import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsControllerI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.ScoreModelI;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.BioJsHTMLOutput;
-import jalview.io.FeaturesFile;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.HtmlSvgOutput;
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
*
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());
+ viewport.setIncludeHiddenRegion(false);
}
else
{
- alignmentToExport = viewport.getAlignment().getHiddenSequences()
- .getFullAlignment();
+ // export all region including visible
+ alignmentToExport = hiddenSeqs.getFullAlignment();
+ viewport.setIncludeHiddenRegion(true);
}
}
- 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);
public FeatureSettings featureSettings;
@Override
+ public FeatureSettingsControllerI getFeatureSettingsUI()
+ {
+ return featureSettings;
+ }
+
+ @Override
public void featureSettings_actionPerformed(ActionEvent e)
{
if (featureSettings != null)
* contents or path to retrieve file
* @param type
* access mode of file (see jalview.io.AlignFile)
- * @return true if features file was parsed corectly.
+ * @return true if features file was parsed correctly.
*/
public boolean parseFeaturesFile(String file, String type)
{
- boolean featuresFile = false;
- try
- {
- featuresFile = new FeaturesFile(file, type).parse(viewport
- .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
- .getFeatureRenderer().getFeatureColours(), false,
- jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ return avc.parseFeaturesFile(file, type,
+ jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+
+ }
- if (featuresFile)
+ @Override
+ public void refreshFeatureUI(boolean enableIfNecessary)
+ {
+ // note - currently this is only still here rather than in the controller
+ // because of the featureSettings hard reference that is yet to be
+ // abstracted
+ if (enableIfNecessary)
{
viewport.setShowSequenceFeatures(true);
showSeqFeatures.setSelected(true);
- if (alignPanel.getSeqPanel().seqCanvas.fr != null)
- {
- // update the min/max ranges where necessary
- alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true);
- }
- if (featureSettings != null)
- {
- featureSettings.setTableData();
- }
- alignPanel.paintAlignment(true);
}
- return featuresFile;
- }
+ }
@Override
public void dragEnter(DropTargetDragEvent evt)
{
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;
}
- }
- @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);
- }
- }
- }
}
class PrintThread extends Thread
git://source.jalview.org / jalview.git / blobdiff