import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Rectangle;
-import java.util.ArrayList;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
-import java.util.Vector;
import javax.swing.JInternalFrame;
private Rectangle explodedGeometry;
- String viewName;
+ private String viewName;
/*
* Flag set true on the view that should 'gather' multiple views of the same
private AnnotationColumnChooser annotationColumnSelectionState;
- boolean validCharWidth;
-
- public boolean followSelection = true;
-
- private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
-
/**
* Creates a new AlignViewport object.
*
setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
- AlignmentI al = getAlignment();
- al.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+ alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
// We must set conservation and consensus before setting colour,
// as Blosum and Clustal require this to be done
- if (hconsensus == null && !isDataset)
+ if (hconsensus == null && !isDataset)
{
- if (!al.isNucleotide())
+ if (!alignment.isNucleotide())
{
showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
showQuality = Cache.getDefault("SHOW_QUALITY", true);
showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
false);
+ // for now, use consensus options for Information till it gets its own
+ setShowHMMSequenceLogo(showSequenceLogo);
+ setNormaliseHMMSequenceLogo(normaliseSequenceLogo);
+ setShowInformationHistogram(showConsensusHistogram);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
initAutoAnnotation();
// initInformation();
- String colourProperty = al.isNucleotide()
+ String colourProperty = alignment.isNucleotide()
? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
String schemeName = Cache.getProperty(colourProperty);
ResidueColourScheme.NONE);
}
ColourSchemeI colourScheme = ColourSchemeProperty
- .getColourScheme(al, schemeName);
+ .getColourScheme(this, alignment, schemeName);
residueShading = new ResidueShader(colourScheme);
if (colourScheme instanceof UserColourScheme)
if (residueShading != null)
{
- residueShading.setConsensus(hconsensus);
+ residueShading.setConsensus(hconsensus);
}
+ setColourAppliesToAllGroups(true);
}
+
+ boolean validCharWidth;
/**
* {@inheritDoc}
/*
* replace mappings on our alignment
*/
- if (getAlignment() != null && align != null)
+ if (alignment != null && align != null)
{
- getAlignment().setCodonFrames(align.getCodonFrames());
+ alignment.setCodonFrames(align.getCodonFrames());
}
}
}
/**
- * returns the visible column regions of the alignment
+ * Returns an iterator over the visible column regions of the alignment
*
* @param selectedRegionOnly
* true to just return the contigs intersecting with the selected
* area
* @return
*/
- public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+ public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
{
- int[] viscontigs = null;
- int start = 0, end = 0;
+ int start = 0;
+ int end = 0;
if (selectedRegionOnly && selectionGroup != null)
{
start = selectionGroup.getStartRes();
}
else
{
- end = getAlignment().getWidth();
+ end = alignment.getWidth();
}
- viscontigs = getAlignment().getHiddenColumns().getVisibleContigs(start,
- end);
- return viscontigs;
+
+ return (alignment.getHiddenColumns().getVisContigsIterator(start,
+ end, false));
}
/**
return false;
}
+ public boolean followSelection = true;
+
/**
* @return true if view selection should always follow the selections
* broadcast by other selection sources
return StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
}
-
- /**
- *
- * @param pdbEntries
- * @return an array of SequenceI arrays, one for each PDBEntry, listing which
- * sequences in the alignment hold a reference to it
- */
- public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
- {
- List<SequenceI[]> seqvectors = new ArrayList<>();
- for (PDBEntry pdb : pdbEntries)
- {
- List<SequenceI> choosenSeqs = new ArrayList<>();
- for (SequenceI sq : getAlignment().getSequences())
- {
- Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
- .getAllPDBEntries();
- if (pdbRefEntries == null)
- {
- continue;
- }
- for (PDBEntry pdbRefEntry : pdbRefEntries)
- {
- if (pdbRefEntry.getId().equals(pdb.getId()))
- {
- if (pdbRefEntry.getChainCode() != null
- && pdb.getChainCode() != null)
- {
- if (pdbRefEntry.getChainCode().equalsIgnoreCase(
- pdb.getChainCode()) && !choosenSeqs.contains(sq))
- {
- choosenSeqs.add(sq);
- continue;
- }
- }
- else
- {
- if (!choosenSeqs.contains(sq))
- {
- choosenSeqs.add(sq);
- continue;
- }
- }
-
- }
- }
- }
- seqvectors
- .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
- }
- return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
- }
-
+
@Override
public boolean isNormaliseSequenceLogo()
{
return normaliseSequenceLogo;
}
-
- public void setNormaliseSequenceLogo(boolean state)
+ @Override
+public void setNormaliseSequenceLogo(boolean state)
{
normaliseSequenceLogo = state;
}
- public void setNormaliseHMMSequenceLogo(boolean state)
- {
- normaliseHMMSequenceLogo = state;
- }
/**
*
{
return validCharWidth;
}
+
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
newAlignFrame.setTitle(title);
- newAlignFrame.statusBar.setText(MessageManager
+ newAlignFrame.setStatus(MessageManager
.formatMessage("label.successfully_loaded_file", new Object[]
{ title }));
fr.setTransparency(featureSettings.getTransparency());
}
- @Override
- public boolean isNormaliseHMMSequenceLogo()
+ public String getViewName()
{
- return normaliseHMMSequenceLogo;
+ return viewName;
}
+ public void setViewName(String viewName)
+ {
+ this.viewName = viewName;
+ }
}
git://source.jalview.org / jalview.git / blobdiff