import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.api.AlignCalcManagerI;
+import jalview.api.AlignExportSettingsI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeaturesDisplayedI;
import jalview.commands.CommandI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Annotation;
/**
* results of cDNA complement consensus visible portion of view
*/
- protected Hashtable[] hcomplementConsensus = null;
+ protected Hashtable<String, Object>[] hcomplementConsensus = null;
/**
* results of secondary structure base pair consensus for visible portion of
* view
*/
- protected Hashtable[] hStrucConsensus = null;
+ protected Hashtable<String, Object>[] hStrucConsensus = null;
protected Conservation hconservation = null;
}
@Override
- public void setComplementConsensusHash(Hashtable[] hconsensus)
+ public void setComplementConsensusHash(
+ Hashtable<String, Object>[] hconsensus)
{
this.hcomplementConsensus = hconsensus;
}
}
@Override
- public Hashtable[] getComplementConsensusHash()
+ public Hashtable<String, Object>[] getComplementConsensusHash()
{
return hcomplementConsensus;
}
@Override
- public Hashtable[] getRnaStructureConsensusHash()
+ public Hashtable<String, Object>[] getRnaStructureConsensusHash()
{
return hStrucConsensus;
}
@Override
- public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
+ public void setRnaStructureConsensusHash(
+ Hashtable<String, Object>[] hStrucConsensus)
{
this.hStrucConsensus = hStrucConsensus;
}
} while (end < max);
- int[][] startEnd = new int[regions.size()][2];
+ // int[][] startEnd = new int[regions.size()][2];
return regions;
}
* TODO reorder the annotation rows according to group/sequence ordering on
* alignment
*/
- boolean sortg = true;
+ // boolean sortg = true;
// remove old automatic annotation
// add any new annotation
public void clearSequenceColours()
{
sequenceColours.clear();
- };
+ }
@Override
public AlignViewportI getCodingComplement()
}
@Override
+ public AlignmentExportData getAlignExportData(AlignExportSettingsI options)
+ {
+ AlignmentI alignmentToExport = null;
+ String[] omitHidden = null;
+ alignmentToExport = null;
+
+ if (hasHiddenColumns() && !options.isExportHiddenColumns())
+ {
+ omitHidden = getViewAsString(false,
+ options.isExportHiddenSequences());
+ }
+
+ int[] alignmentStartEnd = new int[2];
+ if (hasHiddenRows() && options.isExportHiddenSequences())
+ {
+ alignmentToExport = getAlignment().getHiddenSequences()
+ .getFullAlignment();
+ }
+ else
+ {
+ alignmentToExport = getAlignment();
+ }
+ alignmentStartEnd = getAlignment().getHiddenColumns()
+ .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
+ AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
+ omitHidden, alignmentStartEnd);
+ return ed;
+ }
+
+ @Override
public boolean isNormaliseSequenceLogo()
{
return normaliseSequenceLogo;
{
hmmNormaliseSequenceLogo = state;
}
-
/**
* flag set to indicate if structure views might be out of sync with sequences
* in the alignment