package jalview.datamodel;
import jalview.analysis.AlignSeq;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
import jalview.util.StringUtils;
import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
+import com.stevesoft.pat.Regex;
+
import fr.orsay.lri.varna.models.rna.RNA;
/**
checkValidRange();
}
- com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
- "[/][0-9]{1,}[-][0-9]{1,}$");
+ Regex limitrx = new Regex("[/][0-9]{1,}[-][0-9]{1,}$");
- com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex("[0-9]{1,}$");
+ Regex endrx = new Regex("[0-9]{1,}$");
void parseId()
{
int endRes = 0;
for (int j = 0; j < sequence.length; j++)
{
- if (!jalview.util.Comparison.isGap(sequence[j]))
+ if (!Comparison.isGap(sequence[j]))
{
endRes++;
}
// Rely on end being at least as long as the length of the sequence.
while ((i < sequence.length) && (j <= end) && (j <= pos))
{
- if (!jalview.util.Comparison.isGap(sequence[i]))
+ if (!Comparison.isGap(sequence[i]))
{
j++;
}
int seqlen = sequence.length;
while ((j < i) && (j < seqlen))
{
- if (!jalview.util.Comparison.isGap(sequence[j]))
+ if (!Comparison.isGap(sequence[j]))
{
pos++;
}
*/
public int[] gapMap()
{
- String seq = jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, new String(sequence));
+ String seq = AlignSeq.extractGaps(
+ Comparison.GapChars, new String(sequence));
int[] map = new int[seq.length()];
int j = 0;
int p = 0;
while (j < sequence.length)
{
- if (!jalview.util.Comparison.isGap(sequence[j]))
+ if (!Comparison.isGap(sequence[j]))
{
map[p++] = j;
}
while ((j < seqlen))
{
map[j] = pos;
- if (!jalview.util.Comparison.isGap(sequence[j]))
+ if (!Comparison.isGap(sequence[j]))
{
pos++;
}
int seqlen = sequence.length;
while ((j < seqlen))
{
- if (jalview.util.Comparison.isGap(sequence[j]))
+ if (Comparison.isGap(sequence[j]))
{
if (lastj == -1)
{
boolean ecalc = false, scalc = false;
for (int s = i; s < j; s++)
{
- if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+ if (ResidueProperties.aaIndex[sequence[s]] != 23)
{
if (createNewDs)
{
}
for (int i = 0; i < sequence.length; i++)
{
- if (jalview.util.Comparison.isGap(sequence[i]))
+ if (Comparison.isGap(sequence[i]))
{
return false;
}
// Create a new, valid dataset sequence
SequenceI ds = seq;
ds.setSequence(AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, new String(sequence)));
+ Comparison.GapChars, new String(sequence)));
setDatasetSequence(ds);
ds.setSequenceFeatures(getSequenceFeatures());
seq = this; // and return this sequence as the derived sequence.
if (datasetSequence == null)
{
datasetSequence = new Sequence(getName(), AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, getSequenceAsString()),
+ Comparison.GapChars, getSequenceAsString()),
getStart(), getEnd());
datasetSequence.setSequenceFeatures(getSequenceFeatures());
datasetSequence.setDescription(getDescription());