*/
package jalview.viewmodel;
+import java.awt.Color;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
import jalview.api.AlignCalcManagerI;
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;
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
-import java.awt.Color;
-import java.beans.PropertyChangeSupport;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
/**
* base class holding visualization and analysis attributes and common logic for
* an active alignment view displayed in the GUI
public abstract class AlignmentViewport implements AlignViewportI,
CommandListener, VamsasSource
{
+ protected ViewportRanges ranges;
+
protected ViewStyleI viewStyle = new ViewStyle();
/**
protected AlignmentAnnotation complementConsensus;
+ protected AlignmentAnnotation gapcounts;
+
protected AlignmentAnnotation strucConsensus;
protected AlignmentAnnotation conservation;
}
@Override
+ public AlignmentAnnotation getAlignmentGapAnnotation()
+ {
+ return gapcounts;
+ }
+
+ @Override
public AlignmentAnnotation getComplementConsensusAnnotation()
{
return complementConsensus;
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;
- private int startRes;
-
- private int endRes;
-
- private int startSeq;
-
- private 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);
+ 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()
+ {
+ if (showOccupancy)
+ {
+ 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);
+ }
+ }
+
private void initConservation()
{
if (showConservation)
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;
}
@Override
- public int getStartRes()
- {
- return startRes;
- }
-
- @Override
- public int getEndRes()
- {
- return endRes;
- }
-
- @Override
- 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;
- }
-
- @Override
- 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))
*/
private boolean selectionIsDefinedGroup = false;
-
@Override
public boolean isSelectionDefinedGroup()
{
git://source.jalview.org / jalview.git / blobdiff