import jalview.api.ViewStyleI;
import jalview.api.analysis.ScoreModelI;
import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.Sequence;
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);
+ }
+ alignPanel = new AlignmentPanel(this, viewport);
+ addAlignmentPanel(alignPanel, true);
+ init();
+ }
+
+
/**
* Make a new AlignFrame from existing alignmentPanels
*
*/
void init()
{
- progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+ if (!Jalview.isHeadlessMode())
+ {
+ progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+ }
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
.lastIndexOf(java.io.File.separatorChar) + 1);
}
- /*
- * First save any linked Chimera session.
- */
- Desktop.instance.saveChimeraSessions(file);
-
success = new Jalview2XML().saveAlignment(this, file, shortName);
statusBar.setText(MessageManager.formatMessage(
{
warningMessage("Cannot save file " + fileName + " using format "
+ format, "Alignment output format not supported");
- saveAs_actionPerformed(null);
- // JBPNote need to have a raise_gui flag here
+ if (!Jalview.isHeadlessMode())
+ {
+ saveAs_actionPerformed(null);
+ }
return false;
}
- String[] omitHidden = null;
-
- if (viewport.hasHiddenColumns())
+ AlignmentExportData exportData = getAlignmentForExport(format, viewport);
+ if (exportData.getSettings().isCancelled())
{
- 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);
-
- if (reply == JOptionPane.YES_OPTION)
- {
- omitHidden = viewport.getViewAsString(false);
- }
+ return false;
}
- FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
- viewport.setFeatureRenderer(fr);
- FormatAdapter f = new FormatAdapter(viewport);
+ FormatAdapter f = new FormatAdapter(alignPanel,
+ exportData.getSettings());
String output = f.formatSequences(format,
- viewport.getAlignment(), // class cast exceptions will
+ exportData.getAlignment(), // class cast exceptions will
// occur in the distant future
- omitHidden, f.getCacheSuffixDefault(format),
+ exportData.getOmitHidden(), exportData.getStartEndPostions(),
+ f.getCacheSuffixDefault(format),
viewport.getColumnSelection());
if (output == null)
return success;
}
+
private void warningMessage(String warning, String title)
{
if (new jalview.util.Platform().isHeadless())
@Override
protected void outputText_actionPerformed(ActionEvent e)
{
- String[] omitHidden = null;
- FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
- viewport.setFeatureRenderer(fr);
- if (viewport.hasHiddenColumns())
- {
- 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);
- if (reply == JOptionPane.YES_OPTION)
- {
- omitHidden = viewport.getViewAsString(false);
- }
+ AlignmentExportData exportData = getAlignmentForExport(
+ e.getActionCommand(), viewport);
+ if (exportData.getSettings().isCancelled())
+ {
+ return;
}
-
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
-
try
{
- cap.setText(new FormatAdapter(viewport).formatSequences(
+ cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
+ .formatSequences(
e.getActionCommand(),
- viewport.getAlignment(), omitHidden,
+ exportData.getAlignment(),
+ exportData.getOmitHidden(), exportData.getStartEndPostions(),
viewport.getColumnSelection()));
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
"label.alignment_output_command", new Object[]
}
+ public static AlignmentExportData getAlignmentForExport(String exportFormat,
+ AlignViewportI viewport)
+ {
+ AlignmentI alignmentToExport = null;
+ String[] omitHidden = null;
+ int[] alignmentStartEnd = new int[2];
+
+ HiddenSequences hiddenSeqs = viewport.getAlignment()
+ .getHiddenSequences();
+
+
+ alignmentToExport = viewport.getAlignment();
+ alignmentStartEnd = new int[]
+ { 0, alignmentToExport.getWidth() - 1 };
+
+ boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
+ AlignExportSettings settings = new AlignExportSettings(hasHiddenSeqs,
+ viewport.hasHiddenColumns(), exportFormat);
+ settings.isExportAnnotations();
+
+ if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
+ {
+ omitHidden = viewport.getViewAsString(false);
+ }
+
+ if (hasHiddenSeqs && settings.isExportHiddenSequences())
+ {
+ alignmentToExport = hiddenSeqs.getFullAlignment();
+ }
+ else
+ {
+ alignmentToExport = viewport.getAlignment();
+ alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
+ .getColumnSelection().getHiddenColumns());
+ }
+ AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd,
+ settings);
+ return ed;
+ }
+
+ public 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
+ {
+ 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]);
+ }
+
/**
* DOCUMENT ME!
*
@Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- // new HTMLOutput(alignPanel,
- // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
- // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
new HtmlSvgOutput(null, alignPanel);
}
@Override
public void bioJSMenuItem_actionPerformed(ActionEvent e)
{
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel,
- alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
bjs.exportJalviewAlignmentAsBioJsHtmlFile();
}
public void createImageMap(File file, String image)
if (closeAllTabs)
{
+ /*
+ * this will raise an INTERNAL_FRAME_CLOSED event and this method will
+ * be called recursively, with the frame now in 'closed' state
+ */
this.setClosed(true);
}
} catch (Exception ex)
viewport.getSelectionGroup().getEndRes() + groupAdjustment);
}
+ /*
+ * just extend the last slide command if compatible; but not if in
+ * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
+ */
boolean appendHistoryItem = false;
Deque<CommandI> historyList = viewport.getHistoryList();
- if (historyList != null
+ boolean inSplitFrame = getSplitViewContainer() != null;
+ if (!inSplitFrame && historyList != null
&& historyList.size() > 0
&& historyList.peek() instanceof SlideSequencesCommand)
{
}
String output = new FormatAdapter().formatSequences("Fasta", seqs,
- omitHidden);
+ omitHidden, null);
StringSelection ss = new StringSelection(output);
}
/*
- * Views share the same edits, undo and redo stacks, mappings.
+ * Views share the same edits undo and redo stacks
*/
newap.av.setHistoryList(viewport.getHistoryList());
newap.av.setRedoList(viewport.getRedoList());
- newap.av.getAlignment().setCodonFrames(
- viewport.getAlignment().getCodonFrames());
+
+ /*
+ * Views share the same mappings; need to deregister any new mappings
+ * created by copyAlignPanel, and register the new reference to the shared
+ * mappings
+ */
+ newap.av.replaceMappings(viewport.getAlignment());
newap.av.viewName = getNewViewName(viewTitle);
// temporary flag until SplitFrame is released
boolean asSplitFrame = Cache.getDefault(
- Preferences.ENABLE_SPLIT_FRAME, false);
+ Preferences.ENABLE_SPLIT_FRAME, true);
if (asSplitFrame)
{
/*
al.getCodonFrames().addAll(cf);
final StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
- ssm.addMappings(cf);
+ ssm.registerMappings(cf);
}
else
{
"Exception during translation. Please report this !", ex);
final String msg = MessageManager
.getString("label.error_when_translating_sequences_submit_bug_report");
- final String title = MessageManager
+ final String errorTitle = MessageManager
.getString("label.implementation_error")
+ MessageManager.getString("translation_failed");
- JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+ JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JOptionPane.ERROR_MESSAGE);
return;
}
{
final String msg = MessageManager
.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
- final String title = MessageManager
+ final String errorTitle = MessageManager
.getString("label.translation_failed");
- JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+ JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JOptionPane.WARNING_MESSAGE);
}
else
"label.translation_of_params", new Object[]
{ this.getTitle() });
af.setTitle(newTitle);
- if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, false))
+ if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
- viewport.openSplitFrame(af, new Alignment(seqs),
- al.getCodonFrames());
+ viewport.openSplitFrame(af, new Alignment(seqs));
}
else
{
aa.visible = visible;
}
}
- alignPanel.validateAnnotationDimensions(false);
+ alignPanel.validateAnnotationDimensions(true);
alignPanel.alignmentChanged();
}
git://source.jalview.org / jalview.git / blobdiff