/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
* propagate shift in alignment columns to column selection
*
* @param start beginning of edit
- * @param change shift in edit (-ve or +ve number of columns)
+ * @param left shift in edit (+ve for removal, or -ve for inserts)
*/
public void compensateForEdit(int start, int 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(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.get(i);
- compensateForEdit(sh[0], sh[1]);
+ 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
if (copy.selected!=null) {
selected = new Vector();
for (int i=0,j=copy.selected.size(); i<j; i++) {
- selected.set(i, ((Integer) copy.selected.get(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.get(i);
+ rh = (int[])copy.hiddenColumns.elementAt(i);
if (rh!=null) {
cp = new int[rh.length];
System.arraycopy(rh, 0, cp, 0, rh.length);
- hiddenColumns.set(i, cp);
+ hiddenColumns.setElementAt(cp, i);
}
}
}
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;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff