/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
{
this(al, null, width, height);
}
+
/**
- * Creates a new AlignFrame object with specific width, height and sequenceSetId
+ * Creates a new AlignFrame object with specific width, height and
+ * sequenceSetId
+ *
* @param al
* @param width
* @param height
* @param sequenceSetId
*/
- public AlignFrame(AlignmentI al, int width, int height, String sequenceSetId)
+ public AlignFrame(AlignmentI al, int width, int height,
+ String sequenceSetId)
{
this(al, null, width, height, sequenceSetId);
}
+
/**
- * Creates a new AlignFrame object with specific width, height and sequenceSetId
+ * Creates a new AlignFrame object with specific width, height and
+ * sequenceSetId
+ *
* @param al
* @param width
* @param height
* @param sequenceSetId
* @param viewId
*/
- public AlignFrame(AlignmentI al, int width, int height, String sequenceSetId, String viewId)
+ public AlignFrame(AlignmentI al, int width, int height,
+ String sequenceSetId, String viewId)
{
this(al, null, width, height, sequenceSetId, viewId);
}
+
/**
* new alignment window with hidden columns
*
* @param al
- * AlignmentI
+ * AlignmentI
* @param hiddenColumns
- * ColumnSelection or null
- * @param width Width of alignment frame
- * @param height height of frame.
+ * ColumnSelection or null
+ * @param width
+ * Width of alignment frame
+ * @param height
+ * height of frame.
*/
public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
int width, int height)
{
this(al, hiddenColumns, width, height, null);
}
+
/**
- * Create alignment frame for al with hiddenColumns, a specific width and height, and specific sequenceId
+ * Create alignment frame for al with hiddenColumns, a specific width and
+ * height, and specific sequenceId
+ *
* @param al
* @param hiddenColumns
* @param width
* @param height
- * @param sequenceSetId (may be null)
+ * @param sequenceSetId
+ * (may be null)
*/
public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
int width, int height, String sequenceSetId)
}
/**
- * Create alignment frame for al with hiddenColumns, a specific width and height, and specific sequenceId
+ * Create alignment frame for al with hiddenColumns, a specific width and
+ * height, and specific sequenceId
+ *
* @param al
* @param hiddenColumns
* @param width
* @param height
- * @param sequenceSetId (may be null)
- * @param viewId (may be null)
+ * @param sequenceSetId
+ * (may be null)
+ * @param viewId
+ * (may be null)
*/
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height,
- String sequenceSetId, String viewId)
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ int width, int height, String sequenceSetId, String viewId)
{
setSize(width, height);
viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
* Make a new AlignFrame from exisiting alignmentPanels
*
* @param ap
- * AlignmentPanel
+ * AlignmentPanel
* @param av
- * AlignViewport
+ * AlignViewport
*/
public AlignFrame(AlignmentPanel ap)
{
addAlignmentPanel(ap, false);
init();
}
+
/**
- * initalise the alignframe from the underlying viewport data and the configurations
+ * initalise the alignframe from the underlying viewport data and the
+ * configurations
*/
void init()
{
* button functionality.
*
* @param file
- * valid filename
+ * valid filename
* @param format
- * format of file
+ * format of file
*/
public void setFileName(String file, String format)
{
boolean toggleCols = !evt.isShiftDown();
boolean hide = false;
-
SequenceGroup sg = viewport.getSelectionGroup();
+ // TODO: document ctrl-shift-h for show visible selected area and fix hack so columns for the current selected region get transferred.
+ if (!toggleSeqs && !toggleCols)
+ {
+ // Hide everything by the current selection - this is a hack - we do the invert and then hide
+ // first check that there will be visible columns after the invert.
+ if ((viewport.colSel!=null && viewport.colSel.getSelected()!=null && viewport.colSel.getSelected().size()>0) || (sg!=null && sg.getSize()>0 && sg.getStartRes()<=sg.getEndRes()))
+ {
+ // now invert the sequence set, if required - empty selection implies that no hiding is required.
+ if (sg!=null) {
+ invertSequenceMenuItem_actionPerformed(null);
+ sg = viewport.getSelectionGroup();
+ toggleSeqs = true;
+
+ }
+
+ if (sg!=null && sg.getStartRes()>=0 && sg.getStartRes()<=sg.getEndRes()&& (viewport.colSel==null || viewport.colSel.getSelected()==null || viewport.colSel.getSelected().size()==0))
+ {
+ // synthesize a column selection if none exists. this happens if a single region has been selected rather than whole columns.
+ if (viewport.colSel==null)
+ {
+ viewport.colSel = new ColumnSelection();
+ }
+ for (int cspos = sg.getStartRes(); cspos<=sg.getEndRes(); cspos++) {
+ viewport.colSel.addElement(cspos);
+ }
+ }
+ // finally invert the column selection and get the new sequence selection.
+ invertColSel_actionPerformed(null);
+ toggleCols = true;
+ }
+ }
+
if (toggleSeqs)
{
if (sg != null
* loading from Jalview2XML.java
*
* @param av
- * AlignViewport
+ * AlignViewport
*/
void setMenusFromViewport(AlignViewport av)
{
viewBoxesMenuItem.setSelected(av.showBoxes);
viewTextMenuItem.setSelected(av.showText);
showUnconservedMenuItem.setSelected(av.showUnconserved);
+ showGroupConsensus.setSelected(av.showGroupConsensus);
+ showGroupConservation.setSelected(av.showGroupConservation);
setColourSelected(ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
}
if (progressBarHandlers.contains(new Long(id)))
{
- progressBarHandlers.remove(new Long(id));
+ progressBarHandlers.remove(new Long(id));
}
layout.setRows(layout.getRows() - 1);
}
setMenusForViewport();
validate();
}
- public void registerHandler(final long id, final IProgressIndicatorHandler handler)
+
+ public void registerHandler(final long id,
+ final IProgressIndicatorHandler handler)
{
- if (progressBarHandlers==null || !progressBars.contains(new Long(id)))
+ if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
{
- throw new Error("call setProgressBar before registering the progress bar's handler.");
+ throw new Error(
+ "call setProgressBar before registering the progress bar's handler.");
}
progressBarHandlers.put(new Long(id), handler);
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
if (handler.canCancel())
{
JButton cancel = new JButton("Cancel");
- final IProgressIndicator us=this;
- cancel.addActionListener(new ActionListener() {
+ final IProgressIndicator us = this;
+ cancel.addActionListener(new ActionListener()
+ {
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar("Cancelled "+((JLabel)progressPanel.getComponent(0)).getText(), id);
+ us.setProgressBar("Cancelled "
+ + ((JLabel) progressPanel.getComponent(0)).getText(), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
}
}
+
/**
*
* @return true if any progress bars are still active
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null
- || (currentFileFormat == null
- || !jalview.io.FormatAdapter.isValidIOFormat(currentFileFormat, true))
+ || (currentFileFormat == null || !jalview.io.FormatAdapter
+ .isValidIOFormat(currentFileFormat, true))
|| fileName.startsWith("http"))
{
saveAs_actionPerformed(null);
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void saveAs_actionPerformed(ActionEvent e)
{
{
if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
{
- // JBPNote need to have a raise_gui flag here
- JOptionPane.showInternalMessageDialog(this, "Cannot save file "
- + fileName + " using format " + format,
- "Alignment output format not supported",
- JOptionPane.WARNING_MESSAGE);
+ 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
return false;
}
return success;
}
+ private void warningMessage(String warning, String title)
+ {
+ if (new jalview.util.Platform().isHeadless())
+ {
+ System.err.println("Warning: " + title + "\nWarning: " + warning);
+
+ }
+ else
+ {
+ JOptionPane.showInternalMessageDialog(this, warning, title,
+ JOptionPane.WARNING_MESSAGE);
+ }
+ return;
+ }
+
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void outputText_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void createPNG(File f)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void createEPS(File f)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void printMenuItem_actionPerformed(ActionEvent e)
{
}
/**
- * Close the current view or all views in the alignment frame.
- * If the frame only contains one view then the alignment will be removed from memory.
+ * Close the current view or all views in the alignment frame. If the frame
+ * only contains one view then the alignment will be removed from memory.
*
- * @param closeAllTabs
+ * @param closeAllTabs
*/
public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
{
if (closeAllTabs)
{
- for (int i = 0; i < alignPanels.size(); i++)
+ if (this.isClosed())
{
- AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
- jalview.structure.StructureSelectionManager ssm =
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager();
- ssm.removeStructureViewerListener(ap.seqPanel, null);
- ssm.removeSelectionListener(ap.seqPanel);
- PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
- PaintRefresher.RemoveComponent(ap);
- ap.av.alignment = null;
+ // really close all the windows - otherwise wait till
+ // setClosed(true) is called
+ for (int i = 0; i < alignPanels.size(); i++)
+ {
+ AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+ ap.closePanel();
+ }
}
}
else
{
closeView(alignPanel);
- viewport = null;
}
}
}
}
+ /**
+ * close alignPanel2 and shuffle tabs appropriately.
+ *
+ * @param alignPanel2
+ */
public void closeView(AlignmentPanel alignPanel2)
{
int index = tabbedPane.getSelectedIndex();
int closedindex = tabbedPane.indexOfComponent(alignPanel2);
alignPanels.removeElement(alignPanel2);
- PaintRefresher.RemoveComponent(alignPanel2.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(alignPanel2.idPanel.idCanvas);
- PaintRefresher.RemoveComponent(alignPanel2);
- alignPanel2.av.alignment = null;
-
- if (viewport == alignPanel2.av)
- {
- viewport = null;
- }
+ // Unnecessary
+ // if (viewport == alignPanel2.av)
+ // {
+ // viewport = null;
+ // }
+ alignPanel2.closePanel();
alignPanel2 = null;
-
+
tabbedPane.removeTabAt(closedindex);
tabbedPane.validate();
index--;
}
- this.tabSelectionChanged(index);
+ this.tabSelectionChanged(index);
}
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param up
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void moveSelectedSequences(boolean up)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void copy_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void pasteNew_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void pasteThis_actionPerformed(ActionEvent e)
{
* Paste contents of Jalview clipboard
*
* @param newAlignment
- * true to paste to a new alignment, otherwise add to this.
+ * true to paste to a new alignment, otherwise add to this.
*/
void paste(boolean newAlignment)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void cut_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void delete_actionPerformed(ActionEvent evt)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void deleteGroups_actionPerformed(ActionEvent e)
{
viewport.sequenceColours = null;
viewport.setSelectionGroup(null);
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
}
-
- //else
+
+ // else
{
// if (justifySeqs>0)
{
// alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
}
}
- //}
-
+
+ // }
+
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void findMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void font_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void seqLimit_actionPerformed(ActionEvent e)
{
viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
alignPanel.paintAlignment(true);
}
- /* (non-Javadoc)
+
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
*/
protected void followHighlight_actionPerformed()
{
if (viewport.followHighlight = this.followHighlightMenuItem.getState())
{
- alignPanel.scrollToPosition(alignPanel.seqPanel.seqCanvas.searchResults, false);
+ alignPanel.scrollToPosition(
+ alignPanel.seqPanel.seqCanvas.searchResults, false);
}
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void scaleAbove_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void scaleLeft_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void scaleRight_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
* Set or clear 'Show Sequence Features'
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
alignPanel.getOverviewPanel().updateOverviewImage();
}
}
+
/**
* Set or clear 'Show Sequence Features'
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
{
- viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight.isSelected());
+ viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
+ .isSelected());
if (viewport.getShowSequenceFeaturesHeight())
{
// ensure we're actually displaying features
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void clustalColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void zappoColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void taylorColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void hydrophobicityColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void helixColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void strandColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void turnColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void buriedColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void nucleotideColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void applyToAllGroups_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param cs
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void changeColour(ColourSchemeI cs)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void modifyPID_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void modifyConservation_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void conservationMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void abovePIDThreshold_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void userDefinedColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void PIDColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void BLOSUM62Colour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
alignPanel.paintAlignment(true);
}
+
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void sortLengthMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByLength(viewport.getAlignment());
- addHistoryItem(new OrderCommand("Length Sort", oldOrder, viewport.alignment));
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,
+ viewport.alignment));
alignPanel.paintAlignment(true);
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void PCAMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pwType
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param title
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
void NewTreePanel(String type, String pwType, String title)
{
* DOCUMENT ME!
*
* @param title
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param order
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void addSortByOrderMenuItem(String title,
final AlignmentOrder order)
* Add a new sort by annotation score menu item
*
* @param sort
- * the menu to add the option to
+ * the menu to add the option to
* @param scoreLabel
- * the label used to retrieve scores for each sequence on the
- * alignment
+ * the label used to retrieve scores for each sequence on the
+ * alignment
*/
public void addSortByAnnotScoreMenuItem(JMenu sort,
final String scoreLabel)
* modified.
*
* @param treePanel
- * Displayed tree window.
+ * Displayed tree window.
* @param title
- * SortBy menu item title.
+ * SortBy menu item title.
*/
public void buildTreeMenu()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
{
* current alignment view
*
* @param nf
- * the tree
+ * the tree
* @param title
- * tree viewer title
+ * tree viewer title
* @param input
- * Associated alignment input data (or null)
+ * Associated alignment input data (or null)
* @param w
- * width
+ * width
* @param h
- * height
+ * height
* @param x
- * position
+ * position
* @param y
- * position
+ * position
* @return TreePanel handle
*/
public TreePanel ShowNewickTree(NewickFile nf, String title,
showProducts.removeAll();
final boolean dna = viewport.getAlignment().isNucleotide();
final Alignment ds = dataset;
- String[] ptypes = (selection==null || selection.length==0) ? null
- : CrossRef.findSequenceXrefTypes(dna, selection,
- dataset);
+ String[] ptypes = (selection == null || selection.length == 0) ? null
+ : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
// Object[] prods =
// CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
// selection, dataset, true);
* Try to load a features file onto the alignment.
*
* @param file
- * contents or path to retrieve file
+ * contents or path to retrieve file
* @param type
- * access mode of file (see jalview.io.AlignFile)
+ * access mode of file (see jalview.io.AlignFile)
* @return true if features file was parsed corectly.
*/
public boolean parseFeaturesFile(String file, String type)
{
viewport.showSequenceFeatures = true;
showSeqFeatures.setSelected(true);
+ if (alignPanel.seqPanel.seqCanvas.fr != null)
+ {
+ // update the min/max ranges where necessary
+ alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
+ }
alignPanel.paintAlignment(true);
}
}
java.net.URI uri = new java.net.URI(s);
- java.io.File file = new java.io.File(uri);
- files.add(file);
+ // check to see if we can handle this kind of URI
+ if (uri.getScheme().toLowerCase().startsWith("http"))
+ {
+ files.add(uri.toString());
+ }
+ else
+ {
+ // otherwise preserve old behaviour: catch all for file objects
+ java.io.File file = new java.io.File(uri);
+ files.add(file.toString());
+ }
}
}
} catch (Exception e)
}
/**
- * Attempt to load a "dropped" file: First by testing whether it's and
- * Annotation file, then a JNet file, and finally a features file. If all are
- * false then the user may have dropped an alignment file onto this
+ * Attempt to load a "dropped" file or URL string: First by testing whether
+ * it's and Annotation file, then a JNet file, and finally a features file. If
+ * all are false then the user may have dropped an alignment file onto this
* AlignFrame.
*
* @param file
- * either a filename or a URL string.
+ * either a filename or a URL string.
*/
public void loadJalviewDataFile(String file)
{
try
{
- String protocol = "File";
-
- if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
+ String protocol = jalview.io.FormatAdapter.FILE;
+ String f = file.toLowerCase();
+ if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
+ || f.indexOf("file:") == 0)
{
- protocol = "URL";
+ protocol = jalview.io.FormatAdapter.URL;
}
boolean isAnnotation = new AnnotationFile().readAnnotationFile(
}
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
+ * )
*/
protected void showDbRefs_actionPerformed(ActionEvent e)
{
viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.ActionEvent)
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
+ * ActionEvent)
*/
protected void showNpFeats_actionPerformed(ActionEvent e)
{
}
/**
- * find the viewport amongst the tabs in this alignment frame and close that tab
+ * find the viewport amongst the tabs in this alignment frame and close that
+ * tab
+ *
* @param av
*/
public boolean closeView(AlignViewport av)
return true;
}
Component[] comp = tabbedPane.getComponents();
- for (int i=0;comp!=null && i<comp.length;i++)
+ for (int i = 0; comp != null && i < comp.length; i++)
{
if (comp[i] instanceof AlignmentPanel)
{
}
return false;
}
- protected void build_fetchdbmenu(JMenu webService) {
+
+ protected void build_fetchdbmenu(JMenu webService)
+ {
// Temporary hack - DBRef Fetcher always top level ws entry.
- // TODO We probably want to store a sequence database checklist in preferences and have checkboxes.. rather than individual sources selected here
+ // TODO We probably want to store a sequence database checklist in
+ // preferences and have checkboxes.. rather than individual sources selected
+ // here
JMenu rfetch = new JMenu("Fetch DB References");
rfetch
.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
webService.add(rfetch);
JMenuItem fetchr = new JMenuItem("Standard Databases");
- fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
+ fetchr
+ .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
fetchr.addActionListener(new ActionListener()
{
rfetch.add(fetchr);
JMenu dfetch = new JMenu();
rfetch.add(dfetch);
- jalview.ws.SequenceFetcher sf = SequenceFetcher.getSequenceFetcherSingleton(this);
- String[] otherdb = sf.getOrderedSupportedSources();
+ jalview.ws.SequenceFetcher sf = SequenceFetcher
+ .getSequenceFetcherSingleton(this);
+ String[] otherdb = sf.getOrderedSupportedSources();
// sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
// jalview.util.QuickSort.sort(otherdb, otherdb);
- int comp=0,mcomp=15;
- String mname=null;
- if (otherdb!=null && otherdb.length>0)
+ int comp = 0, mcomp = 15;
+ String mname = null;
+ if (otherdb != null && otherdb.length > 0)
{
- for (int i=0; i<otherdb.length; i++)
+ for (int i = 0; i < otherdb.length; i++)
{
- String dbname =sf.getSourceProxy(otherdb[i]).getDbName();
+ String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
if (mname == null)
{
- mname = "from '"+dbname+"'";
+ mname = "from '" + dbname + "'";
}
fetchr = new JMenuItem(otherdb[i]);
- final String[] dassource = new String[] { otherdb[i] };
+ final String[] dassource = new String[]
+ { otherdb[i] };
fetchr.addActionListener(new ActionListener()
{
public void run()
{
new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(), alignPanel.alignFrame, dassource)
- .fetchDBRefs(false);
+ .getSequenceSelection(), alignPanel.alignFrame,
+ dassource).fetchDBRefs(false);
}
}).start();
}
-
+
});
- fetchr.setToolTipText("Retrieve from "+dbname);
+ fetchr.setToolTipText("Retrieve from " + dbname);
dfetch.add(fetchr);
- if (comp++==mcomp || i==(otherdb.length-1))
+ if (comp++ == mcomp || i == (otherdb.length - 1))
{
- dfetch.setText(mname+" to '"+dbname+"'");
+ dfetch.setText(mname + " to '" + dbname + "'");
rfetch.add(dfetch);
dfetch = new JMenu();
mname = null;
- comp=0;
+ comp = 0;
}
}
}
}
+
/**
- * Left justify the whole alignment.
+ * Left justify the whole alignment.
*/
protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
al.justify(false);
viewport.firePropertyChange("alignment", null, al);
}
+
/**
- * Right justify the whole alignment.
+ * Right justify the whole alignment.
*/
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
al.justify(true);
viewport.firePropertyChange("alignment", null, al);
}
+
public void setShowSeqFeatures(boolean b)
{
showSeqFeatures.setSelected(true);
viewport.setShowSequenceFeatures(true);
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.awt.event.ActionEvent)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
+ * awt.event.ActionEvent)
*/
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowUnconserved(showUnconservedMenuItem.getState());
alignPanel.paintAlignment(true);
}
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ protected void showGroupConsensus_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowGroupConsensus(showGroupConsensus.getState());
+ alignPanel.updateAnnotation();
+
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showGroupConservation_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowGroupConservation(showGroupConservation.getState());
+ alignPanel.updateAnnotation();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
+ {
+ if (viewport.getSelectionGroup() != null)
+ {
+ SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
+ viewport.getSequenceSelection(), viewport.getAlignmentView(
+ true).getSequenceStrings(viewport.getGapCharacter()),
+ viewport.alignment.getGroups());
+ viewport.alignment.deleteAllGroups();
+ viewport.sequenceColours = null;
+ viewport.setSelectionGroup(null);
+ // set view properties for each group
+ for (int g = 0; g < gps.length; g++)
+ {
+ gps[g].setShowunconserved(viewport.getShowUnconserved());
+ gps[g].setIncludeAllConsSymbols(viewport.isIncludeAllConsensusSymbols());
+ viewport.alignment.addGroup(gps[g]);
+ Color col = new Color((int) (Math.random() * 255), (int) (Math
+ .random() * 255), (int) (Math.random() * 255));
+ col = col.brighter();
+ for (Enumeration sq = gps[g].getSequences(null).elements(); sq
+ .hasMoreElements(); viewport.setSequenceColour(
+ (SequenceI) sq.nextElement(), col))
+ ;
+ }
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
+ }
}
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