import jalview.util.Comparison;
import jalview.util.MapList;
import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
import jalview.workers.ComplementConsensusThread;
public abstract class AlignmentViewport implements AlignViewportI,
CommandListener, VamsasSource
{
+ protected ViewportRanges ranges;
+
protected ViewStyleI viewStyle = new ViewStyle();
/**
public void updateConsensus(final AlignmentViewPanel ap)
{
// see note in mantis : issue number 8585
- if ((consensus == null || gapcounts == null) || !autoCalculateConsensus)
+ if (consensus == null || !autoCalculateConsensus)
{
return;
}
protected boolean showConsensus = true;
+ protected boolean showOccupancy = true;
+
private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
protected SequenceAnnotationOrder sortAnnotationsBy = null;
*/
private boolean followHighlight = true;
- // TODO private with getters and setters?
- public int startRes;
-
- public int endRes;
-
- public int startSeq;
-
- public int endSeq;
-
/**
* Property change listener for changes in alignment
*
{
initRNAStructure();
}
- consensus = new AlignmentAnnotation("Consensus", "PID",
+ consensus = new AlignmentAnnotation("Consensus",
+ MessageManager.getString("label.consensus_descr"),
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
initConsensus(consensus);
- gapcounts = new AlignmentAnnotation("Occupancy",
- "Number of aligned positions",
- new Annotation[1], 0f, alignment.getHeight(),
- AlignmentAnnotation.BAR_GRAPH);
- initGapCounts(gapcounts);
+ initGapCounts();
initComplementConsensus();
}
}
/**
- * If this is a protein alignment and there are mappings to cDNA, add the cDNA
- * consensus annotation.
+ * If this is a protein alignment and there are mappings to cDNA, adds the
+ * cDNA consensus annotation and returns true, else returns false.
*/
- public void initComplementConsensus()
+ public boolean initComplementConsensus()
{
if (!alignment.isNucleotide())
{
if (doConsensus)
{
complementConsensus = new AlignmentAnnotation("cDNA Consensus",
- "PID for cDNA", new Annotation[1], 0f, 100f,
+ MessageManager
+ .getString("label.complement_consensus_descr"),
+ new Annotation[1], 0f, 100f,
AlignmentAnnotation.BAR_GRAPH);
initConsensus(complementConsensus);
+ return true;
}
}
}
+ return false;
}
private void initConsensus(AlignmentAnnotation aa)
// these should be extracted from the view model - style and settings for
// derived annotation
- private void initGapCounts(AlignmentAnnotation counts)
+ private void initGapCounts()
{
- counts.hasText = false;
- counts.autoCalculated = true;
- counts.graph = AlignmentAnnotation.BAR_GRAPH;
-
- if (showConsensus)
+ if (showOccupancy)
{
- alignment.addAnnotation(counts);
+ gapcounts = new AlignmentAnnotation("Occupancy",
+ MessageManager.getString("label.occupancy_descr"),
+ new Annotation[1], 0f,
+ alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
+ gapcounts.hasText = true;
+ gapcounts.autoCalculated = true;
+ gapcounts.scaleColLabel = true;
+ gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
+
+ alignment.addAnnotation(gapcounts);
}
}
if (conservation == null)
{
conservation = new AlignmentAnnotation("Conservation",
- "Conservation of total alignment less than "
- + getConsPercGaps() + "% gaps", new Annotation[1],
+ MessageManager.formatMessage("label.conservation_descr",
+ getConsPercGaps()), new Annotation[1],
0f, 11f, AlignmentAnnotation.BAR_GRAPH);
conservation.hasText = true;
conservation.autoCalculated = true;
if (quality == null)
{
quality = new AlignmentAnnotation("Quality",
- "Alignment Quality based on Blosum62 scores",
+ MessageManager.getString("label.quality_descr"),
new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
quality.hasText = true;
quality.autoCalculated = true;
{
if (alignment.hasRNAStructure() && strucConsensus == null)
{
- strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+ strucConsensus = new AlignmentAnnotation("StrucConsensus",
+ MessageManager.getString("label.strucconsensus_descr"),
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
strucConsensus.hasText = true;
strucConsensus.autoCalculated = true;
this.followHighlight = b;
}
- public int getStartRes()
- {
- return startRes;
- }
-
@Override
- public int getEndRes()
- {
- return endRes;
- }
-
- public int getStartSeq()
- {
- return startSeq;
- }
-
- public void setStartRes(int res)
- {
- this.startRes = res;
- }
-
- public void setStartSeq(int seq)
- {
- this.startSeq = seq;
- }
-
- public void setEndRes(int res)
- {
- if (res > alignment.getWidth() - 1)
- {
- // log.System.out.println(" Corrected res from " + res + " to maximum " +
- // (alignment.getWidth()-1));
- res = alignment.getWidth() - 1;
- }
- if (res < 0)
- {
- res = 0;
- }
- this.endRes = res;
- }
-
- public void setEndSeq(int seq)
- {
- if (seq > alignment.getHeight())
- {
- seq = alignment.getHeight();
- }
- if (seq < 0)
- {
- seq = 0;
- }
- this.endSeq = seq;
- }
-
- public int getEndSeq()
+ public ViewportRanges getRanges()
{
- return endSeq;
+ return ranges;
}
/**
* locate 'middle' column (true middle if an odd number visible, left of
* middle if an even number visible)
*/
- int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
+ int middleColumn = ranges.getStartRes()
+ + (ranges.getEndRes() - ranges.getStartRes()) / 2;
final HiddenSequences hiddenSequences = getAlignment()
.getHiddenSequences();
*/
int lastSeq = alignment.getHeight() - 1;
List<AlignedCodonFrame> seqMappings = null;
- for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+ for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
{
sequence = getAlignment().getSequenceAt(seqNo);
if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
git://source.jalview.org / jalview.git / blobdiff