String output = f.formatSequences(format,
exportData.getAlignment(), // class cast exceptions will
// occur in the distant future
- exportData.getOmitHidden(), f.getCacheSuffixDefault(format),
+ exportData.getOmitHidden(), exportData.getStartEndPostions(),
+ f.getCacheSuffixDefault(format),
viewport.getColumnSelection());
if (output == null)
cap.setText(new FormatAdapter(viewport).formatSequences(
e.getActionCommand(),
exportData.getAlignment(),
- exportData.getOmitHidden(),
+ exportData.getOmitHidden(), exportData.getStartEndPostions(),
viewport.getColumnSelection()));
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
"label.alignment_output_command", new Object[]
{
AlignmentI alignmentToExport = null;
String[] omitHidden = null;
+ int[] alignmentStartEnd = new int[2];
FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
viewport.setFeatureRenderer(fr);
HiddenSequences hiddenSeqs = viewport.getAlignment()
.getHiddenSequences();
+
+
+ alignmentToExport = viewport.getAlignment();
+ alignmentStartEnd = new int[]
+ { 0, alignmentToExport.getWidth() - 1 };
+
if (viewport.hasHiddenColumns() || hiddenSeqs.getSize() > 0)
{
int reply = JOptionPane
if (reply == JOptionPane.YES_OPTION)
{
+ // export only visible region
omitHidden = viewport.getViewAsString(false);
+ alignmentToExport = viewport.getAlignment();
+ alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
+ .getColumnSelection().getHiddenColumns());
}
else
{
- alignmentToExport = viewport.getAlignment().getHiddenSequences()
- .getFullAlignment();
+ // export all region including visible
+ alignmentToExport = hiddenSeqs.getFullAlignment();
}
}
- if (alignmentToExport == null)
+
+ return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd);
+ }
+
+ private static int[] getStartEnd(int[] aligmentStartEnd,
+ List<int[]> hiddenCols)
+ {
+ int startPos = aligmentStartEnd[0];
+ int endPos = aligmentStartEnd[1];
+
+ int[] lowestRange = new int[2];
+ int[] higestRange = new int[2];
+
+ for (int[] hiddenCol : hiddenCols)
+ {
+ // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
+
+ lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+ higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+ }
+ // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]);
+ // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]);
+
+ if (lowestRange[0] == 0 && lowestRange[1] == 0)
+ {
+ startPos = aligmentStartEnd[0];
+ }
+ else
+ {
+ startPos = lowestRange[1] + 1;
+ }
+
+ if (higestRange[0] == 0 && higestRange[1] == 0)
+ {
+ endPos = aligmentStartEnd[1];
+ }
+ else
{
- alignmentToExport = viewport.getAlignment();
+ endPos = higestRange[0];
}
- return new ExportData(alignmentToExport, omitHidden);
+
+ // System.out.println("Export range : " + minPos + " - " + maxPos);
+ return new int[]
+ { startPos, endPos };
+ }
+
+ public static void main(String[] args)
+ {
+ ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
+ hiddenCols.add(new int[]
+ { 0, 4 });
+ hiddenCols.add(new int[]
+ { 6, 9 });
+ hiddenCols.add(new int[]
+ { 11, 12 });
+ hiddenCols.add(new int[]
+ { 33, 33 });
+ hiddenCols.add(new int[]
+ { 45, 50 });
+
+ int[] x = getStartEnd(new int[]
+ { 0, 50 }, hiddenCols);
+ // System.out.println("Export range : " + x[0] + " - " + x[1]);
}
/**
}
String output = new FormatAdapter().formatSequences("Fasta", seqs,
- omitHidden);
+ omitHidden, null);
StringSelection ss = new StringSelection(output);
private String[] omitHidden;
- public ExportData(AlignmentI align, String[] ommit)
+ private int[] startEnd;
+
+ public ExportData(AlignmentI align, String[] ommit, int[] startEnd)
{
this.alignment = align;
this.omitHidden = ommit;
- System.out.println();
+ this.startEnd = startEnd;
}
public AlignmentI getAlignment()
{
this.omitHidden = omitHidden;
}
+
+ public int[] getStartEndPostions()
+ {
+ return startEnd;
+ }
+
+ public void setStartEndPostions(int[] startEnd)
+ {
+ this.startEnd = startEnd;
+ }
}
@Override