public String printAnnotations(AlignmentAnnotation[] annotations,
List<SequenceGroup> list, Hashtable properties)
{
- return printAnnotations(annotations, list, properties, null, null, null);
+ return printAnnotations(annotations, list, properties, null, null,
+ null);
}
public final Hashtable hiddenRepSeqs;
- public ViewDef(String vname, HiddenSequences hseqs,
- HiddenColumns hcols, Hashtable hRepSeqs)
+ public ViewDef(String vname, HiddenSequences hseqs, HiddenColumns hcols,
+ Hashtable hRepSeqs)
{
this.viewname = vname;
this.hidseqs = hseqs;
* @return annotation file
*/
public String printAnnotations(AlignmentAnnotation[] annotations,
- List<SequenceGroup> list, Hashtable properties,
- HiddenColumns cs,
+ List<SequenceGroup> list, Hashtable properties, HiddenColumns cs,
AlignmentI al, ViewDef view)
{
if (view != null)
{
row = annotations[i];
- if (!row.visible
- && !row.hasScore()
- && !(row.graphGroup > -1 && graphGroupSeen
- .get(row.graphGroup)))
+ if (!row.visible && !row.hasScore() && !(row.graphGroup > -1
+ && graphGroupSeen.get(row.graphGroup)))
{
continue;
}
writeGroup_Ref(refGroup, row.groupRef);
refGroup = row.groupRef;
- boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;
+ boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText,
+ hasValues = row.hasScore, hasText = false;
// lookahead to check what the annotation row object actually contains.
for (int j = 0; row.annotations != null
&& j < row.annotations.length
if (row.annotations[j] != null)
{
hasLabels |= (row.annotations[j].displayCharacter != null
- && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter
- .equals(" "));
- hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' ');
+ && row.annotations[j].displayCharacter.length() > 0
+ && !row.annotations[j].displayCharacter.equals(" "));
+ hasGlyphs |= (row.annotations[j].secondaryStructure != 0
+ && row.annotations[j].secondaryStructure != ' ');
hasValues |= (!Float.isNaN(row.annotations[j].value)); // NaNs can't
// be
// rendered..
- hasText |= (row.annotations[j].description != null && row.annotations[j].description
- .length() > 0);
+ hasText |= (row.annotations[j].description != null
+ && row.annotations[j].description.length() > 0);
}
}
graphLine.append("\t");
graphLine.append(row.getThreshold().label);
graphLine.append("\t");
- graphLine.append(jalview.util.Format.getHexString(row
- .getThreshold().colour));
+ graphLine.append(jalview.util.Format
+ .getHexString(row.getThreshold().colour));
graphLine.append(newline);
}
if (row.annotations[j].colour != null
&& row.annotations[j].colour != java.awt.Color.black)
{
- text.append(comma
- + "["
- + jalview.util.Format
- .getHexString(row.annotations[j].colour)
- + "]");
+ text.append(comma + "[" + jalview.util.Format
+ .getHexString(row.annotations[j].colour) + "]");
comma = ",";
}
}
for (Map.Entry<Integer, String> combine_statement : graphGroup
.entrySet())
{
- Object[] seqRefAndGroup = graphGroup_refs.get(combine_statement
- .getKey());
+ Object[] seqRefAndGroup = graphGroup_refs
+ .get(combine_statement.getKey());
writeSequence_Ref(refSeq, (SequenceI) seqRefAndGroup[0]);
refSeq = (SequenceI) seqRefAndGroup[0];
if (sg.cs != null)
{
text.append("colour=");
- text.append(ColourSchemeProperty.getColourName(sg.cs
- .getColourScheme()));
+ text.append(ColourSchemeProperty
+ .getColourName(sg.cs.getColourScheme()));
text.append("\t");
if (sg.cs.getThreshold() != 0)
{
String refSeqId = null;
- public boolean annotateAlignmentView(AlignViewportI viewport,
- String file, DataSourceType protocol)
+ public boolean annotateAlignmentView(AlignViewportI viewport, String file,
+ DataSourceType protocol)
{
ColumnSelection colSel = viewport.getColumnSelection();
HiddenColumns hidden = viewport.getAlignment().getHiddenColumns();
{
hidden = new HiddenColumns();
}
- boolean rslt = readAnnotationFile(viewport.getAlignment(), hidden,
- file, protocol);
+ boolean rslt = readAnnotationFile(viewport.getAlignment(), hidden, file,
+ protocol);
if (rslt && (colSel.hasSelectedColumns() || hidden.hasHiddenColumns()))
{
viewport.setColumnSelection(colSel);
System.out.println("Problem reading annotation file: " + ex);
if (nlinesread > 0)
{
- System.out.println("Last read line " + nlinesread + ": '"
- + lastread + "' (first 80 chars) ...");
+ System.out.println("Last read line " + nlinesread + ": '" + lastread
+ + "' (first 80 chars) ...");
}
return false;
}
{
// keep a record of current state and resolve groupRef at end
combineAnnotation_calls
- .add(new Object[] { st, refSeq, groupRef });
+ .add(new Object[]
+ { st, refSeq, groupRef });
modified = true;
continue;
}
else if (token.equalsIgnoreCase(GRAPHLINE))
{
// resolve at end
- deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st,
- refSeq, groupRef });
+ deferredAnnotation_calls
+ .add(new Object[]
+ { GRAPHLINE, st, refSeq, groupRef });
modified = true;
continue;
}
if (refSeqIndex < 1)
{
refSeqIndex = 1;
- System.out
- .println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
+ System.out.println(
+ "WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
}
} catch (Exception ex)
{
{
if (hidden == null)
{
- System.err
- .println("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
+ System.err.println(
+ "Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
+ line);
}
else
(index == 0) ? null : annotations, 0, 0, graphStyle);
annotation.score = score;
- if (!overrideAutoAnnot
- && autoAnnots.containsKey(autoAnnotsKey(annotation, refSeq,
- groupRef)))
+ if (!overrideAutoAnnot && autoAnnots
+ .containsKey(autoAnnotsKey(annotation, refSeq, groupRef)))
{
// skip - we've already got an automatic annotation of this type.
continue;
// TODO: verify that undo/redo with 1:many sequence associated
// annotations can be undone correctly
AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
- annotation
- .createSequenceMapping(referedSeq, refSeqIndex, false);
+ annotation.createSequenceMapping(referedSeq, refSeqIndex,
+ false);
annotation.adjustForAlignment();
referedSeq.addAlignmentAnnotation(annotation);
al.addAnnotation(annotation);
al.setAnnotationIndex(annotation,
- al.getAlignmentAnnotation().length
- - existingAnnotations - 1);
+ al.getAlignmentAnnotation().length - existingAnnotations
+ - 1);
if (groupRef != null)
{
((Vector) groupRefRows.get(groupRef)).addElement(annotation);
// and recover our virgin copy to use again if necessary.
annotation = ann;
- } while (refSeqId != null
- && (referedSeq = al.findName(referedSeq, refSeqId, true)) != null);
+ } while (refSeqId != null && (referedSeq = al.findName(referedSeq,
+ refSeqId, true)) != null);
}
else
{
{
// TODO: specify and implement duplication of alignment annotation
// for multiple group references.
- System.err
- .println("Ignoring 1:many group reference mappings for group name '"
+ System.err.println(
+ "Ignoring 1:many group reference mappings for group name '"
+ groupRef + "'");
}
else
if (rowset != null && rowset.size() > 0)
{
AlignmentAnnotation alan = null;
- for (int elm = 0, elmSize = rowset.size(); elm < elmSize; elm++)
+ for (int elm = 0, elmSize = rowset
+ .size(); elm < elmSize; elm++)
{
alan = (AlignmentAnnotation) rowset.elementAt(elm);
alan.groupRef = theGroup;
{
if (_deferred_args[0] == GRAPHLINE)
{
- addLine(al,
- (StringTokenizer) _deferred_args[1], // st
+ addLine(al, (StringTokenizer) _deferred_args[1], // st
(SequenceI) _deferred_args[2], // refSeq
- (_deferred_args[3] == null) ? null : groupRefLookup
- .get(_deferred_args[3]) // the reference
- // group, or null
+ (_deferred_args[3] == null) ? null
+ : groupRefLookup.get(_deferred_args[3]) // the
+ // reference
+ // group, or
+ // null
);
}
}
int combinecount = 0;
for (Object[] _combine_args : combineAnnotation_calls)
{
- combineAnnotations(al,
- ++combinecount,
+ combineAnnotations(al, ++combinecount,
(StringTokenizer) _combine_args[0], // st
(SequenceI) _combine_args[1], // refSeq
- (_combine_args[2] == null) ? null : groupRefLookup
- .get(_combine_args[2]) // the reference group,
- // or null
+ (_combine_args[2] == null) ? null
+ : groupRefLookup.get(_combine_args[2]) // the reference
+ // group,
+ // or null
);
}
}
int j = string.indexOf("]");
if (i > -1 && j > -1)
{
- colour = ColorUtils.parseColourString(string.substring(i + 1,
- j));
+ colour = ColorUtils.parseColourString(string.substring(i + 1, j));
if (i > 0 && string.charAt(i - 1) == ',')
{
// clip the preceding comma as well
displayChar = token;
}
}
- if (hasSymbols
- && (token.length() == 1 && "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz"
+ if (hasSymbols && (token.length() == 1
+ && "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz"
.contains(token)))
{
// Either this character represents a helix or sheet
}
else
{
- System.err
- .println("Couldn't combine annotations. None are added to alignment yet!");
+ System.err.println(
+ "Couldn't combine annotations. None are added to alignment yet!");
}
}
}
} catch (Exception e)
{
- System.err
- .println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
+ System.err.println(
+ "Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
+ rng + "' - assuming alignment width for group.");
// assume group is full width
sg.setStartRes(0);
}
else
{
- sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);
+ sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1),
+ false);
}
}
}
}
else if (key.equalsIgnoreCase("colour"))
{
- sg.cs.setColourScheme(ColourSchemeProperty
- .getColourScheme(al, value));
+ sg.cs.setColourScheme(
+ ColourSchemeProperty.getColourScheme(al, value));
}
else if (key.equalsIgnoreCase("pidThreshold"))
{
AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation();
if (ala == null)
{
- System.err
- .print("Warning - no annotation to set below for sequence associated annotation:");
+ System.err.print(
+ "Warning - no annotation to set below for sequence associated annotation:");
}
while (st.hasMoreTokens())
{
public String printAnnotationsForView(AlignViewportI viewport)
{
- return printAnnotations(viewport.isShowAnnotation() ? viewport
- .getAlignment().getAlignmentAnnotation() : null, viewport
- .getAlignment().getGroups(), viewport.getAlignment()
- .getProperties(), viewport.getAlignment().getHiddenColumns(),
+ return printAnnotations(
+ viewport.isShowAnnotation()
+ ? viewport.getAlignment().getAlignmentAnnotation()
+ : null,
+ viewport.getAlignment().getGroups(),
+ viewport.getAlignment().getProperties(),
+ viewport.getAlignment().getHiddenColumns(),
viewport.getAlignment(), null);
}
git://source.jalview.org / jalview.git / blobdiff