import jalview.util.MessageManager;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collections;
import java.util.Enumeration;
import java.util.HashSet;
*/
public static AlignmentI createAlignment(CigarArray compactAlignment)
{
- throw new Error(
- MessageManager
- .getString("error.alignment_cigararray_not_implemented"));
+ throw new Error(MessageManager
+ .getString("error.alignment_cigararray_not_implemented"));
// this(compactAlignment.refCigars);
}
return AlignmentUtils.getSequencesByName(this);
}
-
@Override
public SequenceI getSequenceAt(int i)
{
return;
}
// remove annotation very quickly
- AlignmentAnnotation[] t, todelete = new AlignmentAnnotation[annotations.length], tokeep = new AlignmentAnnotation[annotations.length];
+ AlignmentAnnotation[] t,
+ todelete = new AlignmentAnnotation[annotations.length],
+ tokeep = new AlignmentAnnotation[annotations.length];
int i, p, k;
if (gp == null)
{
sqname = sq.getName();
if (sqname.equals(token) // exact match
|| (b && // allow imperfect matches - case varies
- (sqname.equalsIgnoreCase(token))))
+ (sqname.equalsIgnoreCase(token))))
{
return getSequenceAt(i);
}
return -1;
}
-
@Override
public int getHeight()
{
currentSeq = currentSeq.createDatasetSequence();
}
}
- if (seqs.contains(currentSeq))
- {
- return;
- }
+
List<SequenceI> toProcess = new ArrayList<>();
toProcess.add(currentSeq);
while (toProcess.size() > 0)
{
// use a queue ?
SequenceI curDs = toProcess.remove(0);
- if (seqs.contains(curDs))
+
+ if (!seqs.add(curDs))
{
continue;
}
- seqs.add(curDs);
// iterate over database references, making sure we add forward referenced
// sequences
if (curDs.getDBRefs() != null)
}
if (dbr.getMap().getTo().getDatasetSequence() != null)
{
- throw new Error(
- "Implementation error: Map.getTo() for dbref " + dbr
- + " from " + curDs.getName()
- + " is not a dataset sequence.");
+ throw new Error("Implementation error: Map.getTo() for dbref "
+ + dbr + " from " + curDs.getName()
+ + " is not a dataset sequence.");
}
// we recurse to add all forward references to dataset sequences via
// DBRefs/etc
current = getSequenceAt(i);
// This should really be a sequence method
ends[i * 2] = current.findIndex(current.getStart());
- ends[i * 2 + 1] = current.findIndex(current.getStart()
- + current.getLength());
+ ends[i * 2 + 1] = current
+ .findIndex(current.getStart() + current.getLength());
boolean hitres = false;
for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++)
{
{
// TODO JAL-1270 needs test coverage
// currently tested for use in jalview.gui.SequenceFetcher
- boolean samegap = toappend.getGapCharacter() == getGapCharacter();
char oldc = toappend.getGapCharacter();
+ boolean samegap = oldc == getGapCharacter();
boolean hashidden = toappend.getHiddenSequences() != null
&& toappend.getHiddenSequences().hiddenSequences != null;
// get all sequences including any hidden ones
- List<SequenceI> sqs = (hashidden) ? toappend.getHiddenSequences()
- .getFullAlignment().getSequences() : toappend.getSequences();
+ List<SequenceI> sqs = (hashidden)
+ ? toappend.getHiddenSequences().getFullAlignment()
+ .getSequences()
+ : toappend.getSequences();
if (sqs != null)
{
// avoid self append deadlock by
{
if (!samegap)
{
- char[] oldseq = addedsq.getSequence();
- for (int c = 0; c < oldseq.length; c++)
- {
- if (oldseq[c] == oldc)
- {
- oldseq[c] = gapCharacter;
- }
- }
+ addedsq.replace(oldc, gapCharacter);
}
toappendsq.add(addedsq);
}
if (ourval instanceof String)
{
// append strings
- this.setProperty(k, ((String) ourval) + "; "
- + ((String) toapprop));
+ this.setProperty(k,
+ ((String) ourval) + "; " + ((String) toapprop));
}
else
{
@Override
public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
{
- List<AlignmentAnnotation> aa = new ArrayList<>();
AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
if (alignmentAnnotation != null)
{
- for (AlignmentAnnotation a : alignmentAnnotation)
- {
- if (a.getCalcId() == calcId
- || (a.getCalcId() != null && calcId != null && a
- .getCalcId().equals(calcId)))
- {
- aa.add(a);
- }
- }
+ return AlignmentAnnotation.findAnnotation(
+ Arrays.asList(getAlignmentAnnotation()), calcId);
}
- return aa;
+ return Arrays.asList(new AlignmentAnnotation[] {});
}
@Override
public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
String calcId, String label)
{
- ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
- for (AlignmentAnnotation ann : getAlignmentAnnotation())
- {
- if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
- .equals(calcId)))
- && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq))
- && (label == null || (ann.label != null && ann.label
- .equals(label))))
- {
- aa.add(ann);
- }
- }
- return aa;
+ return AlignmentAnnotation.findAnnotations(
+ Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
}
@Override
}
@Override
- public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols)
- {
- int[] alignmentStartEnd = new int[] { 0, getWidth() - 1 };
- int startPos = alignmentStartEnd[0];
- int endPos = alignmentStartEnd[1];
-
- int[] lowestRange = new int[] { -1, -1 };
- int[] higestRange = new int[] { -1, -1 };
-
- for (int[] hiddenCol : hiddenCols)
- {
- lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
- higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
- }
-
- if (lowestRange[0] == -1 && lowestRange[1] == -1)
- {
- startPos = alignmentStartEnd[0];
- }
- else
- {
- startPos = lowestRange[1] + 1;
- }
-
- if (higestRange[0] == -1 && higestRange[1] == -1)
- {
- endPos = alignmentStartEnd[1];
- }
- else
- {
- endPos = higestRange[0] - 1;
- }
- return new int[] { startPos, endPos };
- }
-
- @Override
public void setHiddenColumns(HiddenColumns cols)
{
hiddenCols = cols;