*/
public class ColumnSelection
{
- Vector selected = new Vector();
+ Vector selected = new Vector();
- //Vector of int [] {startCol, endCol}
- Vector hiddenColumns;
+ //Vector of int [] {startCol, endCol}
+ Vector hiddenColumns;
- /**
- * Add a column to the selection
- *
- * @param col index of column
- */
- public void addElement(int col)
+ /**
+ * 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))
{
- Integer column = new Integer(col);
- if (!selected.contains(column))
- {
- selected.addElement(column);
- }
+ selected.addElement(column);
}
+ }
- /**
- * clears column selection
- */
- public void clear()
- {
- selected.removeAllElements();
- }
+ /**
+ * 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);
+ /**
+ * 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);
- }
+ 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)
+ /**
+ * 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++)
{
- Integer colInt;
- for(int i=start; i<end; i++)
+ colInt = new Integer(i);
+ if (selected.contains(colInt))
{
- colInt = new Integer(i);
- if (selected.contains(colInt))
- {
- selected.removeElement(colInt);
- }
+ selected.removeElement(colInt);
}
}
- /**
- *
- * @return Vector containing selected columns as Integers
- */
- public Vector getSelected()
- {
- return selected;
- }
+ }
+ /**
+ *
+ * @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));
- }
+ /**
+ *
+ * @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;
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int columnAt(int i)
+ for (int i = 0; i < selected.size(); i++)
{
- return ((Integer) selected.elementAt(i)).intValue();
+ if (columnAt(i) > max)
+ {
+ max = columnAt(i);
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int size()
+ return max;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getMin()
+ {
+ int min = 1000000000;
+
+ for (int i = 0; i < selected.size(); i++)
{
- return selected.size();
+ if (columnAt(i) < min)
+ {
+ min = columnAt(i);
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getMax()
- {
- int max = -1;
+ return min;
+ }
- for (int i = 0; i < selected.size(); i++)
- {
- if (columnAt(i) > max)
- {
- max = columnAt(i);
- }
- }
- return max;
+ /**
+ * 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);
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getMin()
+ if(hiddenColumns!=null)
{
- int min = 1000000000;
-
- for (int i = 0; i < selected.size(); i++)
+ for(int i=0; i<hiddenColumns.size(); i++)
+ {
+ int[] region = (int[]) hiddenColumns.elementAt(i);
+ if(region[0] > start)
{
- if (columnAt(i) < min)
- {
- min = columnAt(i);
- }
+ region[0] -= change;
+ region[1] -= change;
}
-
- return min;
+ 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);
+ }
+ }
- /**
- * 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)
+ if(hiddenColumns!=null)
{
- for (int i = 0; i < size(); i++)
+ for(int i=0; i<hiddenColumns.size(); i++)
+ {
+ int[] region = (int[]) hiddenColumns.elementAt(i);
+ if(region[0] >= start)
{
- int temp = columnAt(i);
-
- if (temp >= start)
- {
- selected.setElementAt(new Integer(temp - change), i);
- }
+ region[0] -= change;
}
-
- 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;
- }
+ if (region[1]>= start) {
+ region[1] -=change;
}
- }
- /**
- * 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 (region[1]<region[0]) {
+ hiddenColumns.removeElementAt(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;
- }
- }
+ 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];
- }
+ }
+ /**
+ * 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;
+ return shiftrecord.getInverse();
}
- /**
- * 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++;
+ 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;
}
- 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 (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;
}
- 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; // 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;
+ 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;
}
- // and shift the rest.
- this.compensateForEdits(deletions);
}
+ 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)
+ }
+ /**
+ * 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)
{
- int result = column;
- 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 (result >= region[0])
{
- int[] region = (int[]) hiddenColumns.elementAt(i);
- if (result >= region[0])
- {
- result += region[1] - region[0] + 1;
- }
+ result += region[1] - region[0] + 1;
}
}
- return result;
}
+ 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)
+ /**
+ * 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 result = hiddenColumn;
- if (hiddenColumns != null)
+ int index = 0;
+ int gaps = 0;
+ do
{
- int index = 0;
- int gaps = 0;
- do
+ int[] region = (int[]) hiddenColumns.elementAt(index);
+ if (hiddenColumn > region[1])
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if (hiddenColumn > region[1])
- {
- result -= region[1]+1-region[0];
- }
- index++;
+ result -= region[1]+1-region[0];
}
- while (index < hiddenColumns.size());
-
- result -= gaps;
+ index++;
}
+ while (index < hiddenColumns.size());
- return result;
+ result -= gaps;
}
- /**
- * Use this method to determine where the next hiddenRegion starts
- */
- public int findHiddenRegionPosition(int hiddenRegion)
+ return result;
+ }
+
+ /**
+ * Use this method to determine where the next hiddenRegion starts
+ */
+ public int findHiddenRegionPosition(int hiddenRegion)
+ {
+ int result = 0;
+ if (hiddenColumns != null)
{
- int result = 0;
- if (hiddenColumns != null)
+ int index = 0;
+ int gaps = 0;
+ do
{
- int index = 0;
- int gaps = 0;
- do
+ int[] region = (int[]) hiddenColumns.elementAt(index);
+ if(hiddenRegion==0)
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if(hiddenRegion==0)
- {
- return region[0];
- }
-
- gaps += region[1] +1 - region[0];
- result = region[1] +1;
- index++;
+ return region[0];
}
- while(index < hiddenRegion+1);
- result -= gaps;
+ gaps += region[1] +1 - region[0];
+ result = region[1] +1;
+ index++;
}
+ while(index < hiddenRegion+1);
- return result;
+ 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
- */
- public int getHiddenBoundaryRight(int alPos)
+ 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)
{
- if (hiddenColumns != null)
+ int index = 0;
+ do
{
- int index = 0;
- do
- {
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if(alPos < region[0])
- return region[0];
+ int[] region = (int[]) hiddenColumns.elementAt(index);
+ if(alPos < region[0])
+ return region[0];
- index++;
- }
- while(index < hiddenColumns.size());
+ index++;
}
+ while(index < hiddenColumns.size());
+ }
- return alPos;
+ 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)
+ }
+ /**
+ * 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)
{
- if (hiddenColumns != null)
+ int index = hiddenColumns.size()-1;
+ do
{
- int index = hiddenColumns.size()-1;
- do
- {
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if(alPos > region[1])
- return region[1];
+ int[] region = (int[]) hiddenColumns.elementAt(index);
+ if(alPos > region[1])
+ return region[1];
- index--;
- }
- while(index >-1);
+ index--;
}
+ while(index >-1);
+ }
- return alPos;
+ return alPos;
- }
+ }
- public void hideSelectedColumns()
+ public void hideSelectedColumns()
+ {
+ while (size() > 0)
{
- while (size() > 0)
- {
- int column = ( (Integer) getSelected().firstElement()).intValue();
- hideColumns(column);
- }
-
+ 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;
+ public void hideColumns(int start, int end)
+ {
+ if(hiddenColumns==null)
+ hiddenColumns = new Vector();
- for (int i = 0; i < hiddenColumns.size(); i++)
+ 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 = (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;
- }
+ hiddenColumns.removeElementAt(i);
+ overlap = true;
+ break;
}
-
- if(overlap)
+ else if (end < region[0] && start < region[0])
{
- hideColumns(start, end);
+ hiddenColumns.insertElementAt(new int[]
+ {start, end}, i);
+ added = true;
+ break;
}
- 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)
+ if(overlap)
{
- // First find out range of columns to hide
- int min = col, max = col+1;
- while( contains(min) )
- { removeElement(min); min --; }
+ hideColumns(start, end);
+ }
+ else if (!added)
+ hiddenColumns.addElement(new int[] {start, end});
- while( contains(max) )
- { removeElement(max); max ++; }
+ }
- min++; max--;
+ /**
+ * 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 --; }
- hideColumns(min, max);
- }
+ while( contains(max) )
+ { removeElement(max); max ++; }
+
+ min++; max--;
+
+ hideColumns(min, max);
+ }
- public void revealAllHiddenColumns()
+ public void revealAllHiddenColumns()
+ {
+ 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);
+ for (int j = region[0]; j < region[1]+1; j++)
{
- int[] region = (int[]) hiddenColumns.elementAt(i);
- for (int j = region[0]; j < region[1]+1; j++)
- {
- addElement(j);
- }
+ addElement(j);
}
}
-
- hiddenColumns = null;
}
- public void revealHiddenColumns(int res)
+ hiddenColumns = null;
+ }
+
+ 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 = (int[])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);
- }
-
- hiddenColumns.removeElement(region);
- break;
+ addElement(j);
}
+
+ hiddenColumns.removeElement(region);
+ break;
}
- if(hiddenColumns.size()==0)
- hiddenColumns = null;
}
+ if(hiddenColumns.size()==0)
+ hiddenColumns = null;
+ }
- public boolean isVisible(int column)
+ public boolean isVisible(int column)
+ {
+ for(int i=0; i<hiddenColumns.size(); i++)
{
- for(int i=0; i<hiddenColumns.size(); i++)
+ int [] region = (int[])hiddenColumns.elementAt(i);
+ if( column >= region[0] && column <= region[1])
{
- int [] region = (int[])hiddenColumns.elementAt(i);
- if( column >= region[0] && column <= region[1])
- {
- return false;
- }
+ 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);
- }
+ 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);
- }
+ }
+ 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
*/
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;
+ int hideStart, hideEnd;
- for (int j = 0; j < regions.size(); j++)
- {
- region = (int[]) regions.elementAt(j);
- hideStart = region[0];
- hideEnd = region[1];
+ for (int j = 0; j < regions.size(); j++)
+ {
+ region = (int[]) regions.elementAt(j);
+ hideStart = region[0];
+ hideEnd = region[1];
- if(hideStart < start)
- {
- continue;
- }
+ if(hideStart < start)
+ {
+ continue;
+ }
- blockStart = Math.min(blockStart, hideEnd+1);
- blockEnd = Math.min(blockEnd, hideStart);
+ blockStart = Math.min(blockStart, hideEnd+1);
+ blockEnd = Math.min(blockEnd, hideStart);
- if(blockStart>blockEnd)
- {
- break;
- }
+ if(blockStart>blockEnd)
+ {
+ break;
+ }
- visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+ visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
- blockStart = hideEnd+1;
- blockEnd = end;
- }
+ blockStart = hideEnd+1;
+ blockEnd = end;
+ }
- if(end>blockStart)
- visibleSeq.append(seqs[i].getSequence(blockStart, end));
+ if(end>blockStart)
+ visibleSeq.append(seqs[i].getSequence(blockStart, end));
- selection[i] = visibleSeq.toString();
- }
+ selection[i] = visibleSeq.toString();
}
- else
+ }
+ else
+ {
+ for(i=0; i<iSize; i++)
{
- for(i=0; i<iSize; i++)
- {
selection[i] = seqs[i].getSequence(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
+ */
+ public int[] getVisibleContigs(int start, int end) {
+ if (hiddenColumns!=null && hiddenColumns.size()>0)
+ {
+ Vector visiblecontigs=new Vector();
+ Vector regions = getHiddenColumns();
+
+ int vstart = start;
+ int [] region;
+ int hideStart, hideEnd;
+
+ for (int j = 0; vstart<end && j < regions.size(); j++)
+ {
+ region = (int[]) regions.elementAt(j);
+ hideStart = region[0];
+ hideEnd = region[1];
+
+ if(hideEnd < vstart)
+ {
+ continue;
+ }
+ if (hideStart>vstart) {
+ visiblecontigs.addElement(new int[] {vstart, hideStart-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);
+ visiblecontigs.setElementAt(null, i);
+ vcontigs[i*2] = vc[0];
+ vcontigs[i*2+1] = vc[1];
+ }
+ visiblecontigs.clear();
+ return vcontigs;
+ }
+ else
+ {
+ return new int[] { start, end-1 };
}
-
+ }
}
git://source.jalview.org / jalview.git / commitdiff