/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Enumeration;
+import java.util.Collections;
import java.util.List;
import java.util.Vector;
*/
public class ColumnSelection
{
- Vector selected = new Vector();
+ /*
+ * list of selected columns (not ordered)
+ */
+ Vector<Integer> selected = new Vector<Integer>();
- // Vector of int [] {startCol, endCol}
+ /*
+ * list of hidden column [start, end] ranges; the list is maintained in
+ * ascending start column order
+ */
Vector<int[]> hiddenColumns;
/**
}
/**
- * removes col from selection
+ * Removes value 'col' from the selection (not the col'th item)
*
* @param col
* index of column to be removed
if (selected.contains(colInt))
{
+ // if this ever changes to List.remove(), ensure Integer not int argument
+ // as List.remove(int i) removes the i'th item which is wrong
selected.removeElement(colInt);
}
}
}
/**
- *
- * @return Vector containing selected columns as Integers
+ * Returns a list of selected columns. The list contains no duplicates but is
+ * not necessarily ordered.
*/
- public Vector getSelected()
+ public List<Integer> getSelected()
{
return selected;
}
}
/**
- * Column number at position i in selection
- *
- * @param i
- * index into selected columns
- *
- * @return column number in alignment
- */
- public int columnAt(int i)
- {
- return ((Integer) selected.elementAt(i)).intValue();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Answers true if no columns are selected, else false
*/
- public int size()
+ public boolean isEmpty()
{
- return selected.size();
+ return selected == null || selected.isEmpty();
}
/**
{
int max = -1;
- for (int i = 0; i < selected.size(); i++)
+ for (int sel : getSelected())
{
- if (columnAt(i) > max)
+ if (sel > max)
{
- max = columnAt(i);
+ max = sel;
}
}
{
int min = 1000000000;
- for (int i = 0; i < selected.size(); i++)
+ for (int sel : getSelected())
{
- if (columnAt(i) < min)
+ if (sel < min)
{
- min = columnAt(i);
+ min = sel;
}
}
public List<int[]> compensateForEdit(int start, int change)
{
List<int[]> deletedHiddenColumns = null;
- for (int i = 0; i < size(); i++)
+ for (int i = 0; i < selected.size(); i++)
{
- int temp = columnAt(i);
+ int temp = selected.get(i);
if (temp >= start)
{
+ // if this ever changes to List.set(), swap parameter order!!
selected.setElementAt(new Integer(temp - change), i);
}
}
*/
private void compensateForDelEdits(int start, int change)
{
- for (int i = 0; i < size(); i++)
+ for (int i = 0; i < selected.size(); i++)
{
- int temp = columnAt(i);
+ int temp = selected.get(i);
if (temp >= start)
{
+ // if this ever changes to List.set(), must swap parameter order!!!
selected.setElementAt(new Integer(temp - change), i);
}
}
{
if (shiftrecord != null)
{
- Vector shifts = shiftrecord.shifts;
+ final List<int[]> shifts = shiftrecord.getShifts();
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);
+ int[] sh = shifts.get(i);
// compensateForEdit(shifted+sh[0], sh[1]);
compensateForDelEdits(shifted + sh[0], sh[1]);
shifted -= sh[1];
* removes intersection of position,length ranges in deletions from the
* start,end regions marked in intervals.
*
- * @param deletions
+ * @param shifts
* @param intervals
* @return
*/
- private boolean pruneIntervalVector(Vector deletions, Vector intervals)
+ private boolean pruneIntervalVector(final List<int[]> shifts,
+ Vector<int[]> 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);
+ int i = 0, j = intervals.size() - 1, s = 0, t = shifts.size() - 1;
+ int hr[] = intervals.elementAt(i);
+ int sr[] = shifts.get(s);
while (i <= j && s <= t)
{
boolean trailinghn = hr[1] >= sr[0];
{
if (i < j)
{
- hr = (int[]) intervals.elementAt(++i);
+ hr = intervals.elementAt(++i);
}
else
{
{ // leadinghc disjoint or not a deletion
if (s < t)
{
- sr = (int[]) deletions.elementAt(++s);
+ sr = shifts.get(++s);
}
else
{
j--;
if (i <= j)
{
- hr = (int[]) intervals.elementAt(i);
+ hr = intervals.elementAt(i);
}
continue;
}
// sr contained in hr
if (s < t)
{
- sr = (int[]) deletions.elementAt(++s);
+ sr = shifts.get(++s);
}
else
{
// operations.
}
- private boolean pruneColumnList(Vector deletion, Vector list)
+ private boolean pruneColumnList(final List<int[]> shifts,
+ Vector<Integer> list)
{
- int s = 0, t = deletion.size();
- int[] sr = (int[]) list.elementAt(s++);
+ int s = 0, t = shifts.size();
+ int[] sr = shifts.get(s++);
boolean pruned = false;
int i = 0, j = list.size();
while (i < j && s <= t)
{
- int c = ((Integer) list.elementAt(i++)).intValue();
+ int c = list.elementAt(i++).intValue();
if (sr[0] <= c)
{
if (sr[1] + sr[0] >= c)
{
if (s < t)
{
- sr = (int[]) deletion.elementAt(s);
+ sr = shifts.get(s);
}
s++;
}
{
if (deletions != null)
{
- Vector shifts = deletions.shifts;
+ final List<int[]> shifts = deletions.getShifts();
if (shifts != null && shifts.size() > 0)
{
// delete any intervals intersecting.
/**
* This Method is used to return all the HiddenColumn regions
+ *
* @return empty list or List of hidden column intervals
*/
public List<int[]> getHiddenColumns()
{
- return hiddenColumns == null ? Arrays.asList(new int[]
- {}) : hiddenColumns;
+ return hiddenColumns == null ? Collections.<int[]> emptyList()
+ : hiddenColumns;
}
/**
public void hideSelectedColumns()
{
- while (size() > 0)
+ while (!selected.isEmpty())
{
- int column = ((Integer) getSelected().firstElement()).intValue();
+ int column = selected.get(0).intValue();
hideColumns(column);
}
}
+ /**
+ * Adds the specified column range to the hidden columns
+ *
+ * @param start
+ * @param end
+ */
public void hideColumns(int start, int end)
{
if (hiddenColumns == null)
{
- hiddenColumns = new Vector();
+ hiddenColumns = new Vector<int[]>();
}
- boolean added = false;
- boolean overlap = false;
-
+ /*
+ * traverse existing hidden ranges and insert / amend / append as
+ * appropriate
+ */
for (int i = 0; i < hiddenColumns.size(); i++)
{
int[] region = hiddenColumns.elementAt(i);
- if (start <= region[1] && end >= region[0])
+
+ if (end < region[0] - 1)
{
- hiddenColumns.removeElementAt(i);
- overlap = true;
- break;
+ /*
+ * insert discontiguous preceding range
+ */
+ hiddenColumns.insertElementAt(new int[] { start, end }, i);
+ return;
}
- else if (end < region[0] && start < region[0])
+
+ if (end <= region[1])
{
- hiddenColumns.insertElementAt(new int[]
- { start, end }, i);
- added = true;
- break;
+ /*
+ * new range overlaps existing, or is contiguous preceding it - adjust
+ * start column
+ */
+ region[0] = Math.min(region[0], start);
+ return;
}
- }
- if (overlap)
- {
- hideColumns(start, end);
- }
- else if (!added)
- {
- hiddenColumns.addElement(new int[]
- { start, end });
+ if (start <= region[1] + 1)
+ {
+ /*
+ * new range overlaps existing, or is contiguous following it - adjust
+ * start and end columns
+ */
+ region[0] = Math.min(region[0], start);
+ region[1] = Math.max(region[1], end);
+ return;
+ }
}
+ /*
+ * remaining case is that the new range follows everything else
+ */
+ hiddenColumns.addElement(new int[] { start, end });
}
/**
- * This method will find a range of selected columns around the column
- * specified
+ * Hides the specified column and any adjacent selected columns
*
* @param res
* int
*/
public void hideColumns(int col)
{
- // First find out range of columns to hide
- int min = col, max = col + 1;
+ /*
+ * deselect column (whether selected or not!)
+ */
+ removeElement(col);
+
+ /*
+ * find adjacent selected columns
+ */
+ int min = col - 1, max = col + 1;
while (contains(min))
{
removeElement(min);
max++;
}
+ /*
+ * min, max are now the closest unselected columns
+ */
min++;
max--;
if (min > max)
hideColumns(min, max);
}
+ /**
+ * Unhides, and adds to the selection list, all hidden columns
+ */
public void revealAllHiddenColumns()
{
if (hiddenColumns != null)
hiddenColumns = null;
}
- public void revealHiddenColumns(int res)
+ /**
+ * Reveals, and marks as selected, the hidden column range with the given
+ * start column
+ *
+ * @param start
+ */
+ public void revealHiddenColumns(int start)
{
for (int i = 0; i < hiddenColumns.size(); i++)
{
int[] region = hiddenColumns.elementAt(i);
- if (res == region[0])
+ if (start == region[0])
{
for (int j = region[0]; j < region[1] + 1; j++)
{
{
if (hiddenColumns != null)
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ for (int[] region : hiddenColumns)
{
- int[] region = hiddenColumns.elementAt(i);
if (column >= region[0] && column <= region[1])
{
return false;
{
if (copy.selected != null)
{
- selected = new Vector();
+ selected = new Vector<Integer>();
for (int i = 0, j = copy.selected.size(); i < j; i++)
{
selected.addElement(copy.selected.elementAt(i));
}
if (copy.hiddenColumns != null)
{
- hiddenColumns = new Vector(copy.hiddenColumns.size());
+ hiddenColumns = new Vector<int[]>(copy.hiddenColumns.size());
for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
{
int[] rh, cp;
{
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
- Vector visiblecontigs = new Vector();
+ List<int[]> visiblecontigs = new ArrayList<int[]>();
List<int[]> regions = getHiddenColumns();
int vstart = start;
}
if (hideStart > vstart)
{
- visiblecontigs.addElement(new int[]
- { vstart, hideStart - 1 });
+ visiblecontigs.add(new int[] { vstart, hideStart - 1 });
}
vstart = hideEnd + 1;
}
if (vstart < end)
{
- visiblecontigs.addElement(new int[]
- { vstart, end - 1 });
+ visiblecontigs.add(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);
+ int[] vc = visiblecontigs.get(i);
+ visiblecontigs.set(i, null);
vcontigs[i * 2] = vc[0];
vcontigs[i * 2 + 1] = vc[1];
}
- visiblecontigs.removeAllElements();
+ visiblecontigs.clear();
return vcontigs;
}
else
{
- return new int[]
- { start, end - 1 };
+ return new int[] { start, end - 1 };
}
}
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
// then mangle the alignmentAnnotation annotation array
- Vector annels = new Vector();
+ Vector<Annotation[]> annels = new Vector<Annotation[]>();
Annotation[] els = null;
List<int[]> regions = getHiddenColumns();
int blockStart = start, blockEnd = end;
{
return;
}
- Enumeration e = annels.elements();
+
alignmentAnnotation.annotations = new Annotation[w];
w = 0;
- while (e.hasMoreElements())
+
+ for (Annotation[] chnk : annels)
{
- Annotation[] chnk = (Annotation[]) e.nextElement();
System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
chnk.length);
w += chnk.length;
*/
public void addElementsFrom(ColumnSelection colsel)
{
- if (colsel != null && colsel.size() > 0)
+ if (colsel != null && !colsel.isEmpty())
{
- Enumeration e = colsel.getSelected().elements();
- while (e.hasMoreElements())
+ for (Integer col : colsel.getSelected())
{
- Object eo = e.nextElement();
- if (hiddenColumns != null && isVisible(((Integer) eo).intValue()))
+ if (hiddenColumns != null && isVisible(col.intValue()))
{
- if (!selected.contains(eo))
+ if (!selected.contains(col))
{
- selected.addElement(eo);
+ selected.addElement(col);
}
}
}
*/
public void setElementsFrom(ColumnSelection colsel)
{
- selected = new Vector();
+ selected = new Vector<Integer>();
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())
+ for (Integer col : colsel.getSelected())
{
- selected.addElement(en.nextElement());
+ addElement(col);
}
}
}
* profileseq marked as hidden.
*/
public static ColumnSelection propagateInsertions(SequenceI profileseq,
- Alignment al, AlignmentView input)
+ AlignmentI al, AlignmentView input)
{
int profsqpos = 0;
{
return hiddenColumns != null && hiddenColumns.size() > 0;
}
-
+
/**
*
* @return true if there are more than one set of columns hidden
hideColumns(r[0], r[1]);
}
}
-
+
public boolean filterAnnotations(Annotation[] annotations,
AnnotationFilterParameter filterParams)
{
git://source.jalview.org / jalview.git / blobdiff