/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
* 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.
- *
+ *
+ * Jalview 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
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
import jalview.util.ShiftList;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
/**
* NOTE: Columns are zero based.
{
Vector selected = new Vector();
- //Vector of int [] {startCol, endCol}
- Vector hiddenColumns;
+ // Vector of int [] {startCol, endCol}
+ Vector<int[]> hiddenColumns;
/**
* Add a column to the selection
- *
- * @param col index of column
+ *
+ * @param col
+ * index of column
*/
public void addElement(int col)
{
/**
* removes col from selection
- *
- * @param col index of column to be removed
+ *
+ * @param col
+ * index of column to be removed
*/
public void removeElement(int col)
{
/**
* removes a range of columns from the selection
- * @param start int - first column in range to be removed
- * @param end int - last col
+ *
+ * @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++)
+ for (int i = start; i < end; i++)
{
colInt = new Integer(i);
if (selected.contains(colInt))
}
}
}
+
/**
- *
+ *
* @return Vector containing selected columns as Integers
*/
- public Vector getSelected()
+ public Vector<Integer> getSelected()
{
return selected;
}
/**
- *
- * @param col index to search for in column selection
- *
+ *
+ * @param col
+ * index to search for in column selection
+ *
* @return true if Integer(col) is in selection.
*/
public boolean contains(int col)
}
/**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Column number at position i in selection
+ *
+ * @param i
+ * index into selected columns
+ *
+ * @return column number in alignment
*/
public int columnAt(int i)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int size()
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * rightmost selected column
+ *
+ * @return rightmost column in alignment that is selected
*/
public int getMax()
{
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Leftmost column in selection
+ *
+ * @return column index of leftmost column in selection
*/
public int getMin()
{
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)
+ *
+ * @param start
+ * beginning of edit
+ * @param left
+ * shift in edit (+ve for removal, or -ve for inserts)
*/
- public void compensateForEdit(int start, int change)
+ public List<int[]> compensateForEdit(int start, int change)
{
+ List<int[]> deletedHiddenColumns = null;
for (int i = 0; i < size(); i++)
{
int temp = columnAt(i);
}
}
- if(hiddenColumns!=null)
+ if (hiddenColumns != null)
{
- for(int i=0; i<hiddenColumns.size(); i++)
+ deletedHiddenColumns = new ArrayList<int[]>();
+ int hSize = hiddenColumns.size();
+ for (int i = 0; i < hSize; i++)
{
- int[] region = (int[]) hiddenColumns.elementAt(i);
- if(region[0] > start)
+ int[] region = hiddenColumns.elementAt(i);
+ if (region[0] > start && start + change > region[1])
+ {
+ deletedHiddenColumns.add(region);
+
+ hiddenColumns.removeElementAt(i);
+ i--;
+ hSize--;
+ continue;
+ }
+
+ if (region[0] > start)
{
region[0] -= change;
region[1] -= change;
}
- if(region[0]<0)
+
+ if (region[0] < 0)
+ {
region[0] = 0;
- if(region[1] <0)
- region[1] = 0;
+ }
+
}
+
+ this.revealHiddenColumns(0);
}
+
+ return deletedHiddenColumns;
}
+
/**
- * 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)
+ * 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)
{
}
}
- if(hiddenColumns!=null)
+ if (hiddenColumns != null)
{
- for(int i=0; i<hiddenColumns.size(); i++)
+ for (int i = 0; i < hiddenColumns.size(); i++)
{
- int[] region = (int[]) hiddenColumns.elementAt(i);
- if(region[0] >= start)
+ int[] region = hiddenColumns.elementAt(i);
+ if (region[0] >= start)
{
region[0] -= change;
}
- if (region[1]>= start) {
- region[1] -=change;
+ if (region[1] >= start)
+ {
+ region[1] -= change;
}
- if (region[1]<region[0]) {
+ if (region[1] < region[0])
+ {
hiddenColumns.removeElementAt(i--);
}
- if(region[0]<0)
+ if (region[0] < 0)
+ {
region[0] = 0;
- if(region[1] <0)
+ }
+ if (region[1] < 0)
+ {
region[1] = 0;
+ }
}
}
}
+
/**
- * Adjust hidden column boundaries based on a series of column
- * additions or deletions in visible regions.
+ * 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) {
+ 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++) {
+ 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];
+ // 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.
+ * 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);
+ 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);
+ 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.
+ 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;
+ pruned = true;
j--;
- if (i<=j)
- hr=(int[]) intervals.elementAt(i);
+ if (i <= j)
+ {
+ hr = (int[]) intervals.elementAt(i);
+ }
continue;
}
- if (leadinghc) {
- hr[0]=endshift; // clip c terminal region
- leadinghn=!leadinghn;
- pruned=true;
+ 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;
+ if (!leadinghn)
+ {
+ if (trailinghc)
+ {
+ if (trailinghn)
+ {
+ hr[1] = sr[0] - 1;
+ pruned = true;
}
- } else {
+ }
+ else
+ {
// sr contained in hr
- if (s<t)
- sr=(int[]) deletions.elementAt(++s);
+ if (s < t)
+ {
+ sr = (int[]) deletions.elementAt(++s);
+ }
else
+ {
s++;
+ }
continue;
}
}
}
- return pruned; // true if any interval was removed or modified by operations.
+ 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.
+
+ 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);
+ }
+ 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.
+ * 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) {
+ 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) {
+ if (hiddenColumns != null)
+ {
pruneIntervalVector(shifts, hiddenColumns);
- if (hiddenColumns!=null && hiddenColumns.size()==0) {
- hiddenColumns=null;
+ if (hiddenColumns != null && hiddenColumns.size() == 0)
+ {
+ hiddenColumns = null;
}
}
- if (selected!=null && selected.size()>0) {
+ if (selected != null && selected.size() > 0)
+ {
pruneColumnList(shifts, selected);
- if (selected!=null && selected.size()==0)
- selected=null;
+ 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
+ * @return empty list or List of hidden column intervals
*/
- public Vector getHiddenColumns()
+ public List<int[]> getHiddenColumns()
{
- return hiddenColumns;
+ return hiddenColumns == null ? Arrays.asList(new int[]
+ {}) : hiddenColumns;
}
+
/**
* Return absolute column index for a visible column index
- * @param column int column index in alignment view
+ *
+ * @param column
+ * int column index in alignment view
* @return alignment column index for column
*/
public int adjustForHiddenColumns(int column)
{
for (int i = 0; i < hiddenColumns.size(); i++)
{
- int[] region = (int[]) hiddenColumns.elementAt(i);
+ int[] region = hiddenColumns.elementAt(i);
if (result >= region[0])
{
result += region[1] - region[0] + 1;
}
/**
- * Use this method to find out where a visible column is in the alignment
- * when hidden columns exist
- * @param hiddenColumn int
+ * Use this method to find out where a column will appear in the visible
+ * alignment when hidden columns exist. If the column is not visible, then the
+ * left-most visible column will always be returned.
+ *
+ * @param hiddenColumn
+ * int
* @return int
*/
public int findColumnPosition(int hiddenColumn)
if (hiddenColumns != null)
{
int index = 0;
- int gaps = 0;
+ int[] region;
do
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
+ region = hiddenColumns.elementAt(index++);
if (hiddenColumn > region[1])
{
- result -= region[1]+1-region[0];
+ result -= region[1] + 1 - region[0];
}
- index++;
+ } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
+ if (hiddenColumn > region[0] && hiddenColumn < region[1])
+ {
+ return region[0] + hiddenColumn - result;
}
- while (index < hiddenColumns.size());
-
- result -= gaps;
}
-
- return result;
+ return result; // return the shifted position after removing hidden columns.
}
/**
int gaps = 0;
do
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if(hiddenRegion==0)
+ int[] region = hiddenColumns.elementAt(index);
+ if (hiddenRegion == 0)
{
return region[0];
}
- gaps += region[1] +1 - region[0];
- result = region[1] +1;
+ gaps += region[1] + 1 - region[0];
+ result = region[1] + 1;
index++;
- }
- while(index < hiddenRegion+1);
+ } while (index < hiddenRegion + 1);
result -= gaps;
}
}
/**
- * THis method returns the rightmost limit of a
- * region of an alignment with hidden columns.
- * In otherwords, the next hidden column.
- * @param index int
+ * 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)
{
int index = 0;
do
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if(alPos < region[0])
+ int[] region = hiddenColumns.elementAt(index);
+ if (alPos < region[0])
+ {
return region[0];
+ }
index++;
- }
- while(index < hiddenColumns.size());
+ } 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
+ * This method returns the leftmost limit of a region of an alignment with
+ * hidden columns. In otherwords, the previous hidden column.
+ *
+ * @param index
+ * int
*/
public int getHiddenBoundaryLeft(int alPos)
{
if (hiddenColumns != null)
{
- int index = hiddenColumns.size()-1;
+ int index = hiddenColumns.size() - 1;
do
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if(alPos > region[1])
+ int[] region = hiddenColumns.elementAt(index);
+ if (alPos > region[1])
+ {
return region[1];
+ }
index--;
- }
- while(index >-1);
+ } while (index > -1);
}
return alPos;
{
while (size() > 0)
{
- int column = ( (Integer) getSelected().firstElement()).intValue();
+ int column = getSelected().firstElement().intValue();
hideColumns(column);
}
public void hideColumns(int start, int end)
{
- if(hiddenColumns==null)
+ 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])
+ int[] region = hiddenColumns.elementAt(i);
+ if (start <= region[1] && end >= region[0])
{
hiddenColumns.removeElementAt(i);
overlap = true;
else if (end < region[0] && start < region[0])
{
hiddenColumns.insertElementAt(new int[]
- {start, end}, i);
+ { start, end }, i);
added = true;
break;
}
}
- if(overlap)
+ if (overlap)
{
hideColumns(start, end);
}
else if (!added)
- hiddenColumns.addElement(new int[] {start, end});
+ {
+ hiddenColumns.addElement(new int[]
+ { start, end });
+ }
}
/**
- * This method will find a range of selected columns
- * around the column specified
- * @param res int
+ * 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 --; }
+ int min = col, max = col + 1;
+ while (contains(min))
+ {
+ removeElement(min);
+ min--;
+ }
- while( contains(max) )
- { removeElement(max); max ++; }
+ while (contains(max))
+ {
+ removeElement(max);
+ max++;
+ }
- min++; max--;
+ min++;
+ max--;
+ if (min > max)
+ {
+ min = max;
+ }
hideColumns(min, max);
}
public void revealAllHiddenColumns()
{
- if(hiddenColumns!=null)
+ 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++)
+ int[] region = hiddenColumns.elementAt(i);
+ for (int j = region[0]; j < region[1] + 1; j++)
{
addElement(j);
}
public void revealHiddenColumns(int res)
{
- for(int i=0; i<hiddenColumns.size(); i++)
+ for (int i = 0; i < hiddenColumns.size(); i++)
{
- int [] region = (int[])hiddenColumns.elementAt(i);
- if( res == region[0])
+ int[] region = hiddenColumns.elementAt(i);
+ if (res == region[0])
{
- for (int j = region[0]; j < region[1]+1; j++)
+ for (int j = region[0]; j < region[1] + 1; j++)
{
addElement(j);
}
break;
}
}
- if(hiddenColumns.size()==0)
+ if (hiddenColumns.size() == 0)
+ {
hiddenColumns = null;
+ }
}
public boolean isVisible(int column)
{
- for(int i=0; i<hiddenColumns.size(); i++)
+ if (hiddenColumns != null)
{
- int [] region = (int[])hiddenColumns.elementAt(i);
- if( column >= region[0] && column <= region[1])
+ for (int i = 0; i < hiddenColumns.size(); i++)
{
- return false;
+ int[] region = 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) {
+ 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);
+ for (int i = 0, j = copy.selected.size(); i < j; i++)
+ {
+ selected.addElement(copy.selected.elementAt(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) {
+ if (copy.hiddenColumns != null)
+ {
+ hiddenColumns = new Vector(copy.hiddenColumns.size());
+ for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
+ {
+ int[] rh, cp;
+ rh = copy.hiddenColumns.elementAt(i);
+ if (rh != null)
+ {
cp = new int[rh.length];
System.arraycopy(rh, 0, cp, 0, rh.length);
- hiddenColumns.setElementAt(cp, i);
+ hiddenColumns.addElement(cp);
}
}
}
}
}
+
/**
* ColumnSelection
*/
{
}
- public String[] getVisibleSequenceStrings(int start, int end, SequenceI[] seqs) {
- int i,iSize=seqs.length;
+ 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)
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
{
- for (i=0; i<iSize; i++) {
+ for (i = 0; i < iSize; i++)
+ {
StringBuffer visibleSeq = new StringBuffer();
- Vector regions = getHiddenColumns();
+ List<int[]> regions = getHiddenColumns();
- int blockStart = start, blockEnd=end;
- int [] region;
+ int blockStart = start, blockEnd = end;
+ int[] region;
int hideStart, hideEnd;
for (int j = 0; j < regions.size(); j++)
{
- region = (int[]) regions.elementAt(j);
+ region = regions.get(j);
hideStart = region[0];
hideEnd = region[1];
- if(hideStart < start)
+ if (hideStart < start)
{
continue;
}
- blockStart = Math.min(blockStart, hideEnd+1);
+ blockStart = Math.min(blockStart, hideEnd + 1);
blockEnd = Math.min(blockEnd, hideStart);
- if(blockStart>blockEnd)
+ if (blockStart > blockEnd)
{
break;
}
-
visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
- blockStart = hideEnd+1;
+ blockStart = hideEnd + 1;
blockEnd = end;
}
- if(end>blockStart)
+ if (end > blockStart)
+ {
visibleSeq.append(seqs[i].getSequence(blockStart, end));
+ }
selection[i] = visibleSeq.toString();
}
}
else
{
- for(i=0; i<iSize; i++)
+ for (i = 0; i < iSize; i++)
{
- selection[i] = seqs[i].getSequence(start, end);
+ selection[i] = seqs[i].getSequenceAsString(start, end);
}
}
return selection;
}
+
/**
* return all visible segments between the given start and end boundaries
*
- * @param start (first column inclusive from 0)
- * @param end (last column - not inclusive)
- * @return int[] {i_start, i_end, ..} where intervals lie in start<=i_start<=i_end<end
+ * @param start
+ * (first column inclusive from 0)
+ * @param end
+ * (last column - not inclusive)
+ * @return int[] {i_start, i_end, ..} where intervals lie in
+ * start<=i_start<=i_end<end
*/
- public int[] getVisibleContigs(int start, int end) {
- if (hiddenColumns!=null && hiddenColumns.size()>0)
+ public int[] getVisibleContigs(int start, int end)
+ {
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
{
- Vector visiblecontigs=new Vector();
- Vector regions = getHiddenColumns();
+ Vector visiblecontigs = new Vector();
+ List<int[]> regions = getHiddenColumns();
int vstart = start;
- int [] region;
+ int[] region;
int hideStart, hideEnd;
- for (int j = 0; vstart<end && j < regions.size(); j++)
+ for (int j = 0; vstart < end && j < regions.size(); j++)
{
- region = (int[]) regions.elementAt(j);
+ region = regions.get(j);
hideStart = region[0];
hideEnd = region[1];
- if(hideEnd < vstart)
+ if (hideEnd < vstart)
{
continue;
}
- if (hideStart>vstart) {
- visiblecontigs.addElement(new int[] {vstart, hideStart-1});
+ if (hideStart > vstart)
+ {
+ visiblecontigs.addElement(new int[]
+ { vstart, hideStart - 1 });
}
- vstart=hideEnd+1;
+ vstart = hideEnd + 1;
}
- if(vstart<end)
- visiblecontigs.addElement(new int[] { vstart, end-1});
- int[] vcontigs = new int[visiblecontigs.size()*2];
- for (int i=0,j=visiblecontigs.size(); i<j; i++) {
- int [] vc = (int[]) visiblecontigs.get(i);
+ if (vstart < end)
+ {
+ visiblecontigs.addElement(new int[]
+ { vstart, end - 1 });
+ }
+ int[] vcontigs = new int[visiblecontigs.size() * 2];
+ for (int i = 0, j = visiblecontigs.size(); i < j; i++)
+ {
+ int[] vc = (int[]) visiblecontigs.elementAt(i);
visiblecontigs.setElementAt(null, i);
- vcontigs[i*2] = vc[0];
- vcontigs[i*2+1] = vc[1];
+ vcontigs[i * 2] = vc[0];
+ vcontigs[i * 2 + 1] = vc[1];
}
- visiblecontigs.clear();
+ visiblecontigs.removeAllElements();
return vcontigs;
- }
+ }
else
{
- return new int[] { start, end-1 };
+ return new int[]
+ { start, end - 1 };
}
}
+
+ /**
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
+ *
+ * @param alignmentAnnotation
+ */
+ public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
+ {
+ makeVisibleAnnotation(-1, -1, alignmentAnnotation);
+ }
+
+ /**
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
+ *
+ * @param start
+ * remove any annotation to the right of this column
+ * @param end
+ * remove any annotation to the left of this column
+ * @param alignmentAnnotation
+ * the annotation to operate on
+ */
+ public void makeVisibleAnnotation(int start, int end,
+ AlignmentAnnotation alignmentAnnotation)
+ {
+ if (alignmentAnnotation.annotations == null)
+ {
+ return;
+ }
+ if (start == end && end == -1)
+ {
+ start = 0;
+ end = alignmentAnnotation.annotations.length;
+ }
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
+ {
+ // then mangle the alignmentAnnotation annotation array
+ Vector annels = new Vector();
+ Annotation[] els = null;
+ List<int[]> regions = getHiddenColumns();
+ int blockStart = start, blockEnd = end;
+ int[] region;
+ int hideStart, hideEnd, w = 0;
+
+ for (int j = 0; j < regions.size(); j++)
+ {
+ region = regions.get(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;
+ }
+
+ annels.addElement(els = new Annotation[blockEnd - blockStart]);
+ System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
+ 0, els.length);
+ w += els.length;
+ blockStart = hideEnd + 1;
+ blockEnd = end;
+ }
+
+ if (end > blockStart)
+ {
+ annels.addElement(els = new Annotation[end - blockStart + 1]);
+ if ((els.length + blockStart) <= alignmentAnnotation.annotations.length)
+ {
+ // copy just the visible segment of the annotation row
+ System.arraycopy(alignmentAnnotation.annotations, blockStart,
+ els, 0, els.length);
+ }
+ else
+ {
+ // copy to the end of the annotation row
+ System.arraycopy(alignmentAnnotation.annotations, blockStart,
+ els, 0,
+ (alignmentAnnotation.annotations.length - blockStart));
+ }
+ w += els.length;
+ }
+ if (w == 0)
+ {
+ return;
+ }
+ Enumeration e = annels.elements();
+ alignmentAnnotation.annotations = new Annotation[w];
+ w = 0;
+ while (e.hasMoreElements())
+ {
+ Annotation[] chnk = (Annotation[]) e.nextElement();
+ System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
+ chnk.length);
+ w += chnk.length;
+ }
+ }
+ else
+ {
+ alignmentAnnotation.restrict(start, end);
+ }
+ }
+
+ /**
+ * Invert the column selection from first to end-1. leaves hiddenColumns
+ * untouched (and unselected)
+ *
+ * @param first
+ * @param end
+ */
+ public void invertColumnSelection(int first, int width)
+ {
+ boolean hasHidden = hiddenColumns != null && hiddenColumns.size() > 0;
+ for (int i = first; i < width; i++)
+ {
+ if (contains(i))
+ {
+ removeElement(i);
+ }
+ else
+ {
+ if (!hasHidden || isVisible(i))
+ {
+ addElement(i);
+ }
+ }
+ }
+ }
+
+ /**
+ * add in any unselected columns from the given column selection, excluding
+ * any that are hidden.
+ *
+ * @param colsel
+ */
+ public void addElementsFrom(ColumnSelection colsel)
+ {
+ if (colsel != null && colsel.size() > 0)
+ {
+ Enumeration e = colsel.getSelected().elements();
+ while (e.hasMoreElements())
+ {
+ Object eo = e.nextElement();
+ if (hiddenColumns != null && isVisible(((Integer) eo).intValue()))
+ {
+ if (!selected.contains(eo))
+ {
+ selected.addElement(eo);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * set the selected columns the given column selection, excluding any columns
+ * that are hidden.
+ *
+ * @param colsel
+ */
+ public void setElementsFrom(ColumnSelection colsel)
+ {
+ selected = new Vector();
+ if (colsel.selected != null && colsel.selected.size() > 0)
+ {
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
+ {
+ // only select visible columns in this columns selection
+ selected = new Vector();
+ addElementsFrom(colsel);
+ }
+ else
+ {
+ // add everything regardless
+ Enumeration en = colsel.selected.elements();
+ while (en.hasMoreElements())
+ {
+ selected.addElement(en.nextElement());
+ }
+ }
+ }
+ }
+
+ /**
+ * Add gaps into the sequences aligned to profileseq under the given
+ * AlignmentView
+ *
+ * @param profileseq
+ * @param al
+ * - alignment to have gaps inserted into it
+ * @param input
+ * - alignment view where sequence corresponding to profileseq is
+ * first entry
+ * @return new Column selection for new alignment view, with insertions into
+ * profileseq marked as hidden.
+ */
+ public static ColumnSelection propagateInsertions(SequenceI profileseq,
+ Alignment al, AlignmentView input)
+ {
+ int profsqpos = 0;
+
+ // return propagateInsertions(profileseq, al, )
+ char gc = al.getGapCharacter();
+ Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);
+ ColumnSelection nview = (ColumnSelection) alandcolsel[1];
+ SequenceI origseq = ((SequenceI[]) alandcolsel[0])[profsqpos];
+ nview.propagateInsertions(profileseq, al, origseq);
+ return nview;
+ }
+
+ /**
+ *
+ * @param profileseq
+ * - sequence in al which corresponds to origseq
+ * @param al
+ * - alignment which is to have gaps inserted into it
+ * @param origseq
+ * - sequence corresponding to profileseq which defines gap map for
+ * modifying al
+ */
+ public void propagateInsertions(SequenceI profileseq, AlignmentI al,
+ SequenceI origseq)
+ {
+ char gc = al.getGapCharacter();
+ // recover mapping between sequence's non-gap positions and positions
+ // mapping to view.
+ pruneDeletions(ShiftList.parseMap(origseq.gapMap()));
+ int[] viscontigs = getVisibleContigs(0, profileseq.getLength());
+ int spos = 0;
+ int offset = 0;
+ // input.pruneDeletions(ShiftList.parseMap(((SequenceI[])
+ // alandcolsel[0])[0].gapMap()))
+ // add profile to visible contigs
+ for (int v = 0; v < viscontigs.length; v += 2)
+ {
+ if (viscontigs[v] > spos)
+ {
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
+ {
+ sb.append(gc);
+ }
+ for (int s = 0, ns = al.getHeight(); s < ns; s++)
+ {
+ SequenceI sqobj = al.getSequenceAt(s);
+ if (sqobj != profileseq)
+ {
+ String sq = al.getSequenceAt(s).getSequenceAsString();
+ if (sq.length() <= spos + offset)
+ {
+ // pad sequence
+ int diff = spos + offset - sq.length() - 1;
+ if (diff > 0)
+ {
+ // pad gaps
+ sq = sq + sb;
+ while ((diff = spos + offset - sq.length() - 1) > 0)
+ {
+ // sq = sq
+ // + ((diff >= sb.length()) ? sb.toString() : sb
+ // .substring(0, diff));
+ if (diff >= sb.length())
+ {
+ sq += sb.toString();
+ }
+ else
+ {
+ char[] buf = new char[diff];
+ sb.getChars(0, diff, buf, 0);
+ sq += buf.toString();
+ }
+ }
+ }
+ sq += sb.toString();
+ }
+ else
+ {
+ al.getSequenceAt(s).setSequence(
+ sq.substring(0, spos + offset) + sb.toString()
+ + sq.substring(spos + offset));
+ }
+ }
+ }
+ // offset+=sb.length();
+ }
+ spos = viscontigs[v + 1] + 1;
+ }
+ if ((offset + spos) < profileseq.getLength())
+ {
+ // pad the final region with gaps.
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
+ {
+ sb.append(gc);
+ }
+ for (int s = 0, ns = al.getHeight(); s < ns; s++)
+ {
+ SequenceI sqobj = al.getSequenceAt(s);
+ if (sqobj == profileseq)
+ {
+ continue;
+ }
+ String sq = sqobj.getSequenceAsString();
+ // pad sequence
+ int diff = origseq.getLength() - sq.length();
+ while (diff > 0)
+ {
+ // sq = sq
+ // + ((diff >= sb.length()) ? sb.toString() : sb
+ // .substring(0, diff));
+ if (diff >= sb.length())
+ {
+ sq += sb.toString();
+ }
+ else
+ {
+ char[] buf = new char[diff];
+ sb.getChars(0, diff, buf, 0);
+ sq += buf.toString();
+ }
+ diff = origseq.getLength() - sq.length();
+ }
+ }
+ }
+ }
+
+ /**
+ *
+ * @return true if there are columns marked
+ */
+ public boolean hasSelectedColumns()
+ {
+ return (selected != null && selected.size() > 0);
+ }
+
+ /**
+ *
+ * @return true if there are columns hidden
+ */
+ public boolean hasHiddenColumns()
+ {
+ return hiddenColumns != null && hiddenColumns.size() > 0;
+ }
+
+ /**
+ *
+ * @return true if there are more than one set of columns hidden
+ */
+ public boolean hasManyHiddenColumns()
+ {
+ return hiddenColumns != null && hiddenColumns.size() > 1;
+ }
+
+ /**
+ * mark the columns corresponding to gap characters as hidden in the column
+ * selection
+ *
+ * @param sr
+ */
+ public void hideInsertionsFor(SequenceI sr)
+ {
+ List<int[]> inserts = sr.getInsertions();
+ for (int[] r : inserts)
+ {
+ hideColumns(r[0], r[1]);
+ }
+ }
+
+ public boolean filterAnnotations(Annotation[] annotations,
+ AnnotationFilterParameter filterParams)
+ {
+ this.revealAllHiddenColumns();
+ this.clear();
+ int count = 0;
+ do
+ {
+ if (annotations[count] != null)
+ {
+
+ 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())
+ {
+ itemMatched = true;
+ }
+
+ if (filterParams.isFilterAlphaHelix()
+ && annotations[count].secondaryStructure == 'H')
+ {
+ itemMatched = true;
+ }
+
+ if (filterParams.isFilterBetaSheet()
+ && annotations[count].secondaryStructure == 'E')
+ {
+ itemMatched = true;
+ }
+
+ 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 (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
+ && annotations[count].displayCharacter
+ .matches(regexSearchString))
+ {
+ itemMatched = true;
+ }
+ } catch (java.util.regex.PatternSyntaxException pse)
+ {
+ if (annotations[count].displayCharacter
+ .equals(regexSearchString))
+ {
+ itemMatched = true;
+ }
+ }
+ if (fields.contains(SearchableAnnotationField.DESCRIPTION)
+ && annotations[count].description != null
+ && annotations[count].description
+ .matches(regexSearchString))
+ {
+ itemMatched = true;
+ }
+ }
+
+ if (itemMatched)
+ {
+ this.addElement(count);
+ }
+ }
+ count++;
+ } while (count < annotations.length);
+ return false;
+ }
}
git://source.jalview.org / jalview.git / blobdiff