import jalview.analysis.Dna;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
this(al, hiddenColumns, width, height, null);
}
+
/**
* Create alignment frame for al with hiddenColumns, a specific width and
* height, and specific sequenceId
init();
}
+ public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+ ColumnSelection hiddenColumns, int width, int height)
+ {
+ setSize(width, height);
+
+ if (al.getDataset() == null)
+ {
+ al.setDataset(null);
+ }
+
+ viewport = new AlignViewport(al, hiddenColumns);
+
+ if (hiddenSeqs != null && hiddenSeqs.length > 0)
+ {
+ viewport.hideSequence(hiddenSeqs);
+ viewport.setHasHiddenRows(true);
+ }
+ alignPanel = new AlignmentPanel(this, viewport);
+ addAlignmentPanel(alignPanel, true);
+ init();
+ }
+
+
/**
* Make a new AlignFrame from existing alignmentPanels
*
return false;
}
- ExportData exportData = getAlignmentForExport();
+ ExportData exportData = getAlignmentForExport(format);
FormatAdapter f = new FormatAdapter(viewport);
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)
protected void outputText_actionPerformed(ActionEvent e)
{
- ExportData exportData = getAlignmentForExport();
+ ExportData exportData = getAlignmentForExport(e.getActionCommand());
+ if (exportData.getSettings().isCancelled())
+ {
+ return;
+ }
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
-
try
{
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[]
}
- public ExportData getAlignmentForExport()
+ public ExportData getAlignmentForExport(String exportFomat)
{
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();
- if (viewport.hasHiddenColumns() || hiddenSeqs.getSize() > 0)
+
+
+ alignmentToExport = viewport.getAlignment();
+ alignmentStartEnd = new int[]
+ { 0, alignmentToExport.getWidth() - 1 };
+
+ boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
+ AlignExportSettingI settings = new AlignExportSettings(hasHiddenSeqs,
+ viewport.hasHiddenColumns(), exportFomat);
+ viewport.setExportSettings(settings);
+ settings.isExportAnnotations();
+
+ if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
{
- int reply = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.alignment_contains_hidden_columns"),
- MessageManager
- .getString("action.save_omit_hidden_columns"),
- JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
+ omitHidden = viewport.getViewAsString(false);
+ }
- if (reply == JOptionPane.YES_OPTION)
- {
- omitHidden = viewport.getViewAsString(false);
- }
- else
- {
- alignmentToExport = viewport.getAlignment().getHiddenSequences()
- .getFullAlignment();
- }
+ if (hasHiddenSeqs && settings.isExportHiddenSequences())
+ {
+ alignmentToExport = hiddenSeqs.getFullAlignment();
}
- if (alignmentToExport == null)
+ else
{
alignmentToExport = viewport.getAlignment();
+ alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
+ .getColumnSelection().getHiddenColumns());
+ }
+ return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd,
+ settings);
+ }
+
+ 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];
}
- return new ExportData(alignmentToExport, omitHidden);
+ else
+ {
+ startPos = lowestRange[1] + 1;
+ }
+
+ if (higestRange[0] == 0 && higestRange[1] == 0)
+ {
+ endPos = aligmentStartEnd[1];
+ }
+ else
+ {
+ endPos = higestRange[0];
+ }
+
+ // 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]);
}
/**
@Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- // new HTMLOutput(alignPanel,
- // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
- // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
new HtmlSvgOutput(null, alignPanel);
}
}
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;
+
+ private AlignExportSettingI settings;
+
+ public ExportData(AlignmentI align, String[] ommit, int[] startEnd,
+ AlignExportSettingI settings)
{
this.alignment = align;
this.omitHidden = ommit;
- System.out.println();
+ this.startEnd = startEnd;
+ this.settings = settings;
}
public AlignmentI getAlignment()
{
this.omitHidden = omitHidden;
}
- }
- @Override
- public void hideColumns(List<int[]> colsToHide)
- {
- for (int[] colRange : colsToHide)
+ public int[] getStartEndPostions()
{
- viewport.hideColumns(colRange[0], colRange[1]);
+ return startEnd;
}
- }
+ public void setStartEndPostions(int[] startEnd)
+ {
+ this.startEnd = startEnd;
+ }
- @Override
- public void syncHiddenSequences()
- {
- AlignmentI al = viewport.getAlignment();
- HiddenSequences hiddenSeqs = al.getHiddenSequences();
- for (SequenceI seq : al.getSequencesArray())
- {
- if (seq.isHidden())
- {
- hiddenSeqs.hideSequence(seq);
- }
- }
+ public AlignExportSettingI getSettings()
+ {
+ return settings;
+ }
+
+ public void setSettings(AlignExportSettingI settings)
+ {
+ this.settings = settings;
+ }
}
+
}
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