boolean validCharWidth;
int wrappedWidth;
Font font;
+ boolean seqNameItalics;
AlignmentI alignment;
ColumnSelection colSel = new ColumnSelection();
int threshold;
boolean rightAlignIds = false;
+ Hashtable hiddenRepSequences;
+
/**
* Creates a new AlignViewport object.
String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
String fontSize = Cache.getDefault("FONT_SIZE", "10");
+ seqNameItalics = Cache.getDefault("ID_ITALICS", true);
+
int style = 0;
if (fontStyle.equals("bold"))
11f,
AlignmentAnnotation.BAR_GRAPH);
conservation.hasText = true;
+ conservation.autoCalculated = true;
if (Cache.getDefault("SHOW_CONSERVATION", true))
11f,
AlignmentAnnotation.BAR_GRAPH);
quality.hasText = true;
+ quality.autoCalculated = true;
alignment.addAnnotation(quality);
}
new Annotation[1], 0f, 100f,
AlignmentAnnotation.BAR_GRAPH);
consensus.hasText = true;
+ consensus.autoCalculated = true;
if (Cache.getDefault("SHOW_IDENTITY", true))
{
cons.findQuality();
}
- String sequence = cons.getConsSequence().getSequence();
+ char [] sequence = cons.getConsSequence().getSequence();
float minR;
float minG;
float minB;
{
float value = 0;
- c = sequence.charAt(i);
+ c = sequence[i];
if (Character.isDigit(c))
value = (int) (c - '0');
hasHiddenColumns = true;
}
+ public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+ {
+ int sSize = sg.getSize();
+ if(sSize < 2)
+ return;
+
+ if(hiddenRepSequences==null)
+ hiddenRepSequences = new Hashtable();
+
+ hiddenRepSequences.put(repSequence, sg);
+
+ //Hide all sequences except the repSequence
+ SequenceI [] seqs = new SequenceI[sSize-1];
+ int index = 0;
+ for(int i=0; i<sSize; i++)
+ if(sg.getSequenceAt(i)!=repSequence)
+ {
+ if(index==sSize-1)
+ return;
+
+ seqs[index++] = sg.getSequenceAt(i);
+ }
+
+ hideSequence(seqs);
+
+ }
+
public void hideAllSelectedSeqs()
{
if (selectionGroup == null)
if(seq!=null)
{
for (int i = 0; i < seq.length; i++)
+ {
alignment.getHiddenSequences().hideSequence(seq[i]);
-
+ }
hasHiddenRows = true;
firePropertyChange("alignment", null, alignment.getSequences());
}
public void showSequence(int index)
{
- Vector tmp = alignment.getHiddenSequences().showSequence(index);
+ Vector tmp = alignment.getHiddenSequences().showSequence(index
+ , hiddenRepSequences);
if(tmp.size()>0)
{
if(selectionGroup==null)
selectionGroup = new SequenceGroup();
selectionGroup.setEndRes(alignment.getWidth()-1);
}
- Vector tmp = alignment.getHiddenSequences().showAll();
+ Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
for(int t=0; t<tmp.size(); t++)
{
selectionGroup.addSequence(
}
firePropertyChange("alignment", null, alignment.getSequences());
hasHiddenRows = false;
+ hiddenRepSequences = null;
}
}
+
+
public void invertColumnSelection()
{
for(int i=0; i<alignment.getWidth(); i++)
colSel.addElement(i);
}
}
-
}
-
}
public int adjustForHiddenSeqs(int alignmentIndex)
int start = 0, end = 0;
if(selectedRegionOnly && selectionGroup!=null)
{
- iSize = selectionGroup.getSize(false);
+ iSize = selectionGroup.getSize();
seqs = selectionGroup.getSequencesInOrder(alignment);
start = selectionGroup.getStartRes();
end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
int start = 0, end = 0;
if(selectedRegionOnly && selectionGroup!=null)
{
- iSize = selectionGroup.getSize(false);
+ iSize = selectionGroup.getSize();
seqs = selectionGroup.getSequencesInOrder(alignment);
start = selectionGroup.getStartRes();
end = selectionGroup.getEndRes()+1;
} else {
for(i=0; i<iSize; i++)
{
- selection[i] = seqs[i].getSequence(start, end);
+ selection[i] = seqs[i].getSequenceAsString(start, end);
}
}
resetAllColourSchemes();
- alignment.adjustSequenceAnnotations();
+ // alignment.adjustSequenceAnnotations();
}
if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
{
((ClustalxColourScheme)sg.cs).resetClustalX(
- sg.getSequences(true), sg.getWidth());
+ sg.getSequences(hiddenRepSequences), sg.getWidth());
}
sg.recalcConservation();
}