns==null)
+        hiddenColumns = new Vector();
+
+      boolean added = false;
+      boolean overlap = false;
+
+      for (int i = 0; i < hiddenColumns.size(); i++)
+      {
+        int[] region = (int[]) hiddenColumns.elementAt(i);
+        if ( start<=region[1] && end>=region[0])
+        {
+          hiddenColumns.removeElementAt(i);
+          overlap = true;
+          break;
+        }
+        else if (end < region[0] && start < region[0])
+        {
+          hiddenColumns.insertElementAt(new int[]
+                                        {start, end}, i);
+          added = true;
+          break;
+        }
+      }
+
+      if(overlap)
+      {
+         hideColumns(start, end);
+      }
+      else if (!added)
+        hiddenColumns.addElement(new int[] {start, end});
+
+    }
+
+    /**
+     * This method will find a range of selected columns
+     * around the column specified
+     * @param res int
+     */
+    public void hideColumns(int col)
+    {
+      // First find out range of columns to hide
+      int min = col, max = col+1;
+      while( contains(min) )
+      {  removeElement(min); min --;  }
+
+      while( contains(max) )
+      { removeElement(max);  max ++;  }
+
+      min++; max--;
+
+      hideColumns(min, max);
+    }
+
+    public void revealAllHiddenColumns()
+    {
+      if(hiddenColumns!=null)
+      {
+        for (int i = 0; i < hiddenColumns.size(); i++)
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(i);
+          for (int j = region[0]; j < region[1]+1; j++)
+          {
+            addElement(j);
+          }
+        }
+      }
+
+      hiddenColumns = null;
+    }
+
+    public void revealHiddenColumns(int res)
+    {
+      for(int i=0; i<hiddenColumns.size(); i++)
+      {
+        int [] region = (int[])hiddenColumns.elementAt(i);
+        if( res == region[0])
+        {
+          for (int j = region[0]; j < region[1]+1; j++)
+          {
+            addElement(j);
+          }
+
+          hiddenColumns.removeElement(region);
+          break;
+        }
+      }
+      if(hiddenColumns.size()==0)
+        hiddenColumns = null;
+    }
+
+    public boolean isVisible(int column)
+    {
+      for(int i=0; i<hiddenColumns.size(); i++)
+      {
+        int [] region = (int[])hiddenColumns.elementAt(i);
+        if( column >= region[0] && column <= region[1])
+        {
+          return false;
+        }
+      }
+      return true;
+    }
+    /**
+     * Copy constructor
+     * @param copy
+     */
+    public ColumnSelection(ColumnSelection copy) {
+      if (copy!=null) {
+        if (copy.selected!=null) {
+          selected = new Vector();
+          for (int i=0,j=copy.selected.size(); i<j; i++) {
+            selected.setElementAt( ((Integer) copy.selected.elementAt(i)), i);
+          }
+        }
+        if (copy.hiddenColumns!=null) {
+          hiddenColumns=new Vector();
+          for (int i=0,j=copy.hiddenColumns.size(); i<j; i++) {
+            int[] rh,cp;
+            rh = (int[])copy.hiddenColumns.elementAt(i);
+            if (rh!=null) {
+              cp = new int[rh.length];
+              System.arraycopy(rh, 0, cp, 0, rh.length);
+              hiddenColumns.setElementAt(cp, i);
+            }
+          }
+        }
+      }
+    }
+
+  /**
+   * ColumnSelection
+   */
+  public ColumnSelection()
+  {
+  }
+
+  public String[] getVisibleSequenceStrings(int start, int end, SequenceI[] seqs) {
+    int i,iSize=seqs.length;
+    String selection[] = new String[iSize];
+    if (hiddenColumns!=null && hiddenColumns.size()>0)
+      {
+      for (i=0; i<iSize; i++) {
+        StringBuffer visibleSeq = new StringBuffer();
+        Vector regions = 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
+      {
+        for(i=0; i<iSize; i++)
+        {
+        selection[i] = seqs[i].getSequence(start, end);
+        }
+      }
+      
+    return selection;
+    }
+  
+}