import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.analysis.WUSSParseException;
+import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
* Updates the _rnasecstr field Determines the positions that base pair and
* the positions of helices based on secondary structure from a Stockholm file
*
- * @param RNAannot
+ * @param rnaAnnotation
*/
- private void _updateRnaSecStr(CharSequence RNAannot)
+ private void _updateRnaSecStr(CharSequence rnaAnnotation)
{
try
{
- bps = Rna.getModeleBP(RNAannot);
- _rnasecstr = Rna.getBasePairs(bps);
+ _rnasecstr = Rna.getHelixMap(rnaAnnotation);
invalidrnastruc = -1;
} catch (WUSSParseException px)
{
{
return;
}
- Rna.HelixMap(_rnasecstr);
- // setRNAStruc(RNAannot);
if (_rnasecstr != null && _rnasecstr.length > 0)
{
private boolean isrna;
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#finalize()
- */
- @Override
- protected void finalize() throws Throwable
- {
- sequenceRef = null;
- groupRef = null;
- super.finalize();
- }
-
public static int getGraphValueFromString(String string)
{
if (string.equalsIgnoreCase("BAR_GRAPH"))
}
}
- // JBPNote: what does this do ?
- public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
- {
- bps = Rna.getModeleBP(RNAannot);
- }
-
/**
* Creates a new AlignmentAnnotation object.
*
firstChar = annotations[i].displayCharacter.charAt(0);
// check to see if it looks like a sequence or is secondary structure
// labelling.
- if (annotations[i].secondaryStructure != ' '
- && !hasIcons
- &&
- // Uncomment to only catch case where
- // displayCharacter==secondary
- // Structure
- // to correctly redisplay SS annotation imported from Stockholm,
- // exported to JalviewXML and read back in again.
- // &&
- // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
- firstChar != ' '
- && firstChar != '$'
- && firstChar != 0xCE
- && firstChar != '('
- && firstChar != '['
- && firstChar != '>'
- && firstChar != '{'
- && firstChar != 'A'
- && firstChar != 'B'
- && firstChar != 'C'
- && firstChar != 'D'
- && firstChar != 'E'
- && firstChar != 'F'
- && firstChar != 'G'
- && firstChar != 'H'
- && firstChar != 'I'
- && firstChar != 'J'
- && firstChar != 'K'
- && firstChar != 'L'
- && firstChar != 'M'
- && firstChar != 'N'
- && firstChar != 'O'
- && firstChar != 'P'
- && firstChar != 'Q'
- && firstChar != 'R'
- && firstChar != 'S'
- && firstChar != 'T'
- && firstChar != 'U'
- && firstChar != 'V'
- && firstChar != 'W'
- && firstChar != 'X'
- && firstChar != 'Y'
- && firstChar != 'Z'
+ if (annotations[i].secondaryStructure != ' ' && !hasIcons &&
+ // Uncomment to only catch case where
+ // displayCharacter==secondary
+ // Structure
+ // to correctly redisplay SS annotation imported from Stockholm,
+ // exported to JalviewXML and read back in again.
+ // &&
+ // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
+ firstChar != ' ' && firstChar != '$' && firstChar != 0xCE
+ && firstChar != '(' && firstChar != '[' && firstChar != '>'
+ && firstChar != '{' && firstChar != 'A' && firstChar != 'B'
+ && firstChar != 'C' && firstChar != 'D' && firstChar != 'E'
+ && firstChar != 'F' && firstChar != 'G' && firstChar != 'H'
+ && firstChar != 'I' && firstChar != 'J' && firstChar != 'K'
+ && firstChar != 'L' && firstChar != 'M' && firstChar != 'N'
+ && firstChar != 'O' && firstChar != 'P' && firstChar != 'Q'
+ && firstChar != 'R' && firstChar != 'S' && firstChar != 'T'
+ && firstChar != 'U' && firstChar != 'V' && firstChar != 'W'
+ && firstChar != 'X' && firstChar != 'Y' && firstChar != 'Z'
&& firstChar != '-'
&& firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
{
{
return ((index + offset < 0) || (index + offset) >= max
|| annotations[index + offset] == null
- || (annotations[index + offset].secondaryStructure <= ' ') ? ' '
- : annotations[index + offset].displayCharacter == null
- || annotations[index + offset].displayCharacter
- .length() == 0 ? annotations[index + offset].secondaryStructure
- : annotations[index + offset].displayCharacter
- .charAt(0));
+ || (annotations[index + offset].secondaryStructure <= ' ')
+ ? ' '
+ : annotations[index + offset].displayCharacter == null
+ || annotations[index
+ + offset].displayCharacter
+ .length() == 0
+ ? annotations[index
+ + offset].secondaryStructure
+ : annotations[index
+ + offset].displayCharacter
+ .charAt(0));
}
@Override
for (int i = offset; i < mx; i++)
{
- string[i] = (annotations[i] == null || (annotations[i].secondaryStructure <= 32)) ? ' '
- : (annotations[i].displayCharacter == null
- || annotations[i].displayCharacter.length() == 0 ? annotations[i].secondaryStructure
- : annotations[i].displayCharacter.charAt(0));
+ string[i] = (annotations[i] == null
+ || (annotations[i].secondaryStructure <= 32))
+ ? ' '
+ : (annotations[i].displayCharacter == null
+ || annotations[i].displayCharacter
+ .length() == 0
+ ? annotations[i].secondaryStructure
+ : annotations[i].displayCharacter
+ .charAt(0));
}
return new String(string);
}
this.calcId = annotation.calcId;
if (annotation.properties != null)
{
- properties = new HashMap<String, String>();
+ properties = new HashMap<>();
for (Map.Entry<String, String> val : annotation.properties.entrySet())
{
properties.put(val.getKey(), val.getValue());
if (annotation.sequenceMapping != null)
{
Integer p = null;
- sequenceMapping = new HashMap<Integer, Annotation>();
+ sequenceMapping = new HashMap<>();
Iterator<Integer> pos = annotation.sequenceMapping.keySet()
.iterator();
while (pos.hasNext())
Annotation[] temp = new Annotation[endRes - startRes + 1];
if (startRes < annotations.length)
{
- System.arraycopy(annotations, startRes, temp, 0, endRes - startRes
- + 1);
+ System.arraycopy(annotations, startRes, temp, 0,
+ endRes - startRes + 1);
}
if (sequenceRef != null)
{
int epos = sequenceRef.findPosition(endRes);
if (sequenceMapping != null)
{
- Map<Integer, Annotation> newmapping = new HashMap<Integer, Annotation>();
+ Map<Integer, Annotation> newmapping = new HashMap<>();
Iterator<Integer> e = sequenceMapping.keySet().iterator();
while (e.hasNext())
{
{
return;
}
- sequenceMapping = new HashMap<Integer, Annotation>();
+ sequenceMapping = new HashMap<>();
int seqPos;
{
if (i + 1 < iSize)
{
- System.arraycopy(annotations, i + 1, annotations, i, iSize - i
- - 1);
+ System.arraycopy(annotations, i + 1, annotations, i,
+ iSize - i - 1);
}
iSize--;
}
{
if (sequenceRef != null)
{
- boolean rIsDs = sequenceRef.getDatasetSequence() == null, tIsDs = sequenceI
- .getDatasetSequence() == null;
+ boolean rIsDs = sequenceRef.getDatasetSequence() == null,
+ tIsDs = sequenceI.getDatasetSequence() == null;
if (sequenceRef != sequenceI
- && (rIsDs && !tIsDs && sequenceRef != sequenceI
- .getDatasetSequence())
- && (!rIsDs && tIsDs && sequenceRef.getDatasetSequence() != sequenceI)
- && (!rIsDs && !tIsDs && sequenceRef.getDatasetSequence() != sequenceI
- .getDatasetSequence())
+ && (rIsDs && !tIsDs
+ && sequenceRef != sequenceI.getDatasetSequence())
+ && (!rIsDs && tIsDs
+ && sequenceRef.getDatasetSequence() != sequenceI)
+ && (!rIsDs && !tIsDs
+ && sequenceRef.getDatasetSequence() != sequenceI
+ .getDatasetSequence())
&& !sequenceRef.equals(sequenceI))
{
// if sequenceRef isn't intersecting with sequenceI
{
return;
}
- hidden.makeVisibleAnnotation(this);
+ makeVisibleAnnotation(hidden);
}
public void setPadGaps(boolean padgaps, char gapchar)
/**
* properties associated with the calcId
*/
- protected Map<String, String> properties = new HashMap<String, String>();
+ protected Map<String, String> properties = new HashMap<>();
/**
* base colour for line graphs. If null, will be set automatically by
throw new Error(
"liftOver currently not implemented for transfer of annotation between different types of seqeunce");
}
- boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == sq || sp2sq
- .getTo() == sq.getDatasetSequence()) : false;
+ boolean mapIsTo = (sp2sq != null)
+ ? (sp2sq.getTo() == sq
+ || sp2sq.getTo() == sq.getDatasetSequence())
+ : false;
// TODO build a better annotation element map and get rid of annotations[]
- Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
+ Map<Integer, Annotation> mapForsq = new HashMap<>();
if (sequenceMapping != null)
{
if (sp2sq != null)
{
for (Entry<Integer, Annotation> ie : sequenceMapping.entrySet())
{
- Integer mpos = Integer.valueOf(mapIsTo ? sp2sq
- .getMappedPosition(ie.getKey()) : sp2sq.getPosition(ie
- .getKey()));
+ Integer mpos = Integer
+ .valueOf(mapIsTo ? sp2sq.getMappedPosition(ie.getKey())
+ : sp2sq.getPosition(ie.getKey()));
if (mpos >= sq.getStart() && mpos <= sq.getEnd())
{
mapForsq.put(mpos, ie.getValue());
if (mapping != null)
{
Map<Integer, Annotation> old = sequenceMapping;
- Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
+ Map<Integer, Annotation> remap = new HashMap<>();
int index = -1;
for (int mp[] : mapping.values())
{
{
if (properties == null)
{
- properties = new HashMap<String, String>();
+ properties = new HashMap<>();
}
properties.put(property, value);
}
* up to and excluding the target column; if the count is less
* than 1, the opening bracket is unmatched, so return its match
*/
- String closer = String.valueOf(Rna
- .getMatchingClosingParenthesis(symbol));
+ String closer = String
+ .valueOf(Rna.getMatchingClosingParenthesis(symbol));
String opener = String.valueOf(symbol);
int count = 0;
for (int j = col + 1; j < column; j++)
{
return graphMin < graphMax;
}
+
+ /**
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
+ *
+ * @param hiddenColumns
+ * the set of hidden columns
+ */
+ public void makeVisibleAnnotation(HiddenColumns hiddenColumns)
+ {
+ if (annotations != null)
+ {
+ makeVisibleAnnotation(0, annotations.length, hiddenColumns);
+ }
+ }
+
+ /**
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
+ *
+ * @param start
+ * remove any annotation to the right of this column
+ * @param end
+ * remove any annotation to the left of this column
+ * @param hiddenColumns
+ * the set of hidden columns
+ */
+ public void makeVisibleAnnotation(int start, int end,
+ HiddenColumns hiddenColumns)
+ {
+ if (annotations != null)
+ {
+ if (hiddenColumns.hasHiddenColumns())
+ {
+ removeHiddenAnnotation(start, end, hiddenColumns);
+ }
+ else
+ {
+ restrict(start, end);
+ }
+ }
+ }
+
+ /**
+ * The actual implementation of deleting hidden annotation columns
+ *
+ * @param start
+ * remove any annotation to the right of this column
+ * @param end
+ * remove any annotation to the left of this column
+ * @param hiddenColumns
+ * the set of hidden columns
+ */
+ private void removeHiddenAnnotation(int start, int end,
+ HiddenColumns hiddenColumns)
+ {
+ // mangle the alignmentAnnotation annotation array
+ ArrayList<Annotation[]> annels = new ArrayList<>();
+ Annotation[] els = null;
+
+ int w = 0;
+
+ Iterator<int[]> blocks = hiddenColumns.getVisContigsIterator(start,
+ end + 1, false);
+
+ int copylength;
+ int annotationLength;
+ while (blocks.hasNext())
+ {
+ int[] block = blocks.next();
+ annotationLength = block[1] - block[0] + 1;
+
+ if (blocks.hasNext())
+ {
+ // copy just the visible segment of the annotation row
+ copylength = annotationLength;
+ }
+ else
+ {
+ if (annotationLength + block[0] <= annotations.length)
+ {
+ // copy just the visible segment of the annotation row
+ copylength = annotationLength;
+ }
+ else
+ {
+ // copy to the end of the annotation row
+ copylength = annotations.length - block[0];
+ }
+ }
+
+ els = new Annotation[annotationLength];
+ annels.add(els);
+ System.arraycopy(annotations, block[0], els, 0, copylength);
+ w += annotationLength;
+ }
+
+ if (w != 0)
+ {
+ annotations = new Annotation[w];
+
+ w = 0;
+ for (Annotation[] chnk : annels)
+ {
+ System.arraycopy(chnk, 0, annotations, w, chnk.length);
+ w += chnk.length;
+ }
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff