import java.util.Hashtable;
import java.util.List;
import java.util.Map;
-import java.util.Set;
/**
* base class holding visualization and analysis attributes and common logic for
* @param name
* @see jalview.api.ViewStyleI#setFontName(java.lang.String)
*/
+ @Override
public void setFontName(String name)
{
viewStyle.setFontName(name);
* @param style
* @see jalview.api.ViewStyleI#setFontStyle(int)
*/
+ @Override
public void setFontStyle(int style)
{
viewStyle.setFontStyle(style);
* @param size
* @see jalview.api.ViewStyleI#setFontSize(int)
*/
+ @Override
public void setFontSize(int size)
{
viewStyle.setFontSize(size);
* @return
* @see jalview.api.ViewStyleI#getFontStyle()
*/
+ @Override
public int getFontStyle()
{
return viewStyle.getFontStyle();
* @return
* @see jalview.api.ViewStyleI#getFontName()
*/
+ @Override
public String getFontName()
{
return viewStyle.getFontName();
* @return
* @see jalview.api.ViewStyleI#getFontSize()
*/
+ @Override
public int getFontSize()
{
return viewStyle.getFontSize();
* @param upperCasebold
* @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
*/
+ @Override
public void setUpperCasebold(boolean upperCasebold)
{
viewStyle.setUpperCasebold(upperCasebold);
* @return
* @see jalview.api.ViewStyleI#isUpperCasebold()
*/
+ @Override
public boolean isUpperCasebold()
{
return viewStyle.isUpperCasebold();
* @return
* @see jalview.api.ViewStyleI#isSeqNameItalics()
*/
+ @Override
public boolean isSeqNameItalics()
{
return viewStyle.isSeqNameItalics();
* @param colourByReferenceSeq
* @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
*/
+ @Override
public void setColourByReferenceSeq(boolean colourByReferenceSeq)
{
viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
* @param b
* @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
*/
+ @Override
public void setColourAppliesToAllGroups(boolean b)
{
viewStyle.setColourAppliesToAllGroups(b);
* @return
* @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
*/
+ @Override
public boolean getColourAppliesToAllGroups()
{
return viewStyle.getColourAppliesToAllGroups();
* @return
* @see jalview.api.ViewStyleI#getAbovePIDThreshold()
*/
+ @Override
public boolean getAbovePIDThreshold()
{
return viewStyle.getAbovePIDThreshold();
* @param inc
* @see jalview.api.ViewStyleI#setIncrement(int)
*/
+ @Override
public void setIncrement(int inc)
{
viewStyle.setIncrement(inc);
* @return
* @see jalview.api.ViewStyleI#getIncrement()
*/
+ @Override
public int getIncrement()
{
return viewStyle.getIncrement();
* @param b
* @see jalview.api.ViewStyleI#setConservationSelected(boolean)
*/
+ @Override
public void setConservationSelected(boolean b)
{
viewStyle.setConservationSelected(b);
* @param show
* @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
*/
+ @Override
public void setShowHiddenMarkers(boolean show)
{
viewStyle.setShowHiddenMarkers(show);
* @return
* @see jalview.api.ViewStyleI#getShowHiddenMarkers()
*/
+ @Override
public boolean getShowHiddenMarkers()
{
return viewStyle.getShowHiddenMarkers();
* @param b
* @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
*/
+ @Override
public void setScaleRightWrapped(boolean b)
{
viewStyle.setScaleRightWrapped(b);
* @param b
* @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
*/
+ @Override
public void setScaleLeftWrapped(boolean b)
{
viewStyle.setScaleLeftWrapped(b);
* @param b
* @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
*/
+ @Override
public void setScaleAboveWrapped(boolean b)
{
viewStyle.setScaleAboveWrapped(b);
* @return
* @see jalview.api.ViewStyleI#getScaleLeftWrapped()
*/
+ @Override
public boolean getScaleLeftWrapped()
{
return viewStyle.getScaleLeftWrapped();
* @return
* @see jalview.api.ViewStyleI#getScaleAboveWrapped()
*/
+ @Override
public boolean getScaleAboveWrapped()
{
return viewStyle.getScaleAboveWrapped();
* @return
* @see jalview.api.ViewStyleI#getScaleRightWrapped()
*/
+ @Override
public boolean getScaleRightWrapped()
{
return viewStyle.getScaleRightWrapped();
* @param b
* @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
*/
+ @Override
public void setAbovePIDThreshold(boolean b)
{
viewStyle.setAbovePIDThreshold(b);
* @param thresh
* @see jalview.api.ViewStyleI#setThreshold(int)
*/
+ @Override
public void setThreshold(int thresh)
{
viewStyle.setThreshold(thresh);
* @return
* @see jalview.api.ViewStyleI#getThreshold()
*/
+ @Override
public int getThreshold()
{
return viewStyle.getThreshold();
* @return
* @see jalview.api.ViewStyleI#getShowJVSuffix()
*/
+ @Override
public boolean getShowJVSuffix()
{
return viewStyle.getShowJVSuffix();
* @param b
* @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
*/
+ @Override
public void setShowJVSuffix(boolean b)
{
viewStyle.setShowJVSuffix(b);
* @param state
* @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
*/
+ @Override
public void setWrapAlignment(boolean state)
{
viewStyle.setWrapAlignment(state);
* @param state
* @see jalview.api.ViewStyleI#setShowText(boolean)
*/
+ @Override
public void setShowText(boolean state)
{
viewStyle.setShowText(state);
* @param state
* @see jalview.api.ViewStyleI#setRenderGaps(boolean)
*/
+ @Override
public void setRenderGaps(boolean state)
{
viewStyle.setRenderGaps(state);
* @return
* @see jalview.api.ViewStyleI#getColourText()
*/
+ @Override
public boolean getColourText()
{
return viewStyle.getColourText();
* @param state
* @see jalview.api.ViewStyleI#setColourText(boolean)
*/
+ @Override
public void setColourText(boolean state)
{
viewStyle.setColourText(state);
* @return
* @see jalview.api.ViewStyleI#getWrapAlignment()
*/
+ @Override
public boolean getWrapAlignment()
{
return viewStyle.getWrapAlignment();
* @return
* @see jalview.api.ViewStyleI#getShowText()
*/
+ @Override
public boolean getShowText()
{
return viewStyle.getShowText();
* @return
* @see jalview.api.ViewStyleI#getWrappedWidth()
*/
+ @Override
public int getWrappedWidth()
{
return viewStyle.getWrappedWidth();
* @param w
* @see jalview.api.ViewStyleI#setWrappedWidth(int)
*/
+ @Override
public void setWrappedWidth(int w)
{
viewStyle.setWrappedWidth(w);
* @return
* @see jalview.api.ViewStyleI#getCharHeight()
*/
+ @Override
public int getCharHeight()
{
return viewStyle.getCharHeight();
* @param h
* @see jalview.api.ViewStyleI#setCharHeight(int)
*/
+ @Override
public void setCharHeight(int h)
{
viewStyle.setCharHeight(h);
* @return
* @see jalview.api.ViewStyleI#getCharWidth()
*/
+ @Override
public int getCharWidth()
{
return viewStyle.getCharWidth();
* @param w
* @see jalview.api.ViewStyleI#setCharWidth(int)
*/
+ @Override
public void setCharWidth(int w)
{
viewStyle.setCharWidth(w);
* @return
* @see jalview.api.ViewStyleI#getShowBoxes()
*/
+ @Override
public boolean getShowBoxes()
{
return viewStyle.getShowBoxes();
* @return
* @see jalview.api.ViewStyleI#getShowUnconserved()
*/
+ @Override
public boolean getShowUnconserved()
{
return viewStyle.getShowUnconserved();
* @param showunconserved
* @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
*/
+ @Override
public void setShowUnconserved(boolean showunconserved)
{
viewStyle.setShowUnconserved(showunconserved);
* @param default1
* @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
*/
+ @Override
public void setSeqNameItalics(boolean default1)
{
viewStyle.setSeqNameItalics(default1);
/*
* A separate thread to compute cDNA consensus for a protein alignment
+ * which has mapping to cDNA
*/
final AlignmentI al = this.getAlignment();
if (!al.isNucleotide() && al.getCodonFrames() != null
&& !al.getCodonFrames().isEmpty())
{
- if (calculator
- .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+ /*
+ * fudge - check first mapping is protein-to-nucleotide
+ * (we don't want to do this for protein-to-protein)
+ */
+ AlignedCodonFrame mapping = al.getCodonFrames().iterator().next();
+ // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
+ if (mapping.getdnaToProt()[0].getFromRatio() == 3)
{
- calculator.registerWorker(new ComplementConsensusThread(this, ap));
+ if (calculator
+ .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+ {
+ calculator
+ .registerWorker(new ComplementConsensusThread(this, ap));
+ }
}
}
}
*/
public boolean isColSelChanged(boolean b)
{
- int hc = (colSel == null || colSel.size() == 0) ? -1 : colSel
+ int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel
.hashCode();
if (hc != -1 && hc != colselhash)
{
public void hideSelectedColumns()
{
- if (colSel.size() < 1)
+ if (colSel.isEmpty())
{
return;
}
if (hiddenRepSequences == null)
{
- hiddenRepSequences = new Hashtable();
+ hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
}
hiddenRepSequences.put(repSequence, sg);
{
if (!alignment.isNucleotide())
{
- final Set<AlignedCodonFrame> codonMappings = alignment
+ final List<AlignedCodonFrame> codonMappings = alignment
.getCodonFrames();
if (codonMappings != null && !codonMappings.isEmpty())
{
- complementConsensus = new AlignmentAnnotation("cDNA Consensus",
- "PID for cDNA", new Annotation[1], 0f, 100f,
- AlignmentAnnotation.BAR_GRAPH);
- initConsensus(complementConsensus);
+ // fudge: check mappings are not protein-to-protein
+ // TODO: nicer
+ AlignedCodonFrame mapping = codonMappings.iterator().next();
+ if (mapping.getdnaToProt()[0].getFromRatio() == 3)
+ {
+ complementConsensus = new AlignmentAnnotation("cDNA Consensus",
+ "PID for cDNA", new Annotation[1], 0f, 100f,
+ AlignmentAnnotation.BAR_GRAPH);
+ initConsensus(complementConsensus);
+ }
}
}
}
* @return
* @see jalview.api.ViewStyleI#getTextColour()
*/
+ @Override
public Color getTextColour()
{
return viewStyle.getTextColour();
* @return
* @see jalview.api.ViewStyleI#getTextColour2()
*/
+ @Override
public Color getTextColour2()
{
return viewStyle.getTextColour2();
* @return
* @see jalview.api.ViewStyleI#getThresholdTextColour()
*/
+ @Override
public int getThresholdTextColour()
{
return viewStyle.getThresholdTextColour();
* @return
* @see jalview.api.ViewStyleI#isConservationColourSelected()
*/
+ @Override
public boolean isConservationColourSelected()
{
return viewStyle.isConservationColourSelected();
* @return
* @see jalview.api.ViewStyleI#isRenderGaps()
*/
+ @Override
public boolean isRenderGaps()
{
return viewStyle.isRenderGaps();
* @return
* @see jalview.api.ViewStyleI#isShowColourText()
*/
+ @Override
public boolean isShowColourText()
{
return viewStyle.isShowColourText();
* @param conservationColourSelected
* @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
*/
+ @Override
public void setConservationColourSelected(
boolean conservationColourSelected)
{
* @param showColourText
* @see jalview.api.ViewStyleI#setShowColourText(boolean)
*/
+ @Override
public void setShowColourText(boolean showColourText)
{
viewStyle.setShowColourText(showColourText);
* @param textColour
* @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
*/
+ @Override
public void setTextColour(Color textColour)
{
viewStyle.setTextColour(textColour);
* @param thresholdTextColour
* @see jalview.api.ViewStyleI#setThresholdTextColour(int)
*/
+ @Override
public void setThresholdTextColour(int thresholdTextColour)
{
viewStyle.setThresholdTextColour(thresholdTextColour);
* @param textColour2
* @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
*/
+ @Override
public void setTextColour2(Color textColour2)
{
viewStyle.setTextColour2(textColour2);
* @return
* @see jalview.api.ViewStyleI#getIdWidth()
*/
+ @Override
public int getIdWidth()
{
return viewStyle.getIdWidth();
* @param i
* @see jalview.api.ViewStyleI#setIdWidth(int)
*/
+ @Override
public void setIdWidth(int i)
{
viewStyle.setIdWidth(i);
* @return
* @see jalview.api.ViewStyleI#isCentreColumnLabels()
*/
+ @Override
public boolean isCentreColumnLabels()
{
return viewStyle.isCentreColumnLabels();
* @param centreColumnLabels
* @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
*/
+ @Override
public void setCentreColumnLabels(boolean centreColumnLabels)
{
viewStyle.setCentreColumnLabels(centreColumnLabels);
* @param showdbrefs
* @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
*/
+ @Override
public void setShowDBRefs(boolean showdbrefs)
{
viewStyle.setShowDBRefs(showdbrefs);
* @return
* @see jalview.api.ViewStyleI#isShowDBRefs()
*/
+ @Override
public boolean isShowDBRefs()
{
return viewStyle.isShowDBRefs();
* @return
* @see jalview.api.ViewStyleI#isShowNPFeats()
*/
+ @Override
public boolean isShowNPFeats()
{
return viewStyle.isShowNPFeats();
* @param shownpfeats
* @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
*/
+ @Override
public void setShowNPFeats(boolean shownpfeats)
{
viewStyle.setShowNPFeats(shownpfeats);
return startRes;
}
+ @Override
public int getEndRes()
{
return endRes;
{
return 0;
}
- final Set<AlignedCodonFrame> mappings = proteinAlignment
+ final List<AlignedCodonFrame> mappings = proteinAlignment
.getCodonFrames();
/*